pp Comparative-genomics~FastANI -c 8 -m 32 input_1/xr1.hap1chr1-2.fa input_2/xr1.hap2chr1-2.fa
PID: 2643171
/home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/PortablePipeline/PortablePipeline/scripts/pp 'Comparative-genomics~FastANI' -c 8 -m 32 input_1/xr1.hap1chr1-2.fa input_2/xr1.hap2chr1-2.fa
Checking the realpath of input files.
1
script: /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/PortablePipeline/PortablePipeline/scripts/Comparative-genomics~FastANI
Containers: biocontainers/samtools:v1.7.0_cv4 c2997108/centos7:metacor7 centos:centos6 quay.io/biocontainers/fastani:1.34--h4dfc31f_4
using docker
++ set -o pipefail
+ set -eux
+ set -o pipefail
++ echo input_1/xr1.hap1chr1-2.fa
++ grep '[.]gz$'
++ wc -l
++ true
+ '[' 0 = 1 ']'
++ echo input_2/xr1.hap2chr1-2.fa
++ grep '[.]gz$'
++ wc -l
++ true
+ '[' 0 = 1 ']'
++ basename input_1/xr1.hap1chr1-2.fa
++ basename input_2/xr1.hap2chr1-2.fa
+ FUNC_RUN_DOCKER quay.io/biocontainers/fastani:1.34--h4dfc31f_4 fastANI -q input_1/xr1.hap1chr1-2.fa -r input_2/xr1.hap2chr1-2.fa -o fastANI.xr1.hap1chr1-2.fa.xr1.hap2chr1-2.fa.txt --visualize
+ PP_RUN_IMAGE=quay.io/biocontainers/fastani:1.34--h4dfc31f_4
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20250303_003723_132_26838
+ echo pp20250303_003723_132_26838
++ id -u
++ id -g
+ docker run --name pp20250303_003723_132_26838 -v /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/Comparative-genomics~FastANI:/suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/Comparative-genomics~FastANI -w /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/Comparative-genomics~FastANI -v /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi -u 2007:600 -i --rm quay.io/biocontainers/fastani:1.34--h4dfc31f_4 fastANI -q input_1/xr1.hap1chr1-2.fa -r input_2/xr1.hap2chr1-2.fa -o fastANI.xr1.hap1chr1-2.fa.xr1.hap2chr1-2.fa.txt --visualize
>>>>>>>>>>>>>>>>>>
Reference = [input_2/xr1.hap2chr1-2.fa]
Query = [input_1/xr1.hap1chr1-2.fa]
Kmer size = 16
Fragment length = 3000
Threads = 1
ANI output file = fastANI.xr1.hap1chr1-2.fa.xr1.hap2chr1-2.fa.txt
Sanity Check  = 0
>>>>>>>>>>>>>>>>>>
INFO [thread 0], skch::main, Count of threads executing parallel_for : 1
INFO [thread 0], skch::Sketch::build, window size for minimizer sampling  = 24
INFO [thread 0], skch::Sketch::build, minimizers picked from reference = 909883
INFO [thread 0], skch::Sketch::index, unique minimizers = 773785
INFO [thread 0], skch::Sketch::computeFreqHist, Frequency histogram of minimizers = (1, 734039) ... (186, 1)
INFO [thread 0], skch::Sketch::computeFreqHist, consider all minimizers during lookup.
INFO [thread 0], skch::main, Time spent sketching the reference : 1.20904 sec
INFO [thread 0], skch::main, Start Map 1
INFO [thread 0], skch::main, Time spent mapping fragments in query #1 : 21.8703 sec
INFO [thread 0], skch::main, Time spent post mapping : 0.0148263 sec
INFO [thread 0], skch::main, ready to exit the loop
INFO, skch::main, parallel_for execution finished
+ mkdir -p reformat
+ DO_EXONERATE fastareformat input_1/xr1.hap1chr1-2.fa
+ sed 's/\r//g'
/suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/PortablePipeline/PortablePipeline/scripts/Comparative-genomics~FastANI: 行 33: DO_EXONERATE: コマンドが見つかりません
++ onerror 33
++ status=127
++ script=/suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/PortablePipeline/PortablePipeline/scripts/Comparative-genomics~FastANI
++ line=33
++ shift
++ set +x

------------------------------------------------------------
Error occured on /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/PortablePipeline/PortablePipeline/scripts/Comparative-genomics~FastANI [Line 33]: Status 127

PID: 2643177
User: yoshitake.kazutoshi
Current directory: /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/Comparative-genomics~FastANI
Command line: /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/PortablePipeline/PortablePipeline/scripts/Comparative-genomics~FastANI
------------------------------------------------------------


PID: 2658529
/home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/PortablePipeline/PortablePipeline/scripts/pp 'Comparative-genomics~FastANI' -c 8 -m 32 input_1/xr1.hap1chr1-2.fa input_2/xr1.hap2chr1-2.fa
Checking the realpath of input files.
1
script: /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/PortablePipeline/PortablePipeline/scripts/Comparative-genomics~FastANI
Containers: c2997108/centos7:metacor7 c2997108/ubuntu20:R-2_gplots_genoPlotR_2 centos:centos6 quay.io/biocontainers/fastani:1.34--h4dfc31f_4
using docker
++ set -o pipefail
+ set -eux
+ set -o pipefail
++ echo input_1/xr1.hap1chr1-2.fa
++ grep '[.]gz$'
++ wc -l
++ true
+ '[' 0 = 1 ']'
++ echo input_2/xr1.hap2chr1-2.fa
++ grep '[.]gz$'
++ wc -l
++ true
+ '[' 0 = 1 ']'
++ basename input_1/xr1.hap1chr1-2.fa
++ basename input_2/xr1.hap2chr1-2.fa
+ FUNC_RUN_DOCKER quay.io/biocontainers/fastani:1.34--h4dfc31f_4 fastANI -t 8 -q input_1/xr1.hap1chr1-2.fa -r input_2/xr1.hap2chr1-2.fa -o fastANI.xr1.hap1chr1-2.fa.xr1.hap2chr1-2.fa.txt --visualize
+ PP_RUN_IMAGE=quay.io/biocontainers/fastani:1.34--h4dfc31f_4
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20250303_005201_081_11437
+ echo pp20250303_005201_081_11437
++ id -u
++ id -g
+ docker run --name pp20250303_005201_081_11437 -v /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/Comparative-genomics~FastANI:/suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/Comparative-genomics~FastANI -w /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/Comparative-genomics~FastANI -v /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi -u 2007:600 -i --rm quay.io/biocontainers/fastani:1.34--h4dfc31f_4 fastANI -t 8 -q input_1/xr1.hap1chr1-2.fa -r input_2/xr1.hap2chr1-2.fa -o fastANI.xr1.hap1chr1-2.fa.xr1.hap2chr1-2.fa.txt --visualize
>>>>>>>>>>>>>>>>>>
Reference = [input_2/xr1.hap2chr1-2.fa]
Query = [input_1/xr1.hap1chr1-2.fa]
Kmer size = 16
Fragment length = 3000
Threads = 8
ANI output file = fastANI.xr1.hap1chr1-2.fa.xr1.hap2chr1-2.fa.txt
Sanity Check  = 0
>>>>>>>>>>>>>>>>>>
INFO [thread 0], skch::main, Count of threads executing parallel_for : 8
INFO [thread 0], skch::Sketch::build, window size for minimizer sampling  = 24
INFO [thread 4], skch::main, ready to exit the loop
INFO [thread 0], skch::Sketch::build, minimizers picked from reference = 909883
INFO [thread 3], skch::main, ready to exit the loop
INFO [thread 2], skch::main, ready to exit the loop
INFO [thread 5], skch::main, ready to exit the loop
INFO [thread 6], skch::main, ready to exit the loop
INFO [thread 1], skch::main, ready to exit the loop
INFO [thread 7], skch::main, ready to exit the loop
INFO [thread 0], skch::Sketch::index, unique minimizers = 773785
INFO [thread 0], skch::Sketch::computeFreqHist, Frequency histogram of minimizers = (1, 734039) ... (186, 1)
INFO [thread 0], skch::Sketch::computeFreqHist, consider all minimizers during lookup.
INFO [thread 0], skch::main, Time spent sketching the reference : 1.52038 sec
INFO [thread 0], skch::main, Start Map 1
INFO [thread 0], skch::main, Time spent mapping fragments in query #1 : 22.4838 sec
INFO [thread 0], skch::main, Time spent post mapping : 0.0140316 sec
INFO [thread 0], skch::main, ready to exit the loop
INFO, skch::main, parallel_for execution finished
++ basename input_1/xr1.hap1chr1-2.fa
++ basename input_2/xr1.hap2chr1-2.fa
+ FUNC_RUN_DOCKER c2997108/ubuntu20:R-2_gplots_genoPlotR_2 Rscript /usr/local/FastANI/scripts/visualize.R input_1/xr1.hap1chr1-2.fa input_2/xr1.hap2chr1-2.fa fastANI.xr1.hap1chr1-2.fa.xr1.hap2chr1-2.fa.txt.visual
+ PP_RUN_IMAGE=c2997108/ubuntu20:R-2_gplots_genoPlotR_2
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20250303_005226_504_21727
+ echo pp20250303_005226_504_21727
++ id -u
++ id -g
+ docker run --name pp20250303_005226_504_21727 -v /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/Comparative-genomics~FastANI:/suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/Comparative-genomics~FastANI -w /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/Comparative-genomics~FastANI -v /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi -u 2007:600 -i --rm c2997108/ubuntu20:R-2_gplots_genoPlotR_2 Rscript /usr/local/FastANI/scripts/visualize.R input_1/xr1.hap1chr1-2.fa input_2/xr1.hap2chr1-2.fa fastANI.xr1.hap1chr1-2.fa.xr1.hap2chr1-2.fa.txt.visual
Loading required package: ade4
Loading required package: grid
null device
1
+ post_processing
+ '[' 1 = 1 ']'
+ rm -f /home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/test/Comparative-genomics~FastANI/pp-singularity-flag
+ '[' '' = y ']'
+ echo 0
+ exit