Question: Empty .cfg after running bam2cfg.pl
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gravatar for shannon.soucy
3.4 years ago by
shannon.soucy0 wrote:

I have been trying to run bam2cfg on my bam files generated with bowtie. The first time I tried I didn't have read groups assigned, but I wasn't comparing SV between samples so it didn't really matter- but I got an empty cfg file. So I re-ran bowtie and added the @RG information, thinking this would help- it didn't I'm getting a different error now than I was before- but still an empty .cfg file!

Here is the bam file header with the @RG:

@HD VN:1.0  SO:coordinate
@SQ SN:DL31-cdc21   LN:2955
@SQ SN:tADL-cdc21   LN:3522
@SQ SN:DL1-cdc21    LN:3492
@SQ SN:Hlac-cdc21   LN:2103
@SQ SN:DL31-gyrB    LN:3231
@SQ SN:DL1-gyrB LN:1914
@SQ SN:Hlac-gyrB    LN:1938
@SQ SN:tADL-gyrB    LN:1950
@SQ SN:DL31-polB    LN:5208
@SQ SN:tADL-polB    LN:2730
@SQ SN:DL1-polB LN:2691
@SQ SN:Hlac-polB    LN:2790
@SQ SN:DL31-pol_II  LN:4296
@SQ SN:Hlac-pol_II  LN:4101
@SQ SN:DL1-pol_II   LN:5031
@SQ SN:tADL-pol_II  LN:5067
@SQ SN:DL1-rir1 LN:3144
@SQ SN:DL31-rir1    LN:4302
@SQ SN:Hlac-rir1    LN:3171
@SQ SN:tADL-rir1    LN:3147
@SQ SN:tADL-top6B   LN:2430
@SQ SN:DL1-top6B    LN:2406
@SQ SN:DL31-top6B   LN:4137
@SQ SN:Hlac-top6B   LN:2457
@RG ID:ID:24m8u PL:illumina
@PG ID:bowtie2  PN:bowtie2  VN:2.2.5    CL:"/export/apps/bowtie2-align-s --wrapper basic-0 -x ./merged_mappings/dl_inteins2 -q 24m-3.0u-sick_trim.fastq --rg-id ID:24m8u --rg PL:illumina -S dl_int-3-bowtie2.sam"

and here is the error that i'm getting when I run bam2cfg.pl:

Use of uninitialized value $lib in hash element at bam2cfg.pl line 79, <$bam> line 26.
[Thu Mar  3 15:35:38 2016 bam2cfg.pl] Closing BAM file
[Thu Mar  3 15:35:38 2016 bam2cfg.pl] Send TERM signal for 8930
[Thu Mar  3 15:35:40 2016 bam2cfg.pl] samtools pid process 8930 is still there...
[Thu Mar  3 15:35:40 2016 bam2cfg.pl] invoking kill -9 on 8930 ...
[Thu Mar  3 15:35:40 2016 bam2cfg.pl] Closing samtools process : 8930
Use of uninitialized value $lib in hash element at bam2cfg.pl line 195.

when I run bam2cfg.pl on the test-data I don't have "Use of uninitialized value" warnings.

Can anyone offer any suggestions as to how I need to reformat my bam files so I can get bam2cfg.pl to generate a *.cfg file??

assembly genome • 1.3k views
ADD COMMENTlink modified 3.4 years ago by Pierre Lindenbaum121k • written 3.4 years ago by shannon.soucy0
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