Question

bam-readcount core dump

0

Entering edit mode

5.8 years ago

p2.leo • 0

$ bam-readcount  -f /v2/reference/human_g1k_v37_decoy.fasta -l test.bed /pValSeq/run202/20180430-0002.bam -q 20 -i -d 1000

returns:

Minimum mapping quality is set to 20
Expect library: KapD-20180607-0002 in BAM
Floating point exception (core dumped)

Any ideas?? Tried all other options etc

BAM file from novoalign, exome, reference and bam otherwise ok

$ bam-readcount  -v
bam-readcount version: 0.8.0-unstable-6-963acab-dirty (commit 963acab-dirty)

$ cat test.bed
1   21295970    21295971
1   35250655    35250656

Bam looks or genoyped via GATK reference matches.....

$ samstool view -H 

*@HD    VN:1.0  SO:coordinate
@RG ID:HKL2TBGX5-4-708-501  CN:ATGC DS:i7_sequence=TAATGCGC|sample_type=XTumour|library_id=KapD-20180607-0002|flowcell_id=HKL2TBGX5|sample_id=20180430-0002|nucleic_type=DNA|capture_type=IdtXPC|preservation_type=Fresh|library_type=KapDH|lane=4|run_id=180611_NB501489_0202_AHKL2TBGX5|cohort_id=NBCF_Riccardo_Paul|instrument_id=NB501489|i5_sequence=AGGCTATA|run_start_date=2018-06-11|capture_id=IDTX-20180607-0001|portion_id=A|subject_id=MDA-MB-231   DT:2018-06-11   LB:KapD-20180607-0002   PL:ILLUMINA PM:NB501489 PU:HKL2TBGX5_4  SM:20180430-0002
@PG ID:novoalign    PN:novoalign    VN:V3.08.02 CL:novoalign -o SAM "@RG\tID:HKL2TBGX5-4-708-501\tCN:ATGC\tDS:i7_sequence=TAATGCGC|sample_type=XTumour|library_id=KapD-20180607-0002|flowcell_id=HKL2TBGX5|sample_id=20180430-0002|nucleic_type=DNA|capture_type=IdtXPC|preservation_type=Fresh|library_type=KapDH|lane=4|run_id=180611_NB501489_0202_AHKL2TBGX5|cohort_id=NBCF_Riccardo_Paul|instrument_id=NB501489|i5_sequence=AGGCTATA|run_start_date=2018-06-11|capture_id=IDTX-20180607-0001|portion_id=A|subject_id=MDA-MB-231\tDT:2018-06-11\tLB:KapD-20180607-0002\tPL:ILLUMINA\tPM:NB501489\tPU:HKL2TBGX5_4\tSM:20180430-0002" -c 12 -r All 1 -d /work2/ATG_datasets/clinical-data/v2/reference/human_g1k_v37_decoy_iupac.ndx -f /work/ATG/clinical/fastq/180611_NB501489_0202_AHKL2TBGX5/ATG/HKL2TBGX5-4-708-501_S24_L004_R1_001.fastq.gz /work/ATG/clinical/fastq/180611_NB501489_0202_AHKL2TBGX5/ATG/HKL2TBGX5-4-708-501_S24_L004_R2_001.fastq.gz -F STDFQ --hlimit 7 --trim3HP --rOQ -k -p 5,20 -t 20,4 -i 280,100
@SQ SN:1    LN:249250621    AS:human_g1k_v37_decoy_iupac.ndx
@SQ SN:2    LN:243199373    AS:human_g1k_v37_decoy_iupac.ndx
@SQ SN:3    LN:198022430    AS:human_g1k_v37_decoy_iupac.ndx
@SQ SN:4    LN:191154276    AS:human_g1k_v37_decoy_iupac.ndx
@SQ SN:5    LN:180915260    AS:human_g1k_v37_decoy_iupac.ndx
@SQ SN:6    LN:171115067    AS:human_g1k_v37_decoy_iupac.ndx
@SQ SN:7    LN:159138663    AS:human_g1k_v37_decoy_iupac.ndx
@SQ SN:8    LN:146364022    AS:human_g1k_v37_decoy_iupac.ndx
@SQ SN:9    LN:141213431    AS:human_g1k_v37_decoy_iupac.ndx
@SQ SN:10   LN:135534747    AS:human_g1k_v37_decoy_iupac.ndx
@SQ SN:11   LN:135006516    AS:human_g1k_v37_decoy_iupac.ndx
@SQ SN:12   LN:133851895    AS:human_g1k_v37_decoy_iupac.ndx
@SQ SN:13   LN:115169878    AS:human_g1k_v37_decoy_iupac.ndx
@SQ SN:14   LN:107349540    AS:human_g1k_v37_decoy_iupac.ndx
@SQ SN:15   LN:102531392    AS:human_g1k_v37_decoy_iupac.ndx
@SQ SN:16   LN:90354753 AS:human_g1k_v37_decoy_iupac.ndx
@SQ SN:17   LN:81195210 AS:human_g1k_v37_decoy_iupac.ndx
@SQ SN:18   LN:78077248 AS:human_g1k_v37_decoy_iupac.ndx
@SQ SN:19   LN:59128983 AS:human_g1k_v37_decoy_iupac.ndx
@SQ SN:20   LN:63025520 AS:human_g1k_v37_decoy_iupac.ndx
@SQ SN:21   LN:48129895 AS:human_g1k_v37_decoy_iupac.ndx
@SQ SN:22   LN:51304566 AS:human_g1k_v37_decoy_iupac.ndx
@SQ SN:X    LN:155270560    AS:human_g1k_v37_decoy_iupac.ndx
@SQ SN:Y    LN:59373566 AS:human_g1k_v37_decoy_iupac.ndx
@SQ SN:MT   LN:16569    AS:human_g1k_v37_decoy_iupac.ndx
@SQ SN:GL000207.1   LN:4262 AS:human_g1k_v37_decoy_iupac.ndx
@SQ SN:GL000226.1   LN:15008    AS:human_g1k_v37_decoy_iupac.ndx
@SQ SN:GL000229.1   LN:19913    AS:human_g1k_v37_decoy_iupac.ndx
@SQ SN:GL000231.1   LN:27386    AS:human_g1k_v37_decoy_iupac.ndx
@SQ SN:GL000210.1   LN:27682    AS:human_g1k_v37_decoy_iupac.ndx
@SQ SN:GL000239.1   LN:33824    AS:human_g1k_v37_decoy_iupac.ndx
@SQ SN:GL000235.1   LN:34474    AS:human_g1k_v37_decoy_iupac.ndx
@SQ SN:GL000201.1   LN:36148    AS:human_g1k_v37_decoy_iupac.ndx
@SQ SN:GL000247.1   LN:36422    AS:human_g1k_v37_decoy_iupac.ndx
@SQ SN:GL000245.1   LN:36651    AS:human_g1k_v37_decoy_iupac.ndx
@SQ SN:GL000197.1   LN:37175    AS:human_g1k_v37_decoy_iupac.ndx
@SQ SN:GL000203.1   LN:37498    AS:human_g1k_v37_decoy_iupac.ndx
@SQ SN:GL000246.1   LN:38154    AS:human_g1k_v37_decoy_iupac.ndx
@SQ SN:GL000249.1   LN:38502    AS:human_g1k_v37_decoy_iupac.ndx
@SQ SN:GL000196.1   LN:38914    AS:human_g1k_v37_decoy_iupac.ndx
@SQ SN:GL000248.1   LN:39786    AS:human_g1k_v37_decoy_iupac.ndx
@SQ SN:GL000244.1   LN:39929    AS:human_g1k_v37_decoy_iupac.ndx
@SQ SN:GL000238.1   LN:39939    AS:human_g1k_v37_decoy_iupac.ndx
@SQ SN:GL000202.1   LN:40103    AS:human_g1k_v37_decoy_iupac.ndx
@SQ SN:GL000234.1   LN:40531    AS:human_g1k_v37_decoy_iupac.ndx
@SQ SN:GL000232.1   LN:40652    AS:human_g1k_v37_decoy_iupac.ndx
@SQ SN:GL000206.1   LN:41001    AS:human_g1k_v37_decoy_iupac.ndx
@SQ SN:GL000240.1   LN:41933    AS:human_g1k_v37_decoy_iupac.ndx
@SQ SN:GL000236.1   LN:41934    AS:human_g1k_v37_decoy_iupac.ndx
@SQ SN:GL000241.1   LN:42152    AS:human_g1k_v37_decoy_iupac.ndx
@SQ SN:GL000243.1   LN:43341    AS:human_g1k_v37_decoy_iupac.ndx
@SQ SN:GL000242.1   LN:43523    AS:human_g1k_v37_decoy_iupac.ndx
@SQ SN:GL000230.1   LN:43691    AS:human_g1k_v37_decoy_iupac.ndx
@SQ SN:GL000237.1   LN:45867    AS:human_g1k_v37_decoy_iupac.ndx
@SQ SN:GL000233.1   LN:45941    AS:human_g1k_v37_decoy_iupac.ndx
@SQ SN:GL000204.1   LN:81310    AS:human_g1k_v37_decoy_iupac.ndx
@SQ SN:GL000198.1   LN:90085    AS:human_g1k_v37_decoy_iupac.ndx
@SQ SN:GL000208.1   LN:92689    AS:human_g1k_v37_decoy_iupac.ndx
@SQ SN:GL000191.1   LN:106433   AS:human_g1k_v37_decoy_iupac.ndx
@SQ SN:GL000227.1   LN:128374   AS:human_g1k_v37_decoy_iupac.ndx
@SQ SN:GL000228.1   LN:129120   AS:human_g1k_v37_decoy_iupac.ndx
@SQ SN:GL000214.1   LN:137718   AS:human_g1k_v37_decoy_iupac.ndx
@SQ SN:GL000221.1   LN:155397   AS:human_g1k_v37_decoy_iupac.ndx
@SQ SN:GL000209.1   LN:159169   AS:human_g1k_v37_decoy_iupac.ndx
@SQ SN:GL000218.1   LN:161147   AS:human_g1k_v37_decoy_iupac.ndx
@SQ SN:GL000220.1   LN:161802   AS:human_g1k_v37_decoy_iupac.ndx
@SQ SN:GL000213.1   LN:164239   AS:human_g1k_v37_decoy_iupac.ndx
@SQ SN:GL000211.1   LN:166566   AS:human_g1k_v37_decoy_iupac.ndx
@SQ SN:GL000199.1   LN:169874   AS:human_g1k_v37_decoy_iupac.ndx
@SQ SN:GL000217.1   LN:172149   AS:human_g1k_v37_decoy_iupac.ndx
@SQ SN:GL000216.1   LN:172294   AS:human_g1k_v37_decoy_iupac.ndx
@SQ SN:GL000215.1   LN:172545   AS:human_g1k_v37_decoy_iupac.ndx
@SQ SN:GL000205.1   LN:174588   AS:human_g1k_v37_decoy_iupac.ndx
@SQ SN:GL000219.1   LN:179198   AS:human_g1k_v37_decoy_iupac.ndx
@SQ SN:GL000224.1   LN:179693   AS:human_g1k_v37_decoy_iupac.ndx
@SQ SN:GL000223.1   LN:180455   AS:human_g1k_v37_decoy_iupac.ndx
@SQ SN:GL000195.1   LN:182896   AS:human_g1k_v37_decoy_iupac.ndx
@SQ SN:GL000212.1   LN:186858   AS:human_g1k_v37_decoy_iupac.ndx
@SQ SN:GL000222.1   LN:186861   AS:human_g1k_v37_decoy_iupac.ndx
@SQ SN:GL000200.1   LN:187035   AS:human_g1k_v37_decoy_iupac.ndx
@SQ SN:GL000193.1   LN:189789   AS:human_g1k_v37_decoy_iupac.ndx
@SQ SN:GL000194.1   LN:191469   AS:human_g1k_v37_decoy_iupac.ndx
@SQ SN:GL000225.1   LN:211173   AS:human_g1k_v37_decoy_iupac.ndx
@SQ SN:GL000192.1   LN:547496   AS:human_g1k_v37_decoy_iupac.ndx
@SQ SN:NC_007605    LN:171823   AS:human_g1k_v37_decoy_iupac.ndx
@SQ SN:hs37d5   LN:35477943 AS:human_g1k_v37_decoy_iupac.ndx
@RG ID:HKL2TBGX5-2-708-501  CN:ATGC DS:i7_sequence=TAATGCGC|sample_type=XTumour|library_id=KapD-20180607-0002|flowcell_id=HKL2TBGX5|sample_id=20180430-0002|nucleic_type=DNA|capture_type=IdtXPC|preservation_type=Fresh|library_type=KapDH|lane=2|run_id=180611_NB501489_0202_AHKL2TBGX5|cohort_id=NBCF_Riccardo_Paul|instrument_id=NB501489|i5_sequence=AGGCTATA|run_start_date=2018-06-11|capture_id=IDTX-20180607-0001|portion_id=A|subject_id=MDA-MB-231   DT:2018-06-11   LB:KapD-20180607-0002   PL:ILLUMINA PM:NB501489 PU:HKL2TBGX5_2  SM:20180430-0002
@PG ID:novoalign.1  PN:novoalign    VN:V3.08.02 CL:novoalign -o SAM "@RG\tID:HKL2TBGX5-2-708-501\tCN:ATGC\tDS:i7_sequence=TAATGCGC|sample_type=XTumour|library_id=KapD-20180607-0002|flowcell_id=HKL2TBGX5|sample_id=20180430-0002|nucleic_type=DNA|capture_type=IdtXPC|preservation_type=Fresh|library_type=KapDH|lane=2|run_id=180611_NB501489_0202_AHKL2TBGX5|cohort_id=NBCF_Riccardo_Paul|instrument_id=NB501489|i5_sequence=AGGCTATA|run_start_date=2018-06-11|capture_id=IDTX-20180607-0001|portion_id=A|subject_id=MDA-MB-231\tDT:2018-06-11\tLB:KapD-20180607-0002\tPL:ILLUMINA\tPM:NB501489\tPU:HKL2TBGX5_2\tSM:20180430-0002" -c 12 -r All 1 -d /work2/ATG_datasets/clinical-data/v2/reference/human_g1k_v37_decoy_iupac.ndx -f /work/ATG/clinical/fastq/180611_NB501489_0202_AHKL2TBGX5/ATG/HKL2TBGX5-2-708-501_S10_L002_R1_001.fastq.gz /work/ATG/clinical/fastq/180611_NB501489_0202_AHKL2TBGX5/ATG/HKL2TBGX5-2-708-501_S10_L002_R2_001.fastq.gz -F STDFQ --hlimit 7 --trim3HP --rOQ -k -p 5,20 -t 20,4 -i 280,100
@RG ID:HKL2TBGX5-1-708-501  CN:ATGC DS:i7_sequence=TAATGCGC|sample_type=XTumour|library_id=KapD-20180607-0002|flowcell_id=HKL2TBGX5|sample_id=20180430-0002|nucleic_type=DNA|capture_type=IdtXPC|preservation_type=Fresh|library_type=KapDH|lane=1|run_id=180611_NB501489_0202_AHKL2TBGX5|cohort_id=NBCF_Riccardo_Paul|instrument_id=NB501489|i5_sequence=AGGCTATA|run_start_date=2018-06-11|capture_id=IDTX-20180607-0001|portion_id=A|subject_id=MDA-MB-231   DT:2018-06-11   LB:KapD-20180607-0002   PL:ILLUMINA PM:NB501489 PU:HKL2TBGX5_1  SM:20180430-0002
@PG ID:novoalign.2  PN:novoalign    VN:V3.08.02 CL:novoalign -o SAM "@RG\tID:HKL2TBGX5-1-708-501\tCN:ATGC\tDS:i7_sequence=TAATGCGC|sample_type=XTumour|library_id=KapD-20180607-0002|flowcell_id=HKL2TBGX5|sample_id=20180430-0002|nucleic_type=DNA|capture_type=IdtXPC|preservation_type=Fresh|library_type=KapDH|lane=1|run_id=180611_NB501489_0202_AHKL2TBGX5|cohort_id=NBCF_Riccardo_Paul|instrument_id=NB501489|i5_sequence=AGGCTATA|run_start_date=2018-06-11|capture_id=IDTX-20180607-0001|portion_id=A|subject_id=MDA-MB-231\tDT:2018-06-11\tLB:KapD-20180607-0002\tPL:ILLUMINA\tPM:NB501489\tPU:HKL2TBGX5_1\tSM:20180430-0002" -c 12 -r All 1 -d /work2/ATG_datasets/clinical-data/v2/reference/human_g1k_v37_decoy_iupac.ndx -f /work/ATG/clinical/fastq/180611_NB501489_0202_AHKL2TBGX5/ATG/HKL2TBGX5-1-708-501_S3_L001_R1_001.fastq.gz /work/ATG/clinical/fastq/180611_NB501489_0202_AHKL2TBGX5/ATG/HKL2TBGX5-1-708-501_S3_L001_R2_001.fastq.gz -F STDFQ --hlimit 7 --trim3HP --rOQ -k -p 5,20 -t 20,4 -i 280,100
@RG ID:HKL2TBGX5-3-708-501  CN:ATGC DS:i7_sequence=TAATGCGC|sample_type=XTumour|library_id=KapD-20180607-0002|flowcell_id=HKL2TBGX5|sample_id=20180430-0002|nucleic_type=DNA|capture_type=IdtXPC|preservation_type=Fresh|library_type=KapDH|lane=3|run_id=180611_NB501489_0202_AHKL2TBGX5|cohort_id=NBCF_Riccardo_Paul|instrument_id=NB501489|i5_sequence=AGGCTATA|run_start_date=2018-06-11|capture_id=IDTX-20180607-0001|portion_id=A|subject_id=MDA-MB-231   DT:2018-06-11   LB:KapD-20180607-0002   PL:ILLUMINA PM:NB501489 PU:HKL2TBGX5_3  SM:20180430-0002
@PG ID:novoalign.3  PN:novoalign    VN:V3.08.02 CL:novoalign -o SAM "@RG\tID:HKL2TBGX5-3-708-501\tCN:ATGC\tDS:i7_sequence=TAATGCGC|sample_type=XTumour|library_id=KapD-20180607-0002|flowcell_id=HKL2TBGX5|sample_id=20180430-0002|nucleic_type=DNA|capture_type=IdtXPC|preservation_type=Fresh|library_type=KapDH|lane=3|run_id=180611_NB501489_0202_AHKL2TBGX5|cohort_id=NBCF_Riccardo_Paul|instrument_id=NB501489|i5_sequence=AGGCTATA|run_start_date=2018-06-11|capture_id=IDTX-20180607-0001|portion_id=A|subject_id=MDA-MB-231\tDT:2018-06-11\tLB:KapD-20180607-0002\tPL:ILLUMINA\tPM:NB501489\tPU:HKL2TBGX5_3\tSM:20180430-0002" -c 12 -r All 1 -d /work2/ATG_datasets/clinical-data/v2/reference/human_g1k_v37_decoy_iupac.ndx -f /work/ATG/clinical/fastq/180611_NB501489_0202_AHKL2TBGX5/ATG/HKL2TBGX5-3-708-501_S17_L003_R1_001.fastq.gz /work/ATG/clinical/fastq/180611_NB501489_0202_AHKL2TBGX5/ATG/HKL2TBGX5-3-708-501_S17_L003_R2_001.fastq.gz -F STDFQ --hlimit 7 --trim3HP --rOQ -k -p 5,20 -t 20,4 -i 280,100*

next-gen sequencing • 1.4k views

ADD COMMENT • link updated 5.7 years ago by Biostar 20 • written 5.8 years ago by p2.leo • 0

0

Entering edit mode

Hello,

I cannot solve your problem. But you could have a look at samtools depth as in alternative.

fin swimmer

ADD REPLY • link 5.8 years ago by finswimmer 16k

0

Entering edit mode

Hello p2.leo,

do you need the bam-readcount output for the VarScan2 fpfilter? If not, what do you plan to do with the output? Depending on that, there might be other tools that can do the job and are still being maintained.

ADD REPLY • link 5.7 years ago by ATpoint 82k

0

Entering edit mode

Thanks for the replies, Yes this is a funny one I wanted to use this program because the output in integrated with pVACtools ... and the output is quite verbose.

I think from these suggestions my best bet may be to just try and to the pileup with more standard tools ,as you suggest, and craft a similar output.

Thanks for the suggestions Best Paul

ADD REPLY • link 5.7 years ago by p2.leo • 0

0

Entering edit mode

The most common reason for bam-readcount crashes/core dumps are a mismatch between reference fasta and bam file. Are you sure that none of of your reads goes past the end of the chromosome sizes defined in your fasta?

ADD REPLY • link 5.7 years ago by Chris Miller 22k