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??