c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_4-kegg_4 c2997108/seldla:2.0.7_1 centos:centos6 using singularity +++ basename c2997108/seldla:2.0.7_1 ++ singularity pull --name seldla:2.0.7_1 docker://c2997108/seldla:2.0.7_1 INFO:  Converting OCI blobs to SIF format INFO:  Starting build... Getting image source signatures Skipping fetch of repeat blob sha256:8ba884070f611d31cb2c42eddb691319dc9facf5e0ec67672fcfa135181ab3df Copying blob sha256:07a5b0e61101f14044fa73122bf1f7a913c4c0e694e28edd37048d9a07e1dde1 0 B / 147.57 MiB 1.19 MiB / 147.57 MiB 2.84 MiB / 147.57 MiB 4.80 MiB / 147.57 MiB 6.96 MiB / 147.57 MiB 9.16 MiB / 147.57 MiB 11.35 MiB / 147.57 MiB 13.60 MiB / 147.57 MiB 15.84 MiB / 147.57 MiB 18.08 MiB / 147.57 MiB 20.31 MiB / 147.57 MiB 22.29 MiB / 147.57 MiB 24.49 MiB / 147.57 MiB 26.72 MiB / 147.57 MiB 28.93 MiB / 147.57 MiB 31.08 MiB / 147.57 MiB 33.24 MiB / 147.57 MiB 35.41 MiB / 147.57 MiB 37.51 MiB / 147.57 MiB 39.73 MiB / 147.57 MiB 41.98 MiB / 147.57 MiB 44.18 MiB / 147.57 MiB 46.42 MiB / 147.57 MiB 48.61 MiB / 147.57 MiB 50.71 MiB / 147.57 MiB 52.86 MiB / 147.57 MiB 55.10 MiB / 147.57 MiB 57.33 MiB / 147.57 MiB 59.38 MiB / 147.57 MiB 61.49 MiB / 147.57 MiB 63.76 MiB / 147.57 MiB 65.83 MiB / 147.57 MiB 67.97 MiB / 147.57 MiB 70.21 MiB / 147.57 MiB 72.43 MiB / 147.57 MiB 74.55 MiB / 147.57 MiB 76.78 MiB / 147.57 MiB 79.01 MiB / 147.57 MiB 81.24 MiB / 147.57 MiB 83.47 MiB / 147.57 MiB 85.73 MiB / 147.57 MiB 87.95 MiB / 147.57 MiB 90.20 MiB / 147.57 MiB 92.44 MiB / 147.57 MiB 94.70 MiB / 147.57 MiB 96.90 MiB / 147.57 MiB 99.02 MiB / 147.57 MiB 101.21 MiB / 147.57 MiB 103.40 MiB / 147.57 MiB 103.83 MiB / 147.57 MiB 105.47 MiB / 147.57 MiB 107.07 MiB / 147.57 MiB 108.72 MiB / 147.57 MiB 110.36 MiB / 147.57 MiB 112.35 MiB / 147.57 MiB 114.52 MiB / 147.57 MiB 116.74 MiB / 147.57 MiB 118.83 MiB / 147.57 MiB 120.65 MiB / 147.57 MiB 122.27 MiB / 147.57 MiB 123.77 MiB / 147.57 MiB 126.01 MiB / 147.57 MiB 128.23 MiB / 147.57 MiB 130.51 MiB / 147.57 MiB 132.75 MiB / 147.57 MiB 135.00 MiB / 147.57 MiB 137.25 MiB / 147.57 MiB 139.47 MiB / 147.57 MiB 141.70 MiB / 147.57 MiB 143.90 MiB / 147.57 MiB 146.12 MiB / 147.57 MiB 147.57 MiB / 147.57 MiB 147.57 MiB / 147.57 MiB 147.57 MiB / 147.57 MiB 147.57 MiB / 147.57 MiB 147.57 MiB / 147.57 MiB 147.57 MiB / 147.57 MiB 147.57 MiB / 147.57 MiB 147.57 MiB / 147.57 MiB 15s Copying blob sha256:0f4192275a3aab800be3fbfff469196d8ad1dcf5470d372b6c5958d2db2fb8f0 0 B / 92.26 MiB 541.26 KiB / 92.26 MiB 1.39 MiB / 92.26 MiB 2.90 MiB / 92.26 MiB 5.05 MiB / 92.26 MiB 7.04 MiB / 92.26 MiB 8.55 MiB / 92.26 MiB 10.09 MiB / 92.26 MiB 11.69 MiB / 92.26 MiB 13.27 MiB / 92.26 MiB 15.51 MiB / 92.26 MiB 17.73 MiB / 92.26 MiB 19.89 MiB / 92.26 MiB 22.13 MiB / 92.26 MiB 24.38 MiB / 92.26 MiB 26.63 MiB / 92.26 MiB 28.86 MiB / 92.26 MiB 31.11 MiB / 92.26 MiB 33.35 MiB / 92.26 MiB 35.61 MiB / 92.26 MiB 37.82 MiB / 92.26 MiB 40.04 MiB / 92.26 MiB 42.26 MiB / 92.26 MiB 44.44 MiB / 92.26 MiB 46.61 MiB / 92.26 MiB 48.79 MiB / 92.26 MiB 50.94 MiB / 92.26 MiB 53.01 MiB / 92.26 MiB 55.26 MiB / 92.26 MiB 57.52 MiB / 92.26 MiB 59.77 MiB / 92.26 MiB 62.01 MiB / 92.26 MiB 64.27 MiB / 92.26 MiB 66.39 MiB / 92.26 MiB 68.33 MiB / 92.26 MiB 70.58 MiB / 92.26 MiB 72.73 MiB / 92.26 MiB 74.92 MiB / 92.26 MiB 77.09 MiB / 92.26 MiB 79.28 MiB / 92.26 MiB 81.49 MiB / 92.26 MiB 83.66 MiB / 92.26 MiB 85.86 MiB / 92.26 MiB 88.03 MiB / 92.26 MiB 90.22 MiB / 92.26 MiB 92.26 MiB / 92.26 MiB 92.26 MiB / 92.26 MiB 92.26 MiB / 92.26 MiB 92.26 MiB / 92.26 MiB 92.26 MiB / 92.26 MiB 92.26 MiB / 92.26 MiB 9s Copying blob sha256:847edd25edfb865ec4cf2ebc2a55de50df034ac2d1c8c5d324dc62f7a40603d3 0 B / 37.20 MiB 125.24 KiB / 37.20 MiB 261.24 KiB / 37.20 MiB 421.24 KiB / 37.20 MiB 573.24 KiB / 37.20 MiB 773.24 KiB / 37.20 MiB 989.24 KiB / 37.20 MiB 1.26 MiB / 37.20 MiB 1.57 MiB / 37.20 MiB 1.90 MiB / 37.20 MiB 2.35 MiB / 37.20 MiB 2.83 MiB / 37.20 MiB 3.63 MiB / 37.20 MiB 4.32 MiB / 37.20 MiB 5.11 MiB / 37.20 MiB 6.10 MiB / 37.20 MiB 7.23 MiB / 37.20 MiB 8.53 MiB / 37.20 MiB 10.08 MiB / 37.20 MiB 11.87 MiB / 37.20 MiB 13.86 MiB / 37.20 MiB 16.04 MiB / 37.20 MiB 18.19 MiB / 37.20 MiB 20.40 MiB / 37.20 MiB 22.58 MiB / 37.20 MiB 24.74 MiB / 37.20 MiB 26.91 MiB / 37.20 MiB 29.07 MiB / 37.20 MiB 31.27 MiB / 37.20 MiB 33.29 MiB / 37.20 MiB 35.49 MiB / 37.20 MiB 37.20 MiB / 37.20 MiB 37.20 MiB / 37.20 MiB 37.20 MiB / 37.20 MiB 6s Copying config sha256:8fba1bb06d95c8c4131914913bbdb3533e56a6cf5a780dd38aad59cae4360881 0 B / 1.45 KiB 1.45 KiB / 1.45 KiB 0s Writing manifest to image destination Storing signatures INFO:  Creating SIF file... INFO:  Build complete: /home/user2/.singularity/cache/oci-tmp/d0b9d4ea74d3d92362559e2d0b057feadbf59097b2602dd265e91d9519859fd4/seldla_2.0.7_1.sif +++ dirname c2997108/seldla:2.0.7_1 ++ mkdir -p /home/user2/img/c2997108 +++ basename c2997108/seldla:2.0.7_1 +++ dirname c2997108/seldla:2.0.7_1 ++ mv seldla:2.0.7_1 /home/user2/img/c2997108 ++ set +ex + set -o pipefail ++ echo input_1/fourth_assembly.fasta ++ grep '[.]gz$' ++ wc -l ++ true + '[' 0 = 1 ']' + singularity exec -B /suikou/files/m64g/user2/work/102:/mnt --pwd /mnt /home/user2/img/c2997108/seldla:2.0.7_1 SELDLA --mode=crossbreed --DP=1 -r 10000 --cs=2 --fasta input_1/fourth_assembly.fasta --vcf input_2/male.vcf --family input_3/family.txt Run SELDLA! Clean up VCF input datas: 1293395 cleaned datas: 982888 Split VCF into each family families: 1 cleaned datas: 982887 family 1 datas: 449844 SNP to Block in family No. 1 #chr, pos, 1, 10, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 12, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 13, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 14, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 15, 150, 151, 153, 154, 155, 156, 157, 158, 159, 16, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 18, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 19, 190, 191, 192, 194, 195, 196, 2, 20, 22, 23, 24, 25, 26, 27, 28, 29, 3, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 5, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 6, 61, 62, 63, 64, 65, 66, 67, 69, 7, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 8, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 9, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99 There were 449845 lines. Block to Phase in family No. 1 #info, #chr, pos, 1, 10, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 12, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 13, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 14, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 15, 150, 151, 153, 154, 155, 156, 157, 158, 159, 16, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 18, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 19, 190, 191, 192, 194, 195, 196, 2, 20, 22, 23, 24, 25, 26, 27, 28, 29, 3, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 5, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 6, 61, 62, 63, 64, 65, 66, 67, 69, 7, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 8, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 9, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99 There were 30974 lines. Detect breakpoints corrected Block to Phase in family No. 1 #info, #chr, pos, 1, 10, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 12, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 13, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 14, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 15, 150, 151, 153, 154, 155, 156, 157, 158, 159, 16, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 18, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 19, 190, 191, 192, 194, 195, 196, 2, 20, 22, 23, 24, 25, 26, 27, 28, 29, 3, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 5, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 6, 61, 62, 63, 64, 65, 66, 67, 69, 7, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 8, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 9, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99 There were 30974 lines. make linkage map... #1 26763950 #2 17037520 #3 16611032 #4 16559098 #5 16188409 #6 16141200 #7 16019556 #8 15689898 #9 15578846 #10 15512229 #11 15251664 #12 15214376 #13 14645770 #14 13530936 #15 12816973 #16 12447156 #17 12233494 #18 11440314 #19 10521522 #20 9894482 #21 9800773 #22 9350413 #23 5835804 #24 4454310 #25 4251420 #26 3282730 #27 3118946 #28 2421976 #29 2305716 #30 1318728 #31 789781 #32 731400 #33 633942 #34 599337 #35 527988 #36 456732 #37 454784 #38 424363 #39 401957 #40 269056 #41 176257 #42 173641 #43 97921 Total: 7,215 scaffolds, Located: 903 (12.516), Ordered: 635 (8.801), Ordered in >=1Mbp chr (30): 589 (8.164) Total: 393,296,343 bp, Located: 343,376,400 (87.307), Ordered: 291685068 (74.164), Ordered in >=1Mbp chr (30): 288047071 (73.239) convert VCF to new position convert SNP to new position + post_processing + '[' 1 = 1 ']' + '[' 'singularity exec -B /suikou/files/m64g/user2/work/102:/mnt --pwd /mnt /home/user2/img/' = 'docker run -v $PWD:$PWD -w $PWD -u root -i --rm ' ']' + echo 0 + exit