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Lisle Mose
Mar 26, 2014, 10:08:01 AM3/26/14
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Hello,
We are running into an error running SOAPIndel on a subset of BAM files downloaded from TCGA.
Command line:
perl /datastore/nextgenout4/seqware-analysis/lmose/software/soapIndel/indel_detection.release/indel_detection.ibam.pl soapIndel.mapping.list GRCh37-lite.fa.DB.SPLIT -chr 1+2+3+4+5+6+7+8+9+10+11+12+13+14+15+16+17+18+19+20+21+22+X+Y+MT -wd soap_indel -cpu 4 >> soapIndel.log 2>&1
Sample error message under log directory:
cat log/01_cr_2:1-243199373.log
[24 16:41:01] Reading the insert_size and RG information
[24 16:41:01] Reading the reference sequence
[24 16:41:02] Start reading region(2:1-243199373) from mappings(/datastore/rclbg/nextgenout3/MOSE_TEST/abra/brca/soapIndel.mapping.list.AUTO)
[bam_header_read] EOF marker is absent. The input is probably truncated.
cluster_reads: cluster_reads.cpp:397: void subfd(SAM_FD&): Assertion `it_ins != INS_H.end()' failed.
The default samtools version in the PATH is:
Version: 0.1.19-44428cd
This error doesn't happen for every BAM file. I've not been able to detect a pattern to the failures.
Other tools are able to process all of these files without error (i.e. samtools, freebayes, Pindel, Picard, GATK, etc...)
Any suggestions would be appreciated.
The full stdout/stderr output is appended at the bottom of this post.
Thanks!
Calculating maximal reads length from 1 file(s) in /datastore/rclbg/nextgenout3/MOSE_TEST/abra/brca/soapIndel.mapping.list
1
Done with maximal length: 100.
cd /proj/seq/LBG/nextgenout3/MOSE_TEST/abra/brca/data/125b0a9a-6cbe-4207-9178-e7ff03487e87/soapIndel2/
mkdir -p soap_indel/
if [ -e "soap_indel/RUNNING" ]; then echo "Please delete the 'soap_indel/RUNNING' file first."; exit; fi
touch soap_indel/RUNNING ; rm -f FINISHED
[Mon Mar 24 16:40:57 EDT 2014] 0. Calculate library insert size
mkdir -p mapping.raw log/99_mp
cat /datastore/rclbg/nextgenout3/MOSE_TEST/abra/brca/soapIndel.mapping.list |perl -ne 'chomp;@t=split/\s+/;$f=`basename $t[0]`;chomp $f;$t[4]="BOTH";print "perl /datastore/nextgenout4/seqware-analysis/lmose/software/soapIndel/indel_detection.release/tools/calc_insert_size.ibam.pl $t[0] 0 0 100 $t[4] -pn 100000 -pp -st samtools > mapping.raw/$f.info 2> log/99_mp/$f.info.log \n"' > 00.mapping.raw.sh
perl /datastore/nextgenout4/seqware-analysis/lmose/software/soapIndel/indel_detection.release/tools/run.pl -cpu 4 -pre log/99_mp_ 00.mapping.raw.sh
perl /datastore/nextgenout4/seqware-analysis/lmose/software/soapIndel/indel_detection.release/tools/run_check.pl 00.mapping.raw.sh
-- Checking 00.mapping.raw.sh
-- 00.mapping.raw.sh: Total 1(1); Finished 1; Unfinished 0
cat /datastore/rclbg/nextgenout3/MOSE_TEST/abra/brca/soapIndel.mapping.list |perl -ne 'chomp;@t=split/\s+/;$f=`basename $t[0]`;chomp $f;open(F,"mapping.raw/$f.info") || die "Fatal Error: $f.info does not exist!";$l=<F>;close(F);chomp $l;@t2=split/\s+/,$l;if($t2[1] && $t2[3]) {print $l."\n";@t3=@t2}else{@t2[1..3]=@t3[1..3];print join("\t",@t2),"\n"}' > /datastore/rclbg/nextgenout3/MOSE_TEST/abra/brca/soapIndel.mapping.list.AUTO
cd soap_indel/
rm -rf cluster_align aa_sh aa_sh_cmd log/99_aa_*_running log/99_*_qsub log/0?_* .db
mkdir -p cluster_reads aa_sh aa_sh_cmd result log .db
perl /datastore/nextgenout4/seqware-analysis/lmose/software/soapIndel/indel_detection.release/init.pl -cc
echo -e '[_##_] VERSION: 2.1.4.5\n[_##_] PWD: /proj/seq/LBG/nextgenout3/MOSE_TEST/abra/brca/data/125b0a9a-6cbe-4207-9178-e7ff03487e87/soapIndel2\n[_##_] WORK_DIR: soap_indel/\n[_##_] COMMAND: /datastore/nextgenout4/seqware-analysis/lmose/software/soapIndel/indel_detection.release/indel_detection.ibam.pl /datastore/rclbg/nextgenout3/MOSE_TEST/abra/brca/soapIndel.mapping.list /datastore/rclbg/nextgenout3/MOSE_TEST/abra/brca/ref/GRCh37-lite.fa.DB.SPLIT -chr 1+2+3+4+5+6+7+8+9+10+11+12+13+14+15+16+17+18+19+20+21+22+X+Y+MT -wd soap_indel -cpu 4\n[_##_] CHR: chr1+chr2+chr3+chr4+chr5+chr6+chr7+chr8+chr9+chr10+chr11+chr12+chr13+chr14+chr15+chr16+chr17+chr18+chr19+chr20+chr21+chr22+chrX+chrY+chrMT\n[_##_] MAPPING: /datastore/rclbg/nextgenout3/MOSE_TEST/abra/brca/soapIndel.mapping.list\n[_##_] REFERENCE: /datastore/rclbg/nextgenout3/MOSE_TEST/abra/brca/ref/GRCh37-lite.fa.DB.SPLIT\n[_##_] MAX_READ_LEN: 100\n[_##_] EXT: 100\n[_##_] K: 25\n[_##_] L: 2\n[_##_] MAX_READ_HIT_NUM: 1\n[_##_] MAX_READ_MISMATCH: 3\n[_##_] MAX_NAILS_DISTANCE: 100\n[_##_] MIN_CLUSTER_LEN: 20\n[_##_] MAX_CLUSTER_LEN: 300\n[_##_] OVERLAP_LEN: 100\n[_##_] SD_AMPLIFY: 2\n[_##_] MAX_COVERAGE: 100\n[_##_] MAX_CONTIG: 100\n[_##_] GAP_READS_AS_MATCH: YES\n[_##_] FILTER_READS_BY_SNP: YES\n[_##_] BINARY_INTERNAL_FA: NO\n[_##_] QUALITY_TAB: /datastore/nextgenout4/seqware-analysis/lmose/software/soapIndel/indel_detection.release/filter/Indel.qual.tab\n' > HEAD
echo -e '1:1-249250621\tchr1\n2:1-243199373\tchr2\n3:1-198022430\tchr3\n4:1-191154276\tchr4\n5:1-180915260\tchr5\n6:1-171115067\tchr6\n7:1-159138663\tchr7\n8:1-146364022\tchr8\n9:1-141213431\tchr9\n10:1-135534747\tchr10\n11:1-135006516\tchr11\n12:1-133851895\tchr12\n13:1-115169878\tchr13\n14:1-107349540\tchr14\n15:1-102531392\tchr15\n16:1-90354753\tchr16\n17:1-81195210\tchr17\n18:1-78077248\tchr18\n19:1-59128983\tchr19\n20:1-63025520\tchr20\n21:1-48129895\tchr21\n22:1-51304566\tchr22\nX:1-155270560\tchrX\nY:1-59373566\tchrY\nMT:1-16569\tchrMT' > .need_region.list
#cut -f2 .need_region.list | sort -u > .need_chr.list
cat .need_region.list |perl -ne 'chomp;@t=split/\t/;$chr=$t[1];print "ln -s /datastore/rclbg/nextgenout3/MOSE_TEST/abra/brca/ref/GRCh37-lite.fa.DB.SPLIT/$chr.fa .db/$t[0].fa\n"' | sh
[Mon Mar 24 16:41:01 EDT 2014] 1. Cluster reads around indels
cut -f1 .need_region.list | xargs -I{} echo '/datastore/nextgenout4/seqware-analysis/lmose/software/soapIndel/indel_detection.release/cluster_reads /datastore/rclbg/nextgenout3/MOSE_TEST/abra/brca/soapIndel.mapping.list.AUTO .db/{}.fa {} cluster_reads/{} -l 2 -ext 100 -xnum 1 -sdp 2 -pp -st samtools -mm 3 -il 100 -xl 300 -ol 100 -ml 20 -mx 100 2> log/01_cr_{}.log' > 01.cluster_reads.sh
perl /datastore/nextgenout4/seqware-analysis/lmose/software/soapIndel/indel_detection.release/tools/run.pl -cpu 4 -pre log/99_cr_ 01.cluster_reads.sh
perl /datastore/nextgenout4/seqware-analysis/lmose/software/soapIndel/indel_detection.release/tools/run_check.pl 01.cluster_reads.sh
-- Checking 01.cluster_reads.sh
log/01_cr_1:1-249250621.log: cluster_reads: cluster_reads.cpp:397: void subfd(SAM_FD&): Assertion `it_ins != INS_H.end()' failed.
Warn: Unfinished cmd 01.cluster_reads.sh(1) 0%: /datastore/nextgenout4/seqware-analysis/lmose/software/soapIndel/indel_detection.release/cluster_reads /datastore/rclbg/nextgenout3/MOSE_TEST/abra/brca/soapIndel.mapping.list.AUTO .db/1:1-249250621.fa 1:1-249250621 cluster_reads/1:1-249250621 -l 2 -ext 100 -xnum 1 -sdp 2 -pp -st samtools -mm 3 -il 100 -xl 300 -ol 100 -ml 20 -mx 100 2> log/01_cr_1:1-249250621.log
log/01_cr_2:1-243199373.log: cluster_reads: cluster_reads.cpp:397: void subfd(SAM_FD&): Assertion `it_ins != INS_H.end()' failed.
Warn: Unfinished cmd 01.cluster_reads.sh(2) 0%: /datastore/nextgenout4/seqware-analysis/lmose/software/soapIndel/indel_detection.release/cluster_reads /datastore/rclbg/nextgenout3/MOSE_TEST/abra/brca/soapIndel.mapping.list.AUTO .db/2:1-243199373.fa 2:1-243199373 cluster_reads/2:1-243199373 -l 2 -ext 100 -xnum 1 -sdp 2 -pp -st samtools -mm 3 -il 100 -xl 300 -ol 100 -ml 20 -mx 100 2> log/01_cr_2:1-243199373.log
log/01_cr_3:1-198022430.log: cluster_reads: cluster_reads.cpp:397: void subfd(SAM_FD&): Assertion `it_ins != INS_H.end()' failed.
Warn: Unfinished cmd 01.cluster_reads.sh(3) 0%: /datastore/nextgenout4/seqware-analysis/lmose/software/soapIndel/indel_detection.release/cluster_reads /datastore/rclbg/nextgenout3/MOSE_TEST/abra/brca/soapIndel.mapping.list.AUTO .db/3:1-198022430.fa 3:1-198022430 cluster_reads/3:1-198022430 -l 2 -ext 100 -xnum 1 -sdp 2 -pp -st samtools -mm 3 -il 100 -xl 300 -ol 100 -ml 20 -mx 100 2> log/01_cr_3:1-198022430.log
log/01_cr_4:1-191154276.log: cluster_reads: cluster_reads.cpp:397: void subfd(SAM_FD&): Assertion `it_ins != INS_H.end()' failed.
Warn: Unfinished cmd 01.cluster_reads.sh(4) 0%: /datastore/nextgenout4/seqware-analysis/lmose/software/soapIndel/indel_detection.release/cluster_reads /datastore/rclbg/nextgenout3/MOSE_TEST/abra/brca/soapIndel.mapping.list.AUTO .db/4:1-191154276.fa 4:1-191154276 cluster_reads/4:1-191154276 -l 2 -ext 100 -xnum 1 -sdp 2 -pp -st samtools -mm 3 -il 100 -xl 300 -ol 100 -ml 20 -mx 100 2> log/01_cr_4:1-191154276.log
log/01_cr_5:1-180915260.log: cluster_reads: cluster_reads.cpp:397: void subfd(SAM_FD&): Assertion `it_ins != INS_H.end()' failed.
Warn: Unfinished cmd 01.cluster_reads.sh(5) 0%: /datastore/nextgenout4/seqware-analysis/lmose/software/soapIndel/indel_detection.release/cluster_reads /datastore/rclbg/nextgenout3/MOSE_TEST/abra/brca/soapIndel.mapping.list.AUTO .db/5:1-180915260.fa 5:1-180915260 cluster_reads/5:1-180915260 -l 2 -ext 100 -xnum 1 -sdp 2 -pp -st samtools -mm 3 -il 100 -xl 300 -ol 100 -ml 20 -mx 100 2> log/01_cr_5:1-180915260.log
log/01_cr_6:1-171115067.log: cluster_reads: cluster_reads.cpp:397: void subfd(SAM_FD&): Assertion `it_ins != INS_H.end()' failed.
Warn: Unfinished cmd 01.cluster_reads.sh(6) 0%: /datastore/nextgenout4/seqware-analysis/lmose/software/soapIndel/indel_detection.release/cluster_reads /datastore/rclbg/nextgenout3/MOSE_TEST/abra/brca/soapIndel.mapping.list.AUTO .db/6:1-171115067.fa 6:1-171115067 cluster_reads/6:1-171115067 -l 2 -ext 100 -xnum 1 -sdp 2 -pp -st samtools -mm 3 -il 100 -xl 300 -ol 100 -ml 20 -mx 100 2> log/01_cr_6:1-171115067.log
log/01_cr_7:1-159138663.log: cluster_reads: cluster_reads.cpp:397: void subfd(SAM_FD&): Assertion `it_ins != INS_H.end()' failed.
Warn: Unfinished cmd 01.cluster_reads.sh(7) 0%: /datastore/nextgenout4/seqware-analysis/lmose/software/soapIndel/indel_detection.release/cluster_reads /datastore/rclbg/nextgenout3/MOSE_TEST/abra/brca/soapIndel.mapping.list.AUTO .db/7:1-159138663.fa 7:1-159138663 cluster_reads/7:1-159138663 -l 2 -ext 100 -xnum 1 -sdp 2 -pp -st samtools -mm 3 -il 100 -xl 300 -ol 100 -ml 20 -mx 100 2> log/01_cr_7:1-159138663.log
log/01_cr_8:1-146364022.log: cluster_reads: cluster_reads.cpp:397: void subfd(SAM_FD&): Assertion `it_ins != INS_H.end()' failed.
Warn: Unfinished cmd 01.cluster_reads.sh(8) 0%: /datastore/nextgenout4/seqware-analysis/lmose/software/soapIndel/indel_detection.release/cluster_reads /datastore/rclbg/nextgenout3/MOSE_TEST/abra/brca/soapIndel.mapping.list.AUTO .db/8:1-146364022.fa 8:1-146364022 cluster_reads/8:1-146364022 -l 2 -ext 100 -xnum 1 -sdp 2 -pp -st samtools -mm 3 -il 100 -xl 300 -ol 100 -ml 20 -mx 100 2> log/01_cr_8:1-146364022.log
log/01_cr_9:1-141213431.log: cluster_reads: cluster_reads.cpp:397: void subfd(SAM_FD&): Assertion `it_ins != INS_H.end()' failed.
Warn: Unfinished cmd 01.cluster_reads.sh(9) 0%: /datastore/nextgenout4/seqware-analysis/lmose/software/soapIndel/indel_detection.release/cluster_reads /datastore/rclbg/nextgenout3/MOSE_TEST/abra/brca/soapIndel.mapping.list.AUTO .db/9:1-141213431.fa 9:1-141213431 cluster_reads/9:1-141213431 -l 2 -ext 100 -xnum 1 -sdp 2 -pp -st samtools -mm 3 -il 100 -xl 300 -ol 100 -ml 20 -mx 100 2> log/01_cr_9:1-141213431.log
log/01_cr_10:1-135534747.log: cluster_reads: cluster_reads.cpp:397: void subfd(SAM_FD&): Assertion `it_ins != INS_H.end()' failed.
Warn: Unfinished cmd 01.cluster_reads.sh(10) 0%: /datastore/nextgenout4/seqware-analysis/lmose/software/soapIndel/indel_detection.release/cluster_reads /datastore/rclbg/nextgenout3/MOSE_TEST/abra/brca/soapIndel.mapping.list.AUTO .db/10:1-135534747.fa 10:1-135534747 cluster_reads/10:1-135534747 -l 2 -ext 100 -xnum 1 -sdp 2 -pp -st samtools -mm 3 -il 100 -xl 300 -ol 100 -ml 20 -mx 100 2> log/01_cr_10:1-135534747.log
log/01_cr_11:1-135006516.log: cluster_reads: cluster_reads.cpp:397: void subfd(SAM_FD&): Assertion `it_ins != INS_H.end()' failed.
Warn: Unfinished cmd 01.cluster_reads.sh(11) 0%: /datastore/nextgenout4/seqware-analysis/lmose/software/soapIndel/indel_detection.release/cluster_reads /datastore/rclbg/nextgenout3/MOSE_TEST/abra/brca/soapIndel.mapping.list.AUTO .db/11:1-135006516.fa 11:1-135006516 cluster_reads/11:1-135006516 -l 2 -ext 100 -xnum 1 -sdp 2 -pp -st samtools -mm 3 -il 100 -xl 300 -ol 100 -ml 20 -mx 100 2> log/01_cr_11:1-135006516.log
log/01_cr_12:1-133851895.log: cluster_reads: cluster_reads.cpp:397: void subfd(SAM_FD&): Assertion `it_ins != INS_H.end()' failed.
Warn: Unfinished cmd 01.cluster_reads.sh(12) 0%: /datastore/nextgenout4/seqware-analysis/lmose/software/soapIndel/indel_detection.release/cluster_reads /datastore/rclbg/nextgenout3/MOSE_TEST/abra/brca/soapIndel.mapping.list.AUTO .db/12:1-133851895.fa 12:1-133851895 cluster_reads/12:1-133851895 -l 2 -ext 100 -xnum 1 -sdp 2 -pp -st samtools -mm 3 -il 100 -xl 300 -ol 100 -ml 20 -mx 100 2> log/01_cr_12:1-133851895.log
log/01_cr_13:1-115169878.log: cluster_reads: cluster_reads.cpp:397: void subfd(SAM_FD&): Assertion `it_ins != INS_H.end()' failed.
Warn: Unfinished cmd 01.cluster_reads.sh(13) 0%: /datastore/nextgenout4/seqware-analysis/lmose/software/soapIndel/indel_detection.release/cluster_reads /datastore/rclbg/nextgenout3/MOSE_TEST/abra/brca/soapIndel.mapping.list.AUTO .db/13:1-115169878.fa 13:1-115169878 cluster_reads/13:1-115169878 -l 2 -ext 100 -xnum 1 -sdp 2 -pp -st samtools -mm 3 -il 100 -xl 300 -ol 100 -ml 20 -mx 100 2> log/01_cr_13:1-115169878.log
log/01_cr_14:1-107349540.log: cluster_reads: cluster_reads.cpp:397: void subfd(SAM_FD&): Assertion `it_ins != INS_H.end()' failed.
Warn: Unfinished cmd 01.cluster_reads.sh(14) 0%: /datastore/nextgenout4/seqware-analysis/lmose/software/soapIndel/indel_detection.release/cluster_reads /datastore/rclbg/nextgenout3/MOSE_TEST/abra/brca/soapIndel.mapping.list.AUTO .db/14:1-107349540.fa 14:1-107349540 cluster_reads/14:1-107349540 -l 2 -ext 100 -xnum 1 -sdp 2 -pp -st samtools -mm 3 -il 100 -xl 300 -ol 100 -ml 20 -mx 100 2> log/01_cr_14:1-107349540.log
log/01_cr_15:1-102531392.log: cluster_reads: cluster_reads.cpp:397: void subfd(SAM_FD&): Assertion `it_ins != INS_H.end()' failed.
Warn: Unfinished cmd 01.cluster_reads.sh(15) 0%: /datastore/nextgenout4/seqware-analysis/lmose/software/soapIndel/indel_detection.release/cluster_reads /datastore/rclbg/nextgenout3/MOSE_TEST/abra/brca/soapIndel.mapping.list.AUTO .db/15:1-102531392.fa 15:1-102531392 cluster_reads/15:1-102531392 -l 2 -ext 100 -xnum 1 -sdp 2 -pp -st samtools -mm 3 -il 100 -xl 300 -ol 100 -ml 20 -mx 100 2> log/01_cr_15:1-102531392.log
log/01_cr_16:1-90354753.log: cluster_reads: cluster_reads.cpp:397: void subfd(SAM_FD&): Assertion `it_ins != INS_H.end()' failed.
Warn: Unfinished cmd 01.cluster_reads.sh(16) 0%: /datastore/nextgenout4/seqware-analysis/lmose/software/soapIndel/indel_detection.release/cluster_reads /datastore/rclbg/nextgenout3/MOSE_TEST/abra/brca/soapIndel.mapping.list.AUTO .db/16:1-90354753.fa 16:1-90354753 cluster_reads/16:1-90354753 -l 2 -ext 100 -xnum 1 -sdp 2 -pp -st samtools -mm 3 -il 100 -xl 300 -ol 100 -ml 20 -mx 100 2> log/01_cr_16:1-90354753.log
log/01_cr_17:1-81195210.log: cluster_reads: cluster_reads.cpp:397: void subfd(SAM_FD&): Assertion `it_ins != INS_H.end()' failed.
Warn: Unfinished cmd 01.cluster_reads.sh(17) 0%: /datastore/nextgenout4/seqware-analysis/lmose/software/soapIndel/indel_detection.release/cluster_reads /datastore/rclbg/nextgenout3/MOSE_TEST/abra/brca/soapIndel.mapping.list.AUTO .db/17:1-81195210.fa 17:1-81195210 cluster_reads/17:1-81195210 -l 2 -ext 100 -xnum 1 -sdp 2 -pp -st samtools -mm 3 -il 100 -xl 300 -ol 100 -ml 20 -mx 100 2> log/01_cr_17:1-81195210.log
log/01_cr_18:1-78077248.log: cluster_reads: cluster_reads.cpp:397: void subfd(SAM_FD&): Assertion `it_ins != INS_H.end()' failed.
Warn: Unfinished cmd 01.cluster_reads.sh(18) 0%: /datastore/nextgenout4/seqware-analysis/lmose/software/soapIndel/indel_detection.release/cluster_reads /datastore/rclbg/nextgenout3/MOSE_TEST/abra/brca/soapIndel.mapping.list.AUTO .db/18:1-78077248.fa 18:1-78077248 cluster_reads/18:1-78077248 -l 2 -ext 100 -xnum 1 -sdp 2 -pp -st samtools -mm 3 -il 100 -xl 300 -ol 100 -ml 20 -mx 100 2> log/01_cr_18:1-78077248.log
log/01_cr_19:1-59128983.log: cluster_reads: cluster_reads.cpp:397: void subfd(SAM_FD&): Assertion `it_ins != INS_H.end()' failed.
Warn: Unfinished cmd 01.cluster_reads.sh(19) 0%: /datastore/nextgenout4/seqware-analysis/lmose/software/soapIndel/indel_detection.release/cluster_reads /datastore/rclbg/nextgenout3/MOSE_TEST/abra/brca/soapIndel.mapping.list.AUTO .db/19:1-59128983.fa 19:1-59128983 cluster_reads/19:1-59128983 -l 2 -ext 100 -xnum 1 -sdp 2 -pp -st samtools -mm 3 -il 100 -xl 300 -ol 100 -ml 20 -mx 100 2> log/01_cr_19:1-59128983.log
log/01_cr_20:1-63025520.log: cluster_reads: cluster_reads.cpp:397: void subfd(SAM_FD&): Assertion `it_ins != INS_H.end()' failed.
Warn: Unfinished cmd 01.cluster_reads.sh(20) 0%: /datastore/nextgenout4/seqware-analysis/lmose/software/soapIndel/indel_detection.release/cluster_reads /datastore/rclbg/nextgenout3/MOSE_TEST/abra/brca/soapIndel.mapping.list.AUTO .db/20:1-63025520.fa 20:1-63025520 cluster_reads/20:1-63025520 -l 2 -ext 100 -xnum 1 -sdp 2 -pp -st samtools -mm 3 -il 100 -xl 300 -ol 100 -ml 20 -mx 100 2> log/01_cr_20:1-63025520.log
log/01_cr_21:1-48129895.log: cluster_reads: cluster_reads.cpp:397: void subfd(SAM_FD&): Assertion `it_ins != INS_H.end()' failed.
Warn: Unfinished cmd 01.cluster_reads.sh(21) 0%: /datastore/nextgenout4/seqware-analysis/lmose/software/soapIndel/indel_detection.release/cluster_reads /datastore/rclbg/nextgenout3/MOSE_TEST/abra/brca/soapIndel.mapping.list.AUTO .db/21:1-48129895.fa 21:1-48129895 cluster_reads/21:1-48129895 -l 2 -ext 100 -xnum 1 -sdp 2 -pp -st samtools -mm 3 -il 100 -xl 300 -ol 100 -ml 20 -mx 100 2> log/01_cr_21:1-48129895.log
log/01_cr_22:1-51304566.log: cluster_reads: cluster_reads.cpp:397: void subfd(SAM_FD&): Assertion `it_ins != INS_H.end()' failed.
Warn: Unfinished cmd 01.cluster_reads.sh(22) 0%: /datastore/nextgenout4/seqware-analysis/lmose/software/soapIndel/indel_detection.release/cluster_reads /datastore/rclbg/nextgenout3/MOSE_TEST/abra/brca/soapIndel.mapping.list.AUTO .db/22:1-51304566.fa 22:1-51304566 cluster_reads/22:1-51304566 -l 2 -ext 100 -xnum 1 -sdp 2 -pp -st samtools -mm 3 -il 100 -xl 300 -ol 100 -ml 20 -mx 100 2> log/01_cr_22:1-51304566.log
log/01_cr_X:1-155270560.log: cluster_reads: cluster_reads.cpp:397: void subfd(SAM_FD&): Assertion `it_ins != INS_H.end()' failed.
Warn: Unfinished cmd 01.cluster_reads.sh(23) 0%: /datastore/nextgenout4/seqware-analysis/lmose/software/soapIndel/indel_detection.release/cluster_reads /datastore/rclbg/nextgenout3/MOSE_TEST/abra/brca/soapIndel.mapping.list.AUTO .db/X:1-155270560.fa X:1-155270560 cluster_reads/X:1-155270560 -l 2 -ext 100 -xnum 1 -sdp 2 -pp -st samtools -mm 3 -il 100 -xl 300 -ol 100 -ml 20 -mx 100 2> log/01_cr_X:1-155270560.log
log/01_cr_Y:1-59373566.log: cluster_reads: cluster_reads.cpp:397: void subfd(SAM_FD&): Assertion `it_ins != INS_H.end()' failed.
Warn: Unfinished cmd 01.cluster_reads.sh(24) 0%: /datastore/nextgenout4/seqware-analysis/lmose/software/soapIndel/indel_detection.release/cluster_reads /datastore/rclbg/nextgenout3/MOSE_TEST/abra/brca/soapIndel.mapping.list.AUTO .db/Y:1-59373566.fa Y:1-59373566 cluster_reads/Y:1-59373566 -l 2 -ext 100 -xnum 1 -sdp 2 -pp -st samtools -mm 3 -il 100 -xl 300 -ol 100 -ml 20 -mx 100 2> log/01_cr_Y:1-59373566.log
log/01_cr_MT:1-16569.log: cluster_reads: cluster_reads.cpp:397: void subfd(SAM_FD&): Assertion `it_ins != INS_H.end()' failed.
Warn: Unfinished cmd 01.cluster_reads.sh(25) 0%: /datastore/nextgenout4/seqware-analysis/lmose/software/soapIndel/indel_detection.release/cluster_reads /datastore/rclbg/nextgenout3/MOSE_TEST/abra/brca/soapIndel.mapping.list.AUTO .db/MT:1-16569.fa MT:1-16569 cluster_reads/MT:1-16569 -l 2 -ext 100 -xnum 1 -sdp 2 -pp -st samtools -mm 3 -il 100 -xl 300 -ol 100 -ml 20 -mx 100 2> log/01_cr_MT:1-16569.log
-- 01.cluster_reads.sh: Total 25(25); Finished 0; Unfinished 25
#cat cluster_reads/chr*/chr*.cluster.list > all_cluster.list
[Mon Mar 24 16:43:01 EDT 2014] 2. Do local assembly and alignment to get indels
cut -f1 .need_region.list | xargs -I{} echo 'perl /datastore/nextgenout4/seqware-analysis/lmose/software/soapIndel/indel_detection.release/make_assembly_align_sh.ibam.pl cluster_reads/{}/u.fa cluster_reads/{}/d.fa cluster_assembly cluster_align /datastore/nextgenout4/seqware-analysis/lmose/software/soapIndel/indel_detection.release/map_assembly_8.pl /datastore/nextgenout4/seqware-analysis/lmose/software/soapIndel/indel_detection.release/align_cluster2db_cm4.pl -m cluster_reads/{}/m.fa -k 25 -il 100 -mx 100 -mc 100 -rr | gzip > aa_sh/assemble_align_{}.sh.old.gz ; perl /datastore/nextgenout4/seqware-analysis/lmose/software/soapIndel/indel_detection.release/make_assembly_align_sh.ibam.pl cluster_reads/{}/u.fa cluster_reads/{}/d.fa cluster_assembly cluster_align /datastore/nextgenout4/seqware-analysis/lmose/software/soapIndel/indel_detection.release/assemble_align -m cluster_reads/{}/m.fa -k 25 -l aa_result_list/assemble_align.{}.list -il 100 -mx 100 -mc 100 -rr > aa_sh/assemble_align_{}.sh ; perl /datastore/nextgenout4/seqware-analysis/lmose/software/soapIndel/indel_detection.release/tools/aa_sh_index.pl aa_sh/assemble_align_{}.sh ; perl -e '"'"'BEGIN{$l=`wc -l $ARGV[0]`;chomp $l;$i=1} while ($i<=$l) {$r=$i+200 > $l ? $l-$i+1 : 200; print "perl /datastore/nextgenout4/seqware-analysis/lmose/software/soapIndel/indel_detection.release/tools/aa_sh_run.pl -cc $ARGV[0] $i $r\n"; $i+=200}'"'"' aa_sh/assemble_align_{}.sh > aa_sh_cmd/run_{}.sh ; perl /datastore/nextgenout4/seqware-analysis/lmose/software/soapIndel/indel_detection.release/tools/run.pl -cpu 4 -pre log/99_aa_{}_ -pp -c aa_sh_cmd/run_{}.sh 2> log/02_aa_{}.log ; mkdir -p result/{} ; perl /datastore/nextgenout4/seqware-analysis/lmose/software/soapIndel/indel_detection.release/filter/merge_result.pl aa_result_list/assemble_align.{}.list - -e aa_result_none/assemble_align.{}.none.list -pp > result/{}/{}.variation.raw 2> log/03_mr_{}.log ; perl /datastore/nextgenout4/seqware-analysis/lmose/software/soapIndel/indel_detection.release/filter/filter_raw2.pl result/{}/{}.variation.raw -w 30 -m 3 > result/{}/{}.variation.raw2 ; sort -k3,3 -k5,5n -T ./ result/{}/{}.variation.raw2 -o result/{}/{}.variation.sorted ; rm result/{}/{}.variation.raw2 ; perl /datastore/nextgenout4/seqware-analysis/lmose/software/soapIndel/indel_detection.release/filter/filter_result_2.pl result/{}/{}.variation.sorted -w 30 -n 2 -k 25 > result/{}/{}.variation.noq.list ; cat result/{}/{}.variation.noq.list |perl -ne '"'"'@t=split /\t/;if ($t[16]=~/ID/) {print}'"'"' > result/{}/{}.indel.noq.list ; cp HEAD result/{}/{}.HEAD ; cat log/*_{}.log | grep "^\[_##_]" >> result/{}/{}.HEAD ; perl /datastore/nextgenout4/seqware-analysis/lmose/software/soapIndel/indel_detection.release/tools/list2VCF4.pl result/{}/{}.indel.noq.list -head result/{}/{}.HEAD -db .db/{}.fa -noq > result/{}/{}.indel.noq.vcf ; gzip result/{}/{}.variation.raw ; perl /datastore/nextgenout4/seqware-analysis/lmose/software/soapIndel/indel_detection.release/filter/filter_result_2.pl result/{}/{}.variation.sorted -k 25 -nof -q /datastore/nextgenout4/seqware-analysis/lmose/software/soapIndel/indel_detection.release/filter/Indel.qual.tab > result/{}/{}.variation.list ; perl /datastore/nextgenout4/seqware-analysis/lmose/software/soapIndel/indel_detection.release/tools/list2VCF4.pl result/{}/{}.variation.list -head result/{}/{}.HEAD -db .db/{}.fa > result/{}/{}.indel.vcf' > 02.assemble_align.sh
perl /datastore/nextgenout4/seqware-analysis/lmose/software/soapIndel/indel_detection.release/tools/run_check.pl 02.assemble_align.sh
-- Checking 02.assemble_align.sh
log/03_mr_1:1-249250621.log: None file exists in aa_result_list/assemble_align.1:1-249250621.list!
log/03_mr_2:1-243199373.log: None file exists in aa_result_list/assemble_align.2:1-243199373.list!
log/03_mr_3:1-198022430.log: None file exists in aa_result_list/assemble_align.3:1-198022430.list!
log/03_mr_4:1-191154276.log: None file exists in aa_result_list/assemble_align.4:1-191154276.list!
log/03_mr_5:1-180915260.log: None file exists in aa_result_list/assemble_align.5:1-180915260.list!
log/03_mr_6:1-171115067.log: None file exists in aa_result_list/assemble_align.6:1-171115067.list!
log/03_mr_7:1-159138663.log: None file exists in aa_result_list/assemble_align.7:1-159138663.list!
log/03_mr_8:1-146364022.log: None file exists in aa_result_list/assemble_align.8:1-146364022.list!
log/03_mr_9:1-141213431.log: None file exists in aa_result_list/assemble_align.9:1-141213431.list!
log/03_mr_10:1-135534747.log: None file exists in aa_result_list/assemble_align.10:1-135534747.list!
log/03_mr_11:1-135006516.log: None file exists in aa_result_list/assemble_align.11:1-135006516.list!
log/03_mr_12:1-133851895.log: None file exists in aa_result_list/assemble_align.12:1-133851895.list!
log/03_mr_13:1-115169878.log: None file exists in aa_result_list/assemble_align.13:1-115169878.list!
log/03_mr_14:1-107349540.log: None file exists in aa_result_list/assemble_align.14:1-107349540.list!
log/03_mr_15:1-102531392.log: None file exists in aa_result_list/assemble_align.15:1-102531392.list!
log/03_mr_16:1-90354753.log: None file exists in aa_result_list/assemble_align.16:1-90354753.list!
log/03_mr_17:1-81195210.log: None file exists in aa_result_list/assemble_align.17:1-81195210.list!
log/03_mr_18:1-78077248.log: None file exists in aa_result_list/assemble_align.18:1-78077248.list!
log/03_mr_19:1-59128983.log: None file exists in aa_result_list/assemble_align.19:1-59128983.list!
log/03_mr_20:1-63025520.log: None file exists in aa_result_list/assemble_align.20:1-63025520.list!
log/03_mr_21:1-48129895.log: None file exists in aa_result_list/assemble_align.21:1-48129895.list!
log/03_mr_22:1-51304566.log: None file exists in aa_result_list/assemble_align.22:1-51304566.list!
log/03_mr_X:1-155270560.log: None file exists in aa_result_list/assemble_align.X:1-155270560.list!
log/03_mr_Y:1-59373566.log: None file exists in aa_result_list/assemble_align.Y:1-59373566.list!
log/03_mr_MT:1-16569.log: None file exists in aa_result_list/assemble_align.MT:1-16569.list!
-- 02.assemble_align.sh: Total 50(25); Finished 50; Unfinished 0
perl /datastore/nextgenout4/seqware-analysis/lmose/software/soapIndel/indel_detection.release/tools/run_check.pl 02.assemble_align.sh -r 'rm -rf cluster_assembly/chr*/ cluster_align/chr*/' &
#cat log/99_aa_*_running/*|perl -ne 'if (/\[A|^$|\] START\[\d+\]|\] END\[\d+\]|\] ALREADY_FINISHED$/) {if (/^\[(A\w+)\] \[.+\] Done \(Total (\d+)s/) {$l{$1}{$2}++;$all{$1}{n}++;$all{$1}{t}+=$2;} if (/ cluster_assembly\/chr.+\/\d+\/(chr.+)\.fa/) {$cl="Error Cluster: $1\n"} next} print "$cl$_"; $cl=""; END{foreach $t ("ASSEM", "ALIGN") {printf "%s:%ds/%d=%.3fs ",$t,$all{$t}{t},$all{$t}{n},$all{$t}{t}/$all{$t}{n}; print join(" ",map {"$_:$l{$t}{$_}"} sort {$a<=>$b} keys %{$l{$t}}),"\n"}}'
#cat .need_region.list |perl -ne 'BEGIN{print "mv result result.raw; mkdir result; cd result\n"}chomp;@t=split/\t/;$chr=$t[1];print "mkdir $chr; cd $chr; ";while(<result/$t[0]/$t[0].*>){/$t[0]([^\/]+)$/;print "ln ../../result.raw/$t[0]/$t[0]$1 $chr$1; ";}print "cd ../\n"' > mv.sh; sh mv.sh
#perl /datastore/nextgenout4/seqware-analysis/lmose/software/soapIndel/indel_detection.release/statistics.pl result/chr*/chr*.variation.list -q 10 > result/stat.q10.tab
wait
cd /proj/seq/LBG/nextgenout3/MOSE_TEST/abra/brca/data/125b0a9a-6cbe-4207-9178-e7ff03487e87/soapIndel2/
[Mon Mar 24 16:43:09 EDT 2014] Done detection
rm -f soap_indel/RUNNING
touch soap_indel/FINISHED
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