pp annotation~BRAKER3 -c 8 -m 32 input_1/ input_2/parasite.fa Checking the realpath of input files. 0 input_1/ 1 /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/input_1/S_l1_1.fq.gz 1 /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/input_1/S_l1_2.fq.gz 0 input_2/parasite.fa 0 0 /home/yoshitake.kazutoshi/work -> /data/yoshitake.kazutoshi/work /home/yoshitake.kazutoshi/work/pp-dev -> /data/yoshitake.kazutoshi/work/pp-dev /home/yoshitake.kazutoshi/work/pp-dev/yoshitake -> /data/yoshitake.kazutoshi/work/pp-dev/yoshitake /home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -> /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test /home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 -> /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 /data/yoshitake.kazutoshi/work /data/yoshitake.kazutoshi/work/pp-dev /data/yoshitake.kazutoshi/work/pp-dev/yoshitake /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 biocontainers/emboss:v6.6.0dfsg-7b1-deb_cv1 c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_3-kegg_2 c2997108/ubuntu-18:braker2_hisat2_5 centos:centos6 quay.io/biocontainers/gffread:0.12.7--h9a82719_0 quay.io/biocontainers/hisat2:2.2.0--py36hf0b53f7_4 quay.io/biocontainers/prinseq:0.20.4 quay.io/biocontainers/samtools:1.9--h10a08f8_12 quay.io/biocontainers/seqkit:0.12.1--0 using docker ++ docker pull biocontainers/emboss:v6.6.0dfsg-7b1-deb_cv1 v6.6.0dfsg-7b1-deb_cv1: Pulling from biocontainers/emboss 478cd0aa93c0: Pulling fs layer 94d6a239eb0e: Pulling fs layer e8e87313e9cb: Pulling fs layer 1badce2e48be: Pulling fs layer 732b6ad56c57: Pulling fs layer f464fdba1cc8: Pulling fs layer f8a34b82a572: Pulling fs layer 1badce2e48be: Waiting 732b6ad56c57: Waiting f8a34b82a572: Waiting f464fdba1cc8: Waiting 94d6a239eb0e: Download complete e8e87313e9cb: Download complete 478cd0aa93c0: Download complete Checking the realpath of input files. 0 input_1/ 1 /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/input_1/S_l1_1.fq.gz 1 /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/input_1/S_l1_2.fq.gz 0 input_2/parasite.fa 0 0 /home/yoshitake.kazutoshi/work -> /data/yoshitake.kazutoshi/work /home/yoshitake.kazutoshi/work/pp-dev -> /data/yoshitake.kazutoshi/work/pp-dev /home/yoshitake.kazutoshi/work/pp-dev/yoshitake -> /data/yoshitake.kazutoshi/work/pp-dev/yoshitake /home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -> /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test /home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 -> /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 /data/yoshitake.kazutoshi/work /data/yoshitake.kazutoshi/work/pp-dev /data/yoshitake.kazutoshi/work/pp-dev/yoshitake /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 biocontainers/emboss:v6.6.0dfsg-7b1-deb_cv1 c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_3-kegg_2 c2997108/ubuntu-18:braker2_hisat2_5 centos:centos6 quay.io/biocontainers/gffread:0.12.7--h9a82719_0 quay.io/biocontainers/hisat2:2.2.0--py36hf0b53f7_4 quay.io/biocontainers/prinseq:0.20.4 quay.io/biocontainers/samtools:1.9--h10a08f8_12 quay.io/biocontainers/seqkit:0.12.1--0 using docker ++ docker pull biocontainers/emboss:v6.6.0dfsg-7b1-deb_cv1 v6.6.0dfsg-7b1-deb_cv1: Pulling from biocontainers/emboss 478cd0aa93c0: Pulling fs layer 94d6a239eb0e: Pulling fs layer e8e87313e9cb: Pulling fs layer 1badce2e48be: Pulling fs layer 732b6ad56c57: Pulling fs layer f464fdba1cc8: Pulling fs layer f8a34b82a572: Pulling fs layer 1badce2e48be: Waiting 732b6ad56c57: Waiting f8a34b82a572: Waiting f464fdba1cc8: Waiting Checking the realpath of input files. 0 input_1/ 1 /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/input_1/S_l1_1.fq.gz 1 /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/input_1/S_l1_2.fq.gz 0 input_2/parasite.fa 0 0 /home/yoshitake.kazutoshi/work -> /data/yoshitake.kazutoshi/work /home/yoshitake.kazutoshi/work/pp-dev -> /data/yoshitake.kazutoshi/work/pp-dev /home/yoshitake.kazutoshi/work/pp-dev/yoshitake -> /data/yoshitake.kazutoshi/work/pp-dev/yoshitake /home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -> /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test /home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 -> /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 /data/yoshitake.kazutoshi/work /data/yoshitake.kazutoshi/work/pp-dev /data/yoshitake.kazutoshi/work/pp-dev/yoshitake /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 biocontainers/emboss:v6.6.0dfsg-7b1-deb_cv1 c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_3-kegg_2 c2997108/ubuntu-18:braker2_hisat2_5 centos:centos6 quay.io/biocontainers/gffread:0.12.7--h9a82719_0 quay.io/biocontainers/hisat2:2.2.0--py36hf0b53f7_4 quay.io/biocontainers/prinseq:0.20.4 quay.io/biocontainers/samtools:1.9--h10a08f8_12 quay.io/biocontainers/seqkit:0.12.1--0 using podman ++ podman pull centos:centos6 Resolved "centos" as an alias (/etc/containers/registries.conf.d/000-shortnames.conf) Trying to pull quay.io/centos/centos:centos6... Getting image source signatures Copying blob sha256:ff50d722b38227ec8f2bbf0cdbce428b66745077c173d8117d91376128fa532e Copying config sha256:d0957ffdf8a2ea8c8925903862b65a1b6850dbb019f88d45e927d3d5a3fa0c31 Writing manifest to image destination Storing signatures d0957ffdf8a2ea8c8925903862b65a1b6850dbb019f88d45e927d3d5a3fa0c31 ++ set +ex + set -o pipefail ++ find input_1// ++ egrep '(_R1.*|_1)[.]f(ast|)q$' ++ echo '' + r1= ++ find input_1// ++ egrep '(_R1.*|_1)[.]f(ast|)q[.]gz$' + r1gz=input_1//S_l1_1.fq.gz + '[' input_1//S_l1_1.fq.gz = '' ']' + r2= ++ for i in $r1gz +++ echo input_1//S_l1_1.fq.gz +++ egrep '_1[.]f(ast|)q[.]gz$' +++ wc -l ++ '[' 1 = 1 ']' ++ echo input_1//S_l1_1.fq.gz ++ sed 's/_1[.]f\(ast\|\)q[.]gz/_2.f\1q.gz/' + r2gz=input_1//S_l1_2.fq.gz + echo '#Check paired-end' #Check paired-end + ls input_1//S_l1_2.fq.gz ++ echo input_2/parasite.fa ++ grep '[.]gz$' ++ wc -l ++ true + '[' 0 = 1 ']' + awk '{if($0~"^>"){sub(/ .*/,"",$0)}; print $0}' input_2/parasite.fa + sed 's/\r//' + input_2=input_2/parasite.fa.ref.fa ++ basename '' ++ basename '' + '[' '!=' gmes_linux_64.tar.gz -o '!=' gm_key_64.gz ']' /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/PortablePipeline/PortablePipeline/scripts/annotation~BRAKER3: 64 行: [: 引数が多すぎます + FUNC_RUN_PODMAN quay.io/biocontainers/hisat2:2.2.0--py36hf0b53f7_4 hisat2-build -p 8 input_2/parasite.fa.ref.fa hisat2_index + PP_RUN_IMAGE=quay.io/biocontainers/hisat2:2.2.0--py36hf0b53f7_4 + shift + PP_RUN_DOCKER_CMD=("${@}") ++ date +%Y%m%d_%H%M%S_%3N + PPDOCNAME=pp20231113_200501_353_7108 + echo pp20231113_200501_353_7108 ++ echo quay.io/biocontainers/hisat2:2.2.0--py36hf0b53f7_4 ++ awk -F/ '{if(NF==2){$0="docker.io/"$0}; print $0}' + PP_RUN_IMAGE=quay.io/biocontainers/hisat2:2.2.0--py36hf0b53f7_4 + podman run --name pp20231113_200501_353_7108 -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 -w /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 -v /data/yoshitake.kazutoshi/work:/data/yoshitake.kazutoshi/work -v /data/yoshitake.kazutoshi/work/pp-dev:/data/yoshitake.kazutoshi/work/pp-dev -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 -i --rm quay.io/biocontainers/hisat2:2.2.0--py36hf0b53f7_4 hisat2-build -p 8 input_2/parasite.fa.ref.fa hisat2_index Settings: Output files: "hisat2_index.*.ht2" Line rate: 6 (line is 64 bytes) Lines per side: 1 (side is 64 bytes) Offset rate: 4 (one in 16) FTable chars: 10 Strings: unpacked Local offset rate: 3 (one in 8) Local fTable chars: 6 Local sequence length: 57344 Local sequence overlap between two consecutive indexes: 1024 Endianness: little Actual local endianness: little Sanity checking: disabled Assertions: disabled Random seed: 0 Sizeofs: void*:8, int:4, long:8, size_t:8 Input files DNA, FASTA: input_2/parasite.fa.ref.fa Reading reference sizes Time reading reference sizes: 00:00:00 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:00 Time to read SNPs and splice sites: 00:00:00 Using parameters --bmax 317396 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 317396 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:00 Allocating rank array Ranking v-sort output Ranking v-sort output time: 00:00:00 Invoking Larsson-Sadakane on ranks Invoking Larsson-Sadakane on ranks time: 00:00:00 Sanity-checking and returning Building samples Reserving space for 86 sample suffixes Generating random suffixes QSorting 86 sample offsets, eliminating duplicates QSorting sample offsets, eliminating duplicates time: 00:00:00 Multikey QSorting 86 samples (Using difference cover) Multikey QSorting samples time: 00:00:00 Calculating bucket sizes Splitting and merging Splitting and merging time: 00:00:00 Split 12, merged 39; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 7, merged 4; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 1, merged 4; iterating... Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 229528 (target: 317395) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering GFM loop Getting block 1 of 59 Reserving size (317396) for bucket 1 Getting block 2 of 59 Reserving size (317396) for bucket 2 Getting block 3 of 59 Reserving size (317396) for bucket 3 Calculating Z arrays for bucket 1 Getting block 4 of 59 Reserving size (317396) for bucket 4 Calculating Z arrays for bucket 3 Calculating Z arrays for bucket 2 Entering block accumulator loop for bucket 1: Getting block 5 of 59 Reserving size (317396) for bucket 5 Calculating Z arrays for bucket 4 Calculating Z arrays for bucket 5 Entering block accumulator loop for bucket 3: Entering block accumulator loop for bucket 2: Entering block accumulator loop for bucket 5: Entering block accumulator loop for bucket 4: Getting block 6 of 59 Reserving size (317396) for bucket 6 Calculating Z arrays for bucket 6 Entering block accumulator loop for bucket 6: Getting block 7 of 59 Reserving size (317396) for bucket 7 Calculating Z arrays for bucket 7 Entering block accumulator loop for bucket 7: Getting block 8 of 59 Reserving size (317396) for bucket 8 Calculating Z arrays for bucket 8 Entering block accumulator loop for bucket 8: bucket 1: 10% bucket 4: 10% bucket 2: 10% bucket 5: 10% bucket 6: 10% bucket 7: 10% bucket 8: 10% bucket 3: 10% bucket 1: 20% bucket 2: 20% bucket 4: 20% bucket 6: 20% bucket 7: 20% bucket 8: 20% bucket 5: 20% bucket 3: 20% bucket 1: 30% bucket 2: 30% bucket 4: 30% bucket 6: 30% bucket 3: 30% bucket 7: 30% bucket 8: 30% bucket 5: 30% bucket 2: 40% bucket 1: 40% bucket 4: 40% bucket 3: 40% bucket 6: 40% bucket 7: 40% bucket 2: 50% bucket 8: 40% bucket 5: 40% bucket 1: 50% bucket 4: 50% bucket 2: 60% bucket 3: 50% bucket 6: 50% bucket 7: 50% bucket 5: 50% bucket 8: 50% bucket 1: 60% bucket 2: 70% bucket 4: 60% bucket 3: 60% bucket 7: 60% bucket 6: 60% bucket 8: 60% bucket 5: 60% bucket 1: 70% bucket 2: 80% bucket 3: 70% bucket 4: 70% bucket 7: 70% bucket 1: 80% bucket 6: 70% bucket 8: 70% bucket 5: 70% bucket 2: 90% bucket 3: 80% bucket 4: 80% bucket 1: 90% bucket 7: 80% bucket 6: 80% bucket 5: 80% bucket 8: 80% bucket 2: 100% Sorting block of length 315861 for bucket 2 (Using difference cover) bucket 3: 90% bucket 4: 90% bucket 1: 100% Sorting block of length 25236 for bucket 1 (Using difference cover) Sorting block time: 00:00:00 Returning block of 25237 for bucket 1 bucket 6: 90% bucket 7: 90% Getting block 9 of 59 Reserving size (317396) for bucket 9 Calculating Z arrays for bucket 9 Entering block accumulator loop for bucket 9: bucket 8: 90% bucket 5: 90% bucket 3: 100% Sorting block of length 179737 for bucket 3 (Using difference cover) bucket 4: 100% Sorting block of length 231987 for bucket 4 (Using difference cover) bucket 6: 100% Sorting block of length 192174 for bucket 6 (Using difference cover) bucket 7: 100% Sorting block of length 212349 for bucket 7 (Using difference cover) bucket 9: 10% bucket 8: 100% Sorting block of length 240099 for bucket 8 (Using difference cover) bucket 5: 100% Sorting block of length 261431 for bucket 5 (Using difference cover) Sorting block time: 00:00:00 Returning block of 315862 for bucket 2 Sorting block time: 00:00:00 Returning block of 179738 for bucket 3 bucket 9: 20% Getting block 10 of 59 Reserving size (317396) for bucket 10 Calculating Z arrays for bucket 10 Entering block accumulator loop for bucket 10: Getting block 11 of 59 Reserving size (317396) for bucket 11 Calculating Z arrays for bucket 11 Entering block accumulator loop for bucket 11: Sorting block time: 00:00:00 Returning block of 231988 for bucket 4 Sorting block time: 00:00:00 Returning block of 192175 for bucket 6 Sorting block time: 00:00:00 Returning block of 212350 for bucket 7 Getting block 12 of 59 Reserving size (317396) for bucket 12 Calculating Z arrays for bucket 12 Entering block accumulator loop for bucket 12: Getting block 13 of 59 Reserving size (317396) for bucket 13 Calculating Z arrays for bucket 13 Entering block accumulator loop for bucket 13: Getting block 14 of 59 Reserving size (317396) for bucket 14 Calculating Z arrays for bucket 14 Entering block accumulator loop for bucket 14: Sorting block time: 00:00:00 Returning block of 240100 for bucket 8 bucket 9: 30% bucket 10: 10% Sorting block time: 00:00:00 Returning block of 261432 for bucket 5 Getting block 15 of 59 Reserving size (317396) for bucket 15 Calculating Z arrays for bucket 15 Entering block accumulator loop for bucket 15: bucket 11: 10% Getting block 16 of 59 Reserving size (317396) for bucket 16 Calculating Z arrays for bucket 16 Entering block accumulator loop for bucket 16: bucket 12: 10% bucket 13: 10% bucket 14: 10% bucket 9: 40% bucket 10: 20% bucket 11: 20% bucket 15: 10% bucket 16: 10% bucket 12: 20% bucket 14: 20% bucket 13: 20% bucket 9: 50% bucket 10: 30% bucket 11: 30% bucket 15: 20% bucket 14: 30% bucket 12: 30% bucket 16: 20% bucket 13: 30% bucket 9: 60% bucket 10: 40% bucket 11: 40% bucket 15: 30% bucket 14: 40% bucket 12: 40% bucket 9: 70% bucket 10: 50% bucket 13: 40% bucket 16: 30% bucket 11: 50% bucket 14: 50% bucket 15: 40% bucket 12: 50% bucket 10: 60% bucket 9: 80% bucket 13: 50% bucket 16: 40% bucket 14: 60% bucket 11: 60% bucket 15: 50% bucket 10: 70% bucket 12: 60% bucket 9: 90% bucket 13: 60% bucket 16: 50% bucket 14: 70% bucket 11: 70% bucket 10: 80% bucket 9: 100% Sorting block of length 236608 for bucket 9 (Using difference cover) bucket 12: 70% bucket 15: 60% bucket 13: 70% bucket 16: 60% bucket 14: 80% bucket 10: 90% bucket 11: 80% bucket 12: 80% bucket 15: 70% bucket 13: 80% bucket 16: 70% bucket 14: 90% Sorting block time: 00:00:00 Returning block of 236609 for bucket 9 bucket 10: 100% Sorting block of length 157060 for bucket 10 (Using difference cover) bucket 11: 90% Getting block 17 of 59 Reserving size (317396) for bucket 17 Calculating Z arrays for bucket 17 Entering block accumulator loop for bucket 17: bucket 12: 90% bucket 15: 80% bucket 13: 90% bucket 16: 80% bucket 14: 100% Sorting block of length 153879 for bucket 14 (Using difference cover) bucket 11: 100% Sorting block of length 209880 for bucket 11 (Using difference cover) Sorting block time: 00:00:00 Returning block of 157061 for bucket 10 bucket 12: 100% Sorting block of length 194732 for bucket 12 (Using difference cover) bucket 17: 10% Getting block 18 of 59 Reserving size (317396) for bucket 18 Calculating Z arrays for bucket 18 Entering block accumulator loop for bucket 18: bucket 15: 90% bucket 13: 100% Sorting block of length 287453 for bucket 13 (Using difference cover) bucket 16: 90% Sorting block time: 00:00:00 Returning block of 153880 for bucket 14 Getting block 19 of 59 Reserving size (317396) for bucket 19 Calculating Z arrays for bucket 19 Entering block accumulator loop for bucket 19: bucket 17: 20% bucket 18: 10% bucket 15: 100% Sorting block of length 236203 for bucket 15 (Using difference cover) Sorting block time: 00:00:00 Returning block of 194733 for bucket 12 bucket 16: 100% Sorting block of length 250076 for bucket 16 (Using difference cover) Sorting block time: 00:00:00 Returning block of 209881 for bucket 11 Getting block 20 of 59 Reserving size (317396) for bucket 20 Calculating Z arrays for bucket 20 Entering block accumulator loop for bucket 20: bucket 19: 10% Getting block 21 of 59 Reserving size (317396) for bucket 21 Calculating Z arrays for bucket 21 Entering block accumulator loop for bucket 21: bucket 17: 30% bucket 18: 20% Sorting block time: 00:00:00 Returning block of 287454 for bucket 13 Getting block 22 of 59 Reserving size (317396) for bucket 22 Calculating Z arrays for bucket 22 Entering block accumulator loop for bucket 22: bucket 20: 10% bucket 19: 20% Sorting block time: 00:00:00 Returning block of 236204 for bucket 15 bucket 17: 40% bucket 18: 30% bucket 21: 10% Sorting block time: 00:00:00 Returning block of 250077 for bucket 16 Getting block 23 of 59 Reserving size (317396) for bucket 23 Calculating Z arrays for bucket 23 Entering block accumulator loop for bucket 23: Getting block 24 of 59 Reserving size (317396) for bucket 24 Calculating Z arrays for bucket 24 Entering block accumulator loop for bucket 24: bucket 22: 10% bucket 20: 20% bucket 19: 30% bucket 17: 50% bucket 18: 40% bucket 21: 20% bucket 23: 10% bucket 24: 10% bucket 22: 20% bucket 20: 30% bucket 17: 60% bucket 19: 40% bucket 18: 50% bucket 21: 30% bucket 17: 70% bucket 22: 30% bucket 23: 20% bucket 24: 20% bucket 20: 40% bucket 18: 60% bucket 19: 50% bucket 21: 40% bucket 17: 80% bucket 18: 70% bucket 23: 30% bucket 22: 40% bucket 20: 50% bucket 24: 30% bucket 19: 60% bucket 21: 50% bucket 17: 90% bucket 18: 80% bucket 23: 40% bucket 22: 50% bucket 20: 60% bucket 24: 40% bucket 19: 70% bucket 21: 60% bucket 17: 100% Sorting block of length 255385 for bucket 17 (Using difference cover) bucket 18: 90% bucket 23: 50% bucket 20: 70% bucket 22: 60% bucket 24: 50% bucket 19: 80% bucket 21: 70% bucket 18: 100% Sorting block of length 193039 for bucket 18 (Using difference cover) bucket 23: 60% bucket 24: 60% bucket 22: 70% bucket 19: 90% Sorting block time: 00:00:00 Returning block of 255386 for bucket 17 bucket 20: 80% bucket 21: 80% Getting block 25 of 59 Reserving size (317396) for bucket 25 Calculating Z arrays for bucket 25 Entering block accumulator loop for bucket 25: Sorting block time: 00:00:00 Returning block of 193040 for bucket 18 bucket 23: 70% Getting block 26 of 59 Reserving size (317396) for bucket 26 Calculating Z arrays for bucket 26 Entering block accumulator loop for bucket 26: bucket 19: 100% Sorting block of length 223267 for bucket 19 (Using difference cover) bucket 22: 80% bucket 24: 70% bucket 20: 90% bucket 21: 90% bucket 25: 10% bucket 26: 10% bucket 23: 80% bucket 22: 90% bucket 24: 80% bucket 25: 20% bucket 20: 100% Sorting block of length 317369 for bucket 20 (Using difference cover) bucket 21: 100% Sorting block of length 193747 for bucket 21 (Using difference cover) Sorting block time: 00:00:00 Returning block of 223268 for bucket 19 bucket 26: 20% bucket 23: 90% bucket 22: 100% Sorting block of length 271332 for bucket 22 (Using difference cover) bucket 24: 90% bucket 25: 30% Sorting block time: 00:00:00 Returning block of 193748 for bucket 21 bucket 26: 30% bucket 23: 100% Sorting block of length 167037 for bucket 23 (Using difference cover) bucket 25: 40% bucket 24: 100% Sorting block of length 171287 for bucket 24 (Using difference cover) Sorting block time: 00:00:00 Returning block of 317370 for bucket 20 bucket 26: 40% Sorting block time: 00:00:00 Returning block of 271333 for bucket 22 bucket 25: 50% Sorting block time: 00:00:00 Returning block of 167038 for bucket 23 bucket 26: 50% Sorting block time: 00:00:00 Returning block of 171288 for bucket 24 bucket 25: 60% bucket 26: 60% bucket 25: 70% bucket 25: 80% bucket 26: 70% bucket 25: 90% bucket 26: 80% bucket 25: 100% Sorting block of length 296970 for bucket 25 (Using difference cover) bucket 26: 90% Sorting block time: 00:00:00 Returning block of 296971 for bucket 25 bucket 26: 100% Sorting block of length 261601 for bucket 26 (Using difference cover) Sorting block time: 00:00:00 Returning block of 261602 for bucket 26 Getting block 27 of 59 Reserving size (317396) for bucket 27 Calculating Z arrays for bucket 27 Entering block accumulator loop for bucket 27: Getting block 28 of 59 Reserving size (317396) for bucket 28 Calculating Z arrays for bucket 28 Entering block accumulator loop for bucket 28: Getting block 29 of 59 Reserving size (317396) for bucket 29 Calculating Z arrays for bucket 29 Entering block accumulator loop for bucket 29: Getting block 30 of 59 Reserving size (317396) for bucket 30 Calculating Z arrays for bucket 30 Entering block accumulator loop for bucket 30: Getting block 31 of 59 Reserving size (317396) for bucket 31 Calculating Z arrays for bucket 31 Entering block accumulator loop for bucket 31: Getting block 32 of 59 Reserving size (317396) for bucket 32 Calculating Z arrays for bucket 32 Entering block accumulator loop for bucket 32: Getting block 33 of 59 Reserving size (317396) for bucket 33 Calculating Z arrays for bucket 33 Entering block accumulator loop for bucket 33: Getting block 34 of 59 Reserving size (317396) for bucket 34 Calculating Z arrays for bucket 34 Entering block accumulator loop for bucket 34: bucket 27: 10% bucket 28: 10% bucket 29: 10% bucket 32: 10% bucket 33: 10% bucket 31: 10% bucket 30: 10% bucket 34: 10% bucket 27: 20% bucket 28: 20% bucket 32: 20% bucket 33: 20% bucket 29: 20% bucket 31: 20% bucket 30: 20% bucket 34: 20% bucket 27: 30% bucket 28: 30% bucket 33: 30% bucket 32: 30% bucket 29: 30% bucket 31: 30% bucket 34: 30% bucket 30: 30% bucket 28: 40% bucket 27: 40% bucket 33: 40% bucket 32: 40% bucket 29: 40% bucket 30: 40% bucket 31: 40% bucket 28: 50% bucket 27: 50% bucket 34: 40% bucket 33: 50% bucket 29: 50% bucket 32: 50% bucket 31: 50% bucket 27: 60% bucket 30: 50% bucket 34: 50% bucket 28: 60% bucket 33: 60% bucket 29: 60% bucket 32: 60% bucket 27: 70% bucket 34: 60% bucket 28: 70% bucket 33: 70% bucket 30: 60% bucket 31: 60% bucket 32: 70% bucket 29: 70% bucket 27: 80% bucket 34: 70% bucket 28: 80% bucket 33: 80% bucket 31: 70% bucket 32: 80% bucket 30: 70% bucket 29: 80% bucket 27: 90% bucket 28: 90% bucket 34: 80% bucket 33: 90% bucket 32: 90% bucket 31: 80% bucket 30: 80% bucket 29: 90% bucket 28: 100% Sorting block of length 258899 for bucket 28 (Using difference cover) bucket 27: 100% Sorting block of length 103285 for bucket 27 (Using difference cover) bucket 34: 90% bucket 32: 100% Sorting block of length 304022 for bucket 32 (Using difference cover) bucket 33: 100% Sorting block of length 220734 for bucket 33 (Using difference cover) bucket 31: 90% bucket 30: 90% bucket 29: 100% Sorting block of length 298284 for bucket 29 (Using difference cover) Sorting block time: 00:00:00 Returning block of 103286 for bucket 27 Getting block 35 of 59 Reserving size (317396) for bucket 35 Calculating Z arrays for bucket 35 Entering block accumulator loop for bucket 35: bucket 34: 100% Sorting block of length 157583 for bucket 34 (Using difference cover) Sorting block time: 00:00:00 Returning block of 258900 for bucket 28 bucket 31: 100% Sorting block of length 291711 for bucket 31 (Using difference cover) Sorting block time: 00:00:00 Returning block of 220735 for bucket 33 Getting block 36 of 59 Reserving size (317396) for bucket 36 Calculating Z arrays for bucket 36 Entering block accumulator loop for bucket 36: Getting block 37 of 59 Reserving size (317396) for bucket 37 Calculating Z arrays for bucket 37 Entering block accumulator loop for bucket 37: bucket 30: 100% Sorting block of length 243228 for bucket 30 (Using difference cover) Sorting block time: 00:00:00 Returning block of 304023 for bucket 32 bucket 35: 10% Sorting block time: 00:00:00 Returning block of 157584 for bucket 34 Getting block 38 of 59 Reserving size (317396) for bucket 38 Calculating Z arrays for bucket 38 Entering block accumulator loop for bucket 38: Getting block 39 of 59 Reserving size (317396) for bucket 39 Calculating Z arrays for bucket 39 Entering block accumulator loop for bucket 39: Sorting block time: 00:00:00 Returning block of 298285 for bucket 29 bucket 36: 10% bucket 37: 10% Getting block 40 of 59 Reserving size (317396) for bucket 40 Calculating Z arrays for bucket 40 Entering block accumulator loop for bucket 40: bucket 35: 20% Sorting block time: 00:00:00 Returning block of 291712 for bucket 31 Sorting block time: 00:00:00 Returning block of 243229 for bucket 30 bucket 38: 10% bucket 39: 10% Getting block 41 of 59 Reserving size (317396) for bucket 41 Calculating Z arrays for bucket 41 Entering block accumulator loop for bucket 41: Getting block 42 of 59 Reserving size (317396) for bucket 42 Calculating Z arrays for bucket 42 Entering block accumulator loop for bucket 42: bucket 40: 10% bucket 37: 20% bucket 36: 20% bucket 35: 30% bucket 38: 20% bucket 39: 20% bucket 40: 20% bucket 41: 10% bucket 42: 10% bucket 37: 30% bucket 35: 40% bucket 36: 30% bucket 38: 30% bucket 40: 30% bucket 41: 20% bucket 42: 20% bucket 37: 40% bucket 39: 30% bucket 35: 50% bucket 38: 40% bucket 40: 40% bucket 36: 40% bucket 37: 50% bucket 41: 30% bucket 42: 30% bucket 35: 60% bucket 39: 40% bucket 38: 50% bucket 40: 50% bucket 37: 60% bucket 41: 40% bucket 42: 40% bucket 36: 50% bucket 35: 70% bucket 39: 50% bucket 40: 60% bucket 38: 60% bucket 37: 70% bucket 41: 50% bucket 42: 50% bucket 35: 80% bucket 40: 70% bucket 39: 60% bucket 38: 70% bucket 36: 60% bucket 37: 80% bucket 41: 60% bucket 42: 60% bucket 40: 80% bucket 38: 80% bucket 35: 90% bucket 39: 70% bucket 37: 90% bucket 36: 70% bucket 41: 70% bucket 42: 70% bucket 38: 90% bucket 40: 90% bucket 35: 100% Sorting block of length 237486 for bucket 35 (Using difference cover) bucket 37: 100% Sorting block of length 291568 for bucket 37 (Using difference cover) bucket 39: 80% bucket 41: 80% bucket 42: 80% bucket 36: 80% bucket 38: 100% Sorting block of length 244260 for bucket 38 (Using difference cover) bucket 40: 100% Sorting block of length 233272 for bucket 40 (Using difference cover) bucket 39: 90% bucket 42: 90% bucket 41: 90% Sorting block time: 00:00:00 Returning block of 237487 for bucket 35 Sorting block time: 00:00:00 Returning block of 291569 for bucket 37 bucket 36: 90% Getting block 43 of 59 Reserving size (317396) for bucket 43 Calculating Z arrays for bucket 43 Entering block accumulator loop for bucket 43: Getting block 44 of 59 Reserving size (317396) for bucket 44 Calculating Z arrays for bucket 44 Entering block accumulator loop for bucket 44: Sorting block time: 00:00:00 Returning block of 244261 for bucket 38 Sorting block time: 00:00:00 Returning block of 233273 for bucket 40 Getting block 45 of 59 Reserving size (317396) for bucket 45 Calculating Z arrays for bucket 45 Entering block accumulator loop for bucket 45: bucket 42: 100% Sorting block of length 297133 for bucket 42 (Using difference cover) bucket 41: 100% Sorting block of length 250351 for bucket 41 (Using difference cover) Getting block 46 of 59 Reserving size (317396) for bucket 46 Calculating Z arrays for bucket 46 Entering block accumulator loop for bucket 46: bucket 39: 100% Sorting block of length 214666 for bucket 39 (Using difference cover) bucket 36: 100% Sorting block of length 101213 for bucket 36 (Using difference cover) bucket 44: 10% bucket 45: 10% bucket 46: 10% bucket 43: 10% Sorting block time: 00:00:01 Returning block of 101214 for bucket 36 Sorting block time: 00:00:01 Returning block of 250352 for bucket 41 Getting block 47 of 59 Reserving size (317396) for bucket 47 Calculating Z arrays for bucket 47 Entering block accumulator loop for bucket 47: Sorting block time: 00:00:01 Returning block of 214667 for bucket 39 Sorting block time: 00:00:01 Returning block of 297134 for bucket 42 Getting block 48 of 59 Reserving size (317396) for bucket 48 Calculating Z arrays for bucket 48 Entering block accumulator loop for bucket 48: Getting block 49 of 59 Reserving size (317396) for bucket 49 Calculating Z arrays for bucket 49 Entering block accumulator loop for bucket 49: bucket 44: 20% Getting block 50 of 59 Reserving size (317396) for bucket 50 Calculating Z arrays for bucket 50 Entering block accumulator loop for bucket 50: bucket 45: 20% bucket 43: 20% bucket 46: 20% bucket 48: 10% bucket 49: 10% bucket 47: 10% bucket 43: 30% bucket 44: 30% bucket 45: 30% bucket 50: 10% bucket 46: 30% bucket 43: 40% bucket 48: 20% bucket 49: 20% bucket 44: 40% bucket 45: 40% bucket 50: 20% bucket 47: 20% bucket 43: 50% bucket 46: 40% bucket 48: 30% bucket 49: 30% bucket 44: 50% bucket 45: 50% bucket 50: 30% bucket 43: 60% bucket 47: 30% bucket 48: 40% bucket 46: 50% bucket 49: 40% bucket 44: 60% bucket 45: 60% bucket 43: 70% bucket 50: 40% bucket 48: 50% bucket 47: 40% bucket 46: 60% bucket 49: 50% bucket 44: 70% bucket 43: 80% bucket 45: 70% bucket 50: 50% bucket 48: 60% bucket 49: 60% bucket 46: 70% bucket 43: 90% bucket 44: 80% bucket 45: 80% bucket 47: 50% bucket 50: 60% bucket 48: 70% bucket 43: 100% Sorting block of length 300961 for bucket 43 (Using difference cover) bucket 49: 70% bucket 44: 90% bucket 46: 80% bucket 45: 90% bucket 47: 60% bucket 50: 70% bucket 48: 80% bucket 44: 100% Sorting block of length 286470 for bucket 44 (Using difference cover) bucket 49: 80% bucket 45: 100% Sorting block of length 309474 for bucket 45 (Using difference cover) bucket 46: 90% bucket 50: 80% Sorting block time: 00:00:00 Returning block of 300962 for bucket 43 bucket 47: 70% bucket 48: 90% bucket 49: 90% Getting block 51 of 59 Reserving size (317396) for bucket 51 Calculating Z arrays for bucket 51 Entering block accumulator loop for bucket 51: bucket 46: 100% Sorting block of length 209376 for bucket 46 (Using difference cover) Sorting block time: 00:00:00 Returning block of 286471 for bucket 44 Sorting block time: 00:00:00 Returning block of 309475 for bucket 45 bucket 50: 90% bucket 48: 100% Sorting block of length 188712 for bucket 48 (Using difference cover) Getting block 52 of 59 Reserving size (317396) for bucket 52 Calculating Z arrays for bucket 52 Entering block accumulator loop for bucket 52: bucket 47: 80% Getting block 53 of 59 Reserving size (317396) for bucket 53 Calculating Z arrays for bucket 53 Entering block accumulator loop for bucket 53: bucket 49: 100% Sorting block of length 317074 for bucket 49 (Using difference cover) bucket 51: 10% Sorting block time: 00:00:00 Returning block of 209377 for bucket 46 bucket 50: 100% Sorting block of length 272545 for bucket 50 (Using difference cover) Getting block 54 of 59 Reserving size (317396) for bucket 54 Calculating Z arrays for bucket 54 Entering block accumulator loop for bucket 54: Sorting block time: 00:00:00 Returning block of 188713 for bucket 48 bucket 53: 10% Getting block 55 of 59 Reserving size (317396) for bucket 55 Calculating Z arrays for bucket 55 bucket 51: 20% bucket 52: 10% Entering block accumulator loop for bucket 55: bucket 47: 90% Sorting block time: 00:00:00 Returning block of 317075 for bucket 49 bucket 54: 10% bucket 52: 20% bucket 53: 20% Getting block 56 of 59 Reserving size (317396) for bucket 56 Calculating Z arrays for bucket 56 Entering block accumulator loop for bucket 56: bucket 51: 30% bucket 55: 10% Sorting block time: 00:00:00 Returning block of 272546 for bucket 50 Getting block 57 of 59 Reserving size (317396) for bucket 57 Calculating Z arrays for bucket 57 Entering block accumulator loop for bucket 57: bucket 47: 100% Sorting block of length 266355 for bucket 47 (Using difference cover) bucket 52: 30% bucket 54: 20% bucket 56: 10% bucket 51: 40% bucket 53: 30% bucket 55: 20% bucket 57: 10% bucket 52: 40% bucket 56: 20% bucket 54: 30% bucket 51: 50% bucket 53: 40% bucket 55: 30% bucket 57: 20% Sorting block time: 00:00:00 Returning block of 266356 for bucket 47 bucket 52: 50% bucket 56: 30% bucket 54: 40% bucket 53: 50% bucket 51: 60% Getting block 58 of 59 Reserving size (317396) for bucket 58 Calculating Z arrays for bucket 58 Entering block accumulator loop for bucket 58: bucket 55: 40% bucket 57: 30% bucket 56: 40% bucket 52: 60% bucket 54: 50% bucket 51: 70% bucket 53: 60% bucket 55: 50% bucket 57: 40% bucket 58: 10% bucket 56: 50% bucket 52: 70% bucket 54: 60% bucket 51: 80% bucket 53: 70% bucket 55: 60% bucket 57: 50% bucket 56: 60% bucket 52: 80% bucket 51: 90% bucket 54: 70% bucket 58: 20% bucket 55: 70% bucket 53: 80% bucket 57: 60% bucket 56: 70% bucket 52: 90% bucket 54: 80% bucket 51: 100% Sorting block of length 111013 for bucket 51 (Using difference cover) bucket 55: 80% bucket 58: 30% bucket 53: 90% bucket 57: 70% bucket 56: 80% bucket 52: 100% Sorting block of length 297672 for bucket 52 (Using difference cover) bucket 54: 90% bucket 55: 90% Sorting block time: 00:00:00 Returning block of 111014 for bucket 51 Getting block 59 of 59 Reserving size (317396) for bucket 59 Calculating Z arrays for bucket 59 Entering block accumulator loop for bucket 59: bucket 53: 100% Sorting block of length 205886 for bucket 53 (Using difference cover) bucket 57: 80% bucket 56: 90% bucket 58: 40% bucket 59: 10% Sorting block time: 00:00:00 Returning block of 297673 for bucket 52 bucket 55: 100% Sorting block of length 242121 for bucket 55 (Using difference cover) bucket 57: 90% bucket 56: 100% Sorting block of length 187618 for bucket 56 (Using difference cover) bucket 59: 20% bucket 54: 100% Sorting block of length 150210 for bucket 54 (Using difference cover) Sorting block time: 00:00:00 Returning block of 205887 for bucket 53 bucket 58: 50% bucket 59: 30% bucket 57: 100% Sorting block of length 281318 for bucket 57 (Using difference cover) Sorting block time: 00:00:00 Returning block of 150211 for bucket 54 Sorting block time: 00:00:00 Returning block of 187619 for bucket 56 bucket 59: 40% bucket 58: 60% Sorting block time: 00:00:00 Returning block of 242122 for bucket 55 bucket 59: 50% bucket 58: 70% Sorting block time: 00:00:00 Returning block of 281319 for bucket 57 bucket 59: 60% bucket 58: 80% bucket 59: 70% bucket 58: 90% bucket 59: 80% bucket 58: 100% Sorting block of length 125664 for bucket 58 (Using difference cover) bucket 59: 90% Sorting block time: 00:00:00 Returning block of 125665 for bucket 58 bucket 59: 100% Sorting block of length 306213 for bucket 59 (Using difference cover) Sorting block time: 00:00:00 Returning block of 306214 for bucket 59 Exited GFM loop fchr[A]: 0 fchr[C]: 5036868 fchr[G]: 6776772 fchr[T]: 8516403 fchr[$]: 13542234 Exiting GFM::buildToDisk() Returning from initFromVector Wrote 8743985 bytes to primary GFM file: hisat2_index.1.ht2 Wrote 3385564 bytes to secondary GFM file: hisat2_index.2.ht2 Re-opening _in1 and _in2 as input streams Returning from GFM constructor Returning from initFromVector Wrote 11673573 bytes to primary GFM file: hisat2_index.5.ht2 Wrote 3394706 bytes to secondary GFM file: hisat2_index.6.ht2 Re-opening _in5 and _in5 as input streams Returning from HGFM constructor Headers: len: 13542234 gbwtLen: 13542235 nodes: 13542235 sz: 3385559 gbwtSz: 3385559 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 0 eftabSz: 0 ftabLen: 1048577 ftabSz: 4194308 offsLen: 846390 offsSz: 3385560 lineSz: 64 sideSz: 64 sideGbwtSz: 48 sideGbwtLen: 192 numSides: 70533 numLines: 70533 gbwtTotLen: 4514112 gbwtTotSz: 4514112 reverse: 0 linearFM: Yes Total time for call to driver() for forward index: 00:00:12 + mkdir -p output.prinseq + for i in $r1gz + xargs '-d\n' -I '{}' -P 8 bash -c '{}' ++ echo input_1//S_l1_1.fq.gz ++ egrep '_1[.]f(ast|)q[.]gz$' ++ wc -l + '[' 1 = 1 ']' ++ echo input_1//S_l1_1.fq.gz ++ sed 's/_1[.]f\(ast\|\)q[.]gz/_2.f\1q.gz/' + j=input_1//S_l1_2.fq.gz ++ basename input_1//S_l1_1.fq.gz .gz + i2=S_l1_1.fq ++ basename input_1//S_l1_2.fq.gz .gz + j2=S_l1_2.fq ++ basename input_1//S_l1_1.fq.gz + echo zcat input_1//S_l1_1.fq.gz '>' 'S_l1_1.fq;' zcat input_1//S_l1_2.fq.gz '>' 'S_l1_2.fq;' 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/pp-podman-list;' podman run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -v /data/yoshitake.kazutoshi/work:/data/yoshitake.kazutoshi/work -v /data/yoshitake.kazutoshi/work/pp-dev:/data/yoshitake.kazutoshi/work/pp-dev -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 -u root -i --rm quay.io/biocontainers/prinseq:0.20.4 prinseq-lite.pl -fastq S_l1_1.fq -fastq2 S_l1_2.fq -out_good output.prinseq/S_l1_1.fq -out_bad null -out_format 3 -trim_tail_right 5 -trim_qual_right 20 -ns_max_p 20 -min_len 30 -trim_qual_window 5 '>' log.prinseq.S_l1_1.fq.gz '2>&1' ';' mv output.prinseq/S_l1_1.fq_1.fastq 'output.prinseq/S_l1_1.fq;' mv output.prinseq/S_l1_1.fq_2.fastq 'output.prinseq/S_l1_2.fq;rm' -f S_l1_1.fq S_l1_2.fq + rm -f output.prinseq/S_l1_1.fq_1_singletons.fastq output.prinseq/S_l1_1.fq_2_singletons.fastq ++ find output.prinseq/ ++ egrep '(_R1.*|_1)[.]f(ast|)q$' + r1=output.prinseq/S_l1_1.fq + echo '' + for i in $r1 + xargs '-d\n' -I '{}' -P 1 bash -c '{}' ++ echo output.prinseq/S_l1_1.fq ++ egrep '_1[.]f(ast|)q$' ++ wc -l + '[' 1 = 1 ']' ++ echo output.prinseq/S_l1_1.fq ++ sed 's/_1[.]f\(ast\|\)q/_2.f\1q/' + j=output.prinseq/S_l1_2.fq ++ basename output.prinseq/S_l1_1.fq ++ basename output.prinseq/S_l1_1.fq ++ basename output.prinseq/S_l1_1.fq + echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/pp-podman-list;' podman run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -v /data/yoshitake.kazutoshi/work:/data/yoshitake.kazutoshi/work -v /data/yoshitake.kazutoshi/work/pp-dev:/data/yoshitake.kazutoshi/work/pp-dev -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 -u root -i --rm quay.io/biocontainers/hisat2:2.2.0--py36hf0b53f7_4 hisat2 --rna-strandness RF -p 8 --dta --dta-cufflinks -x hisat2_index -1 output.prinseq/S_l1_1.fq -2 output.prinseq/S_l1_2.fq --rg-id output.prinseq/S_l1_1.fq --rg SM:output.prinseq/S_l1_1.fq '2>' log.hisat2.S_l1_1.fq '|(PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/pp-podman-list;' podman run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -v /data/yoshitake.kazutoshi/work:/data/yoshitake.kazutoshi/work -v /data/yoshitake.kazutoshi/work/pp-dev:/data/yoshitake.kazutoshi/work/pp-dev -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 -u root -i --rm quay.io/biocontainers/samtools:1.9--h10a08f8_12 samtools sort -@ 8 -o S_l1_1.fq.bam ');' 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/pp-podman-list;' podman run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -v /data/yoshitake.kazutoshi/work:/data/yoshitake.kazutoshi/work -v /data/yoshitake.kazutoshi/work/pp-dev:/data/yoshitake.kazutoshi/work/pp-dev -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 -u root -i --rm quay.io/biocontainers/samtools:1.9--h10a08f8_12 samtools index S_l1_1.fq.bam ++ basename output.prinseq/S_l1_1.fq + echo S_l1_1.fq.bam [bam_sort_core] merging from 24 files and 8 in-memory blocks... ++ awk '{ORS=","; print $0}' bamlist ++ sed 's/^,//; s/,$//' + bamlist=S_l1_1.fq.bam + FUNC_RUN_PODMAN c2997108/ubuntu-18:braker2_hisat2_5 braker.pl '--genome='\''input_2/parasite.fa.ref.fa'\''' --species=run1 '--bam='\''S_l1_1.fq.bam'\''' '' + PP_RUN_IMAGE=c2997108/ubuntu-18:braker2_hisat2_5 + shift + PP_RUN_DOCKER_CMD=("${@}") ++ date +%Y%m%d_%H%M%S_%3N + PPDOCNAME=pp20231113_212634_649_18183 + echo pp20231113_212634_649_18183 ++ echo c2997108/ubuntu-18:braker2_hisat2_5 ++ awk -F/ '{if(NF==2){$0="docker.io/"$0}; print $0}' + PP_RUN_IMAGE=docker.io/c2997108/ubuntu-18:braker2_hisat2_5 + podman run --name pp20231113_212634_649_18183 -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 -w /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 -v /data/yoshitake.kazutoshi/work:/data/yoshitake.kazutoshi/work -v /data/yoshitake.kazutoshi/work/pp-dev:/data/yoshitake.kazutoshi/work/pp-dev -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 -i --rm docker.io/c2997108/ubuntu-18:braker2_hisat2_5 braker.pl '--genome='\''input_2/parasite.fa.ref.fa'\''' --species=run1 '--bam='\''S_l1_1.fq.bam'\''' '' Error: crun: executable file `braker.pl` not found in $PATH: No such file or directory: OCI runtime attempted to invoke a command that was not found PID: 2523905 pp runtime error. Checking the realpath of input files. 0 input_1/ 1 /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/input_1/S_l1_1.fq.gz 1 /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/input_1/S_l1_2.fq.gz 0 input_2/parasite.fa 0 0 /home/yoshitake.kazutoshi/work -> /data/yoshitake.kazutoshi/work /home/yoshitake.kazutoshi/work/pp-dev -> /data/yoshitake.kazutoshi/work/pp-dev /home/yoshitake.kazutoshi/work/pp-dev/yoshitake -> /data/yoshitake.kazutoshi/work/pp-dev/yoshitake /home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -> /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test /home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 -> /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 /data/yoshitake.kazutoshi/work /data/yoshitake.kazutoshi/work/pp-dev /data/yoshitake.kazutoshi/work/pp-dev/yoshitake /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 biocontainers/emboss:v6.6.0dfsg-7b1-deb_cv1 c2997108/braker:3 c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_3-kegg_2 c2997108/ubuntu-18:braker2_hisat2_5 centos:centos6 quay.io/biocontainers/gffread:0.12.7--h9a82719_0 quay.io/biocontainers/hisat2:2.2.0--py36hf0b53f7_4 quay.io/biocontainers/prinseq:0.20.4 quay.io/biocontainers/samtools:1.9--h10a08f8_12 quay.io/biocontainers/seqkit:0.12.1--0 using podman ++ podman pull centos:centos6 Trying to pull quay.io/centos/centos:centos6... Getting image source signatures Copying blob sha256:ff50d722b38227ec8f2bbf0cdbce428b66745077c173d8117d91376128fa532e Copying config sha256:d0957ffdf8a2ea8c8925903862b65a1b6850dbb019f88d45e927d3d5a3fa0c31 Writing manifest to image destination Storing signatures d0957ffdf8a2ea8c8925903862b65a1b6850dbb019f88d45e927d3d5a3fa0c31 ++ set +ex + set -o pipefail ++ find input_1// ++ egrep '(_R1.*|_1)[.]f(ast|)q$' ++ echo '' + r1= ++ find input_1// ++ egrep '(_R1.*|_1)[.]f(ast|)q[.]gz$' + r1gz=input_1//S_l1_1.fq.gz + '[' input_1//S_l1_1.fq.gz = '' ']' + r2= ++ for i in $r1gz +++ echo input_1//S_l1_1.fq.gz +++ egrep '_1[.]f(ast|)q[.]gz$' +++ wc -l ++ '[' 1 = 1 ']' ++ echo input_1//S_l1_1.fq.gz ++ sed 's/_1[.]f\(ast\|\)q[.]gz/_2.f\1q.gz/' + r2gz=input_1//S_l1_2.fq.gz + echo '#Check paired-end' #Check paired-end + ls input_1//S_l1_2.fq.gz ++ echo input_2/parasite.fa ++ grep '[.]gz$' ++ wc -l ++ true + '[' 0 = 1 ']' + awk '{if($0~"^>"){sub(/ .*/,"",$0)}; print $0}' input_2/parasite.fa + sed 's/\r//' + input_2=input_2/parasite.fa.ref.fa + mkdir -p output.prinseq + for i in $r1gz ++ echo input_1//S_l1_1.fq.gz ++ egrep '_1[.]f(ast|)q[.]gz$' ++ wc -l + '[' 1 = 1 ']' ++ echo input_1//S_l1_1.fq.gz ++ sed 's/_1[.]f\(ast\|\)q[.]gz/_2.f\1q.gz/' + j=input_1//S_l1_2.fq.gz ++ basename input_1//S_l1_1.fq.gz .gz + i2=S_l1_1.fq ++ basename input_1//S_l1_2.fq.gz .gz + j2=S_l1_2.fq ++ basename input_1//S_l1_1.fq.gz + echo zcat input_1//S_l1_1.fq.gz '>' 'S_l1_1.fq;' zcat input_1//S_l1_2.fq.gz '>' 'S_l1_2.fq;' 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/pp-podman-list;' podman run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -v /data/yoshitake.kazutoshi/work:/data/yoshitake.kazutoshi/work -v /data/yoshitake.kazutoshi/work/pp-dev:/data/yoshitake.kazutoshi/work/pp-dev -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 -u root -i --rm quay.io/biocontainers/prinseq:0.20.4 prinseq-lite.pl -fastq S_l1_1.fq -fastq2 S_l1_2.fq -out_good output.prinseq/S_l1_1.fq -out_bad null -out_format 3 -trim_tail_right 5 -trim_qual_right 20 -ns_max_p 20 -min_len 30 -trim_qual_window 5 '>' log.prinseq.S_l1_1.fq.gz '2>&1' ';' mv output.prinseq/S_l1_1.fq_1.fastq 'output.prinseq/S_l1_1.fq;' mv output.prinseq/S_l1_1.fq_2.fastq 'output.prinseq/S_l1_2.fq;rm' -f S_l1_1.fq S_l1_2.fq zcat input_1//S_l1_1.fq.gz > S_l1_1.fq; zcat input_1//S_l1_2.fq.gz > S_l1_2.fq; PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/pp-podman-list; podman run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -v /data/yoshitake.kazutoshi/work:/data/yoshitake.kazutoshi/work -v /data/yoshitake.kazutoshi/work/pp-dev:/data/yoshitake.kazutoshi/work/pp-dev -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 -u root -i --rm quay.io/biocontainers/prinseq:0.20.4 prinseq-lite.pl -fastq S_l1_1.fq -fastq2 S_l1_2.fq -out_good output.prinseq/S_l1_1.fq -out_bad null -out_format 3 -trim_tail_right 5 -trim_qual_right 20 -ns_max_p 20 -min_len 30 -trim_qual_window 5 > log.prinseq.S_l1_1.fq.gz 2>&1 ; mv output.prinseq/S_l1_1.fq_1.fastq output.prinseq/S_l1_1.fq; mv output.prinseq/S_l1_1.fq_2.fastq output.prinseq/S_l1_2.fq;rm -f S_l1_1.fq S_l1_2.fq ++ find output.prinseq/ ++ egrep '(_R1.*|_1)[.]f(ast|)q$' + r1=output.prinseq/S_l1_1.fq + echo '' + for i in $r1 ++ echo output.prinseq/S_l1_1.fq ++ egrep '_1[.]f(ast|)q$' ++ wc -l + '[' 1 = 1 ']' ++ echo output.prinseq/S_l1_1.fq ++ sed 's/_1[.]f\(ast\|\)q/_2.f\1q/' + j=output.prinseq/S_l1_2.fq ++ basename output.prinseq/S_l1_1.fq ++ basename output.prinseq/S_l1_1.fq ++ basename output.prinseq/S_l1_1.fq + echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/pp-podman-list;' podman run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -v /data/yoshitake.kazutoshi/work:/data/yoshitake.kazutoshi/work -v /data/yoshitake.kazutoshi/work/pp-dev:/data/yoshitake.kazutoshi/work/pp-dev -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 -u root -i --rm quay.io/biocontainers/hisat2:2.2.0--py36hf0b53f7_4 hisat2 --rna-strandness RF -p 8 --dta --dta-cufflinks -x hisat2_index -1 output.prinseq/S_l1_1.fq -2 output.prinseq/S_l1_2.fq --rg-id output.prinseq/S_l1_1.fq --rg SM:output.prinseq/S_l1_1.fq '2>' log.hisat2.S_l1_1.fq '|(PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/pp-podman-list;' podman run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -v /data/yoshitake.kazutoshi/work:/data/yoshitake.kazutoshi/work -v /data/yoshitake.kazutoshi/work/pp-dev:/data/yoshitake.kazutoshi/work/pp-dev -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 -u root -i --rm quay.io/biocontainers/samtools:1.9--h10a08f8_12 samtools sort -@ 8 -o S_l1_1.fq.bam ');' 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/pp-podman-list;' podman run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -v /data/yoshitake.kazutoshi/work:/data/yoshitake.kazutoshi/work -v /data/yoshitake.kazutoshi/work/pp-dev:/data/yoshitake.kazutoshi/work/pp-dev -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 -u root -i --rm quay.io/biocontainers/samtools:1.9--h10a08f8_12 samtools index S_l1_1.fq.bam PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/pp-podman-list; podman run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -v /data/yoshitake.kazutoshi/work:/data/yoshitake.kazutoshi/work -v /data/yoshitake.kazutoshi/work/pp-dev:/data/yoshitake.kazutoshi/work/pp-dev -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 -u root -i --rm quay.io/biocontainers/hisat2:2.2.0--py36hf0b53f7_4 hisat2 --rna-strandness RF -p 8 --dta --dta-cufflinks -x hisat2_index -1 output.prinseq/S_l1_1.fq -2 output.prinseq/S_l1_2.fq --rg-id output.prinseq/S_l1_1.fq --rg SM:output.prinseq/S_l1_1.fq 2> log.hisat2.S_l1_1.fq |(PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/pp-podman-list; podman run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -v /data/yoshitake.kazutoshi/work:/data/yoshitake.kazutoshi/work -v /data/yoshitake.kazutoshi/work/pp-dev:/data/yoshitake.kazutoshi/work/pp-dev -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 -u root -i --rm quay.io/biocontainers/samtools:1.9--h10a08f8_12 samtools sort -@ 8 -o S_l1_1.fq.bam ); PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/pp-podman-list; podman run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -v /data/yoshitake.kazutoshi/work:/data/yoshitake.kazutoshi/work -v /data/yoshitake.kazutoshi/work/pp-dev:/data/yoshitake.kazutoshi/work/pp-dev -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 -u root -i --rm quay.io/biocontainers/samtools:1.9--h10a08f8_12 samtools index S_l1_1.fq.bam ++ basename output.prinseq/S_l1_1.fq + echo S_l1_1.fq.bam ++ awk '{ORS=","; print $0}' bamlist ++ sed 's/^,//; s/,$//' + bamlist=S_l1_1.fq.bam + FUNC_RUN_PODMAN c2997108/braker:3 braker.pl --genome=input_2/parasite.fa.ref.fa --species=run1 --bam=S_l1_1.fq.bam '' + PP_RUN_IMAGE=c2997108/braker:3 + shift + PP_RUN_DOCKER_CMD=("${@}") ++ date +%Y%m%d_%H%M%S_%3N + PPDOCNAME=pp20231113_213931_362_22257 + echo pp20231113_213931_362_22257 ++ echo c2997108/braker:3 ++ awk -F/ '{if(NF==2){$0="docker.io/"$0}; print $0}' + PP_RUN_IMAGE=docker.io/c2997108/braker:3 + podman run --name pp20231113_213931_362_22257 -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 -w /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 -v /data/yoshitake.kazutoshi/work:/data/yoshitake.kazutoshi/work -v /data/yoshitake.kazutoshi/work/pp-dev:/data/yoshitake.kazutoshi/work/pp-dev -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 -i --rm docker.io/c2997108/braker:3 braker.pl --genome=input_2/parasite.fa.ref.fa --species=run1 --bam=S_l1_1.fq.bam '' #********************************************************************************** # BRAKER CONFIGURATION #********************************************************************************** # BRAKER CALL: /opt/BRAKER/scripts/braker.pl --genome=input_2/parasite.fa.ref.fa --species=run1 --bam=S_l1_1.fq.bam # Mon Nov 13 12:39:32 2023: braker.pl version 3.0.5 # Mon Nov 13 12:39:32 2023: ERROR: in file /opt/BRAKER/scripts/braker.pl at line 825 Do not have write permission for /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3. Please use command 'chmod' to reset permissions, or specify another working directory with option --workingdir=... PID: 2618332 pp runtime error. Checking the realpath of input files. 0 input_1/ 1 /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/input_1/S_l1_1.fq.gz 1 /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/input_1/S_l1_2.fq.gz 0 input_2/parasite.fa 0 0 /home/yoshitake.kazutoshi/work -> /data/yoshitake.kazutoshi/work /home/yoshitake.kazutoshi/work/pp-dev -> /data/yoshitake.kazutoshi/work/pp-dev /home/yoshitake.kazutoshi/work/pp-dev/yoshitake -> /data/yoshitake.kazutoshi/work/pp-dev/yoshitake /home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -> /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test /home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 -> /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 /data/yoshitake.kazutoshi/work /data/yoshitake.kazutoshi/work/pp-dev /data/yoshitake.kazutoshi/work/pp-dev/yoshitake /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 biocontainers/emboss:v6.6.0dfsg-7b1-deb_cv1 c2997108/braker:3 c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_3-kegg_2 c2997108/ubuntu-18:braker2_hisat2_5 centos:centos6 quay.io/biocontainers/gffread:0.12.7--h9a82719_0 quay.io/biocontainers/hisat2:2.2.0--py36hf0b53f7_4 quay.io/biocontainers/prinseq:0.20.4 quay.io/biocontainers/samtools:1.9--h10a08f8_12 quay.io/biocontainers/seqkit:0.12.1--0 using podman ++ podman pull centos:centos6 Trying to pull quay.io/centos/centos:centos6... Error: parsing image configuration: Get "http://m32s:5001/v2/centos/centos/blobs/sha256:d0957ffdf8a2ea8c8925903862b65a1b6850dbb019f88d45e927d3d5a3fa0c31": dial tcp: lookup m32s on 192.168.200.201:53: no such host PID: 2622182 pp runtime error. Checking the realpath of input files. 0 input_1/ 1 /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/input_1/S_l1_1.fq.gz 1 /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/input_1/S_l1_2.fq.gz 0 input_2/parasite.fa 0 0 /home/yoshitake.kazutoshi/work -> /data/yoshitake.kazutoshi/work /home/yoshitake.kazutoshi/work/pp-dev -> /data/yoshitake.kazutoshi/work/pp-dev /home/yoshitake.kazutoshi/work/pp-dev/yoshitake -> /data/yoshitake.kazutoshi/work/pp-dev/yoshitake /home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -> /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test /home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 -> /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 /data/yoshitake.kazutoshi/work /data/yoshitake.kazutoshi/work/pp-dev /data/yoshitake.kazutoshi/work/pp-dev/yoshitake /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 biocontainers/emboss:v6.6.0dfsg-7b1-deb_cv1 c2997108/braker:3 c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_3-kegg_2 c2997108/ubuntu-18:braker2_hisat2_5 centos:centos6 quay.io/biocontainers/gffread:0.12.7--h9a82719_0 quay.io/biocontainers/hisat2:2.2.0--py36hf0b53f7_4 quay.io/biocontainers/prinseq:0.20.4 quay.io/biocontainers/samtools:1.9--h10a08f8_12 quay.io/biocontainers/seqkit:0.12.1--0 using podman ++ podman pull centos:centos6 Trying to pull quay.io/centos/centos:centos6... Getting image source signatures Copying blob sha256:ff50d722b38227ec8f2bbf0cdbce428b66745077c173d8117d91376128fa532e Copying config sha256:d0957ffdf8a2ea8c8925903862b65a1b6850dbb019f88d45e927d3d5a3fa0c31 Writing manifest to image destination Storing signatures d0957ffdf8a2ea8c8925903862b65a1b6850dbb019f88d45e927d3d5a3fa0c31 ++ set +ex + set -o pipefail ++ find input_1// ++ egrep '(_R1.*|_1)[.]f(ast|)q$' ++ echo '' + r1= ++ find input_1// ++ egrep '(_R1.*|_1)[.]f(ast|)q[.]gz$' + r1gz=input_1//S_l1_1.fq.gz + '[' input_1//S_l1_1.fq.gz = '' ']' + r2= ++ for i in $r1gz +++ echo input_1//S_l1_1.fq.gz +++ egrep '_1[.]f(ast|)q[.]gz$' +++ wc -l ++ '[' 1 = 1 ']' ++ echo input_1//S_l1_1.fq.gz ++ sed 's/_1[.]f\(ast\|\)q[.]gz/_2.f\1q.gz/' + r2gz=input_1//S_l1_2.fq.gz + echo '#Check paired-end' #Check paired-end + ls input_1//S_l1_2.fq.gz ++ echo input_2/parasite.fa ++ grep '[.]gz$' ++ wc -l ++ true + '[' 0 = 1 ']' + awk '{if($0~"^>"){sub(/ .*/,"",$0)}; print $0}' input_2/parasite.fa + sed 's/\r//' + input_2=input_2/parasite.fa.ref.fa + mkdir -p output.prinseq + for i in $r1gz ++ echo input_1//S_l1_1.fq.gz ++ egrep '_1[.]f(ast|)q[.]gz$' ++ wc -l + '[' 1 = 1 ']' ++ echo input_1//S_l1_1.fq.gz ++ sed 's/_1[.]f\(ast\|\)q[.]gz/_2.f\1q.gz/' + j=input_1//S_l1_2.fq.gz ++ basename input_1//S_l1_1.fq.gz .gz + i2=S_l1_1.fq ++ basename input_1//S_l1_2.fq.gz .gz + j2=S_l1_2.fq ++ basename input_1//S_l1_1.fq.gz + echo zcat input_1//S_l1_1.fq.gz '>' 'S_l1_1.fq;' zcat input_1//S_l1_2.fq.gz '>' 'S_l1_2.fq;' 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/pp-podman-list;' podman run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -v /data/yoshitake.kazutoshi/work:/data/yoshitake.kazutoshi/work -v /data/yoshitake.kazutoshi/work/pp-dev:/data/yoshitake.kazutoshi/work/pp-dev -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 -u root -i --rm quay.io/biocontainers/prinseq:0.20.4 prinseq-lite.pl -fastq S_l1_1.fq -fastq2 S_l1_2.fq -out_good output.prinseq/S_l1_1.fq -out_bad null -out_format 3 -trim_tail_right 5 -trim_qual_right 20 -ns_max_p 20 -min_len 30 -trim_qual_window 5 '>' log.prinseq.S_l1_1.fq.gz '2>&1' ';' mv output.prinseq/S_l1_1.fq_1.fastq 'output.prinseq/S_l1_1.fq;' mv output.prinseq/S_l1_1.fq_2.fastq 'output.prinseq/S_l1_2.fq;rm' -f S_l1_1.fq S_l1_2.fq zcat input_1//S_l1_1.fq.gz > S_l1_1.fq; zcat input_1//S_l1_2.fq.gz > S_l1_2.fq; PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/pp-podman-list; podman run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -v /data/yoshitake.kazutoshi/work:/data/yoshitake.kazutoshi/work -v /data/yoshitake.kazutoshi/work/pp-dev:/data/yoshitake.kazutoshi/work/pp-dev -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 -u root -i --rm quay.io/biocontainers/prinseq:0.20.4 prinseq-lite.pl -fastq S_l1_1.fq -fastq2 S_l1_2.fq -out_good output.prinseq/S_l1_1.fq -out_bad null -out_format 3 -trim_tail_right 5 -trim_qual_right 20 -ns_max_p 20 -min_len 30 -trim_qual_window 5 > log.prinseq.S_l1_1.fq.gz 2>&1 ; mv output.prinseq/S_l1_1.fq_1.fastq output.prinseq/S_l1_1.fq; mv output.prinseq/S_l1_1.fq_2.fastq output.prinseq/S_l1_2.fq;rm -f S_l1_1.fq S_l1_2.fq ++ find output.prinseq/ ++ egrep '(_R1.*|_1)[.]f(ast|)q$' + r1=output.prinseq/S_l1_1.fq + echo '' + for i in $r1 ++ echo output.prinseq/S_l1_1.fq ++ egrep '_1[.]f(ast|)q$' ++ wc -l + '[' 1 = 1 ']' ++ echo output.prinseq/S_l1_1.fq ++ sed 's/_1[.]f\(ast\|\)q/_2.f\1q/' + j=output.prinseq/S_l1_2.fq ++ basename output.prinseq/S_l1_1.fq ++ basename output.prinseq/S_l1_1.fq ++ basename output.prinseq/S_l1_1.fq + echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/pp-podman-list;' podman run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -v /data/yoshitake.kazutoshi/work:/data/yoshitake.kazutoshi/work -v /data/yoshitake.kazutoshi/work/pp-dev:/data/yoshitake.kazutoshi/work/pp-dev -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 -u root -i --rm quay.io/biocontainers/hisat2:2.2.0--py36hf0b53f7_4 hisat2 --rna-strandness RF -p 8 --dta --dta-cufflinks -x hisat2_index -1 output.prinseq/S_l1_1.fq -2 output.prinseq/S_l1_2.fq --rg-id output.prinseq/S_l1_1.fq --rg SM:output.prinseq/S_l1_1.fq '2>' log.hisat2.S_l1_1.fq '|(PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/pp-podman-list;' podman run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -v /data/yoshitake.kazutoshi/work:/data/yoshitake.kazutoshi/work -v /data/yoshitake.kazutoshi/work/pp-dev:/data/yoshitake.kazutoshi/work/pp-dev -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 -u root -i --rm quay.io/biocontainers/samtools:1.9--h10a08f8_12 samtools sort -@ 8 -o S_l1_1.fq.bam ');' 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/pp-podman-list;' podman run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -v /data/yoshitake.kazutoshi/work:/data/yoshitake.kazutoshi/work -v /data/yoshitake.kazutoshi/work/pp-dev:/data/yoshitake.kazutoshi/work/pp-dev -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 -u root -i --rm quay.io/biocontainers/samtools:1.9--h10a08f8_12 samtools index S_l1_1.fq.bam PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/pp-podman-list; podman run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -v /data/yoshitake.kazutoshi/work:/data/yoshitake.kazutoshi/work -v /data/yoshitake.kazutoshi/work/pp-dev:/data/yoshitake.kazutoshi/work/pp-dev -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 -u root -i --rm quay.io/biocontainers/hisat2:2.2.0--py36hf0b53f7_4 hisat2 --rna-strandness RF -p 8 --dta --dta-cufflinks -x hisat2_index -1 output.prinseq/S_l1_1.fq -2 output.prinseq/S_l1_2.fq --rg-id output.prinseq/S_l1_1.fq --rg SM:output.prinseq/S_l1_1.fq 2> log.hisat2.S_l1_1.fq |(PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/pp-podman-list; podman run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -v /data/yoshitake.kazutoshi/work:/data/yoshitake.kazutoshi/work -v /data/yoshitake.kazutoshi/work/pp-dev:/data/yoshitake.kazutoshi/work/pp-dev -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 -u root -i --rm quay.io/biocontainers/samtools:1.9--h10a08f8_12 samtools sort -@ 8 -o S_l1_1.fq.bam ); PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/pp-podman-list; podman run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -v /data/yoshitake.kazutoshi/work:/data/yoshitake.kazutoshi/work -v /data/yoshitake.kazutoshi/work/pp-dev:/data/yoshitake.kazutoshi/work/pp-dev -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 -u root -i --rm quay.io/biocontainers/samtools:1.9--h10a08f8_12 samtools index S_l1_1.fq.bam ++ basename output.prinseq/S_l1_1.fq + echo S_l1_1.fq.bam ++ awk '{ORS=","; print $0}' bamlist ++ sed 's/^,//; s/,$//' + bamlist=S_l1_1.fq.bam + FUNC_RUN_PODMAN c2997108/braker:3 braker.pl --genome=input_2/parasite.fa.ref.fa --species=run1 --bam=S_l1_1.fq.bam '' + PP_RUN_IMAGE=c2997108/braker:3 + shift + PP_RUN_DOCKER_CMD=("${@}") ++ date +%Y%m%d_%H%M%S_%3N + PPDOCNAME=pp20231113_214311_517_11050 + echo pp20231113_214311_517_11050 ++ echo c2997108/braker:3 ++ awk -F/ '{if(NF==2){$0="docker.io/"$0}; print $0}' + PP_RUN_IMAGE=docker.io/c2997108/braker:3 + podman run --name pp20231113_214311_517_11050 -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 -w /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 -v /data/yoshitake.kazutoshi/work:/data/yoshitake.kazutoshi/work -v /data/yoshitake.kazutoshi/work/pp-dev:/data/yoshitake.kazutoshi/work/pp-dev -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 -u root -i --rm docker.io/c2997108/braker:3 braker.pl --genome=input_2/parasite.fa.ref.fa --species=run1 --bam=S_l1_1.fq.bam '' # Mon Nov 13 12:43:12 2023: Log information is stored in file /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/braker.log