Problem with RG

[Sophie Blanc]

Hello,

I've been using Platypus as part of the Fast-GBS pipeline for 2 years, and it worked fine.

But recently I have been having problems running Platypus. Maybe it's due to the fact that we updated some of our tools on our server.

Without the RG I have an error indicating that it needs RG. Previously I made it work without it, but anyway I used Picard to add RG, and still it doesn't work... the log file indicates it succeeds to add samples, but my .vcf is empty. The names of the RG are exactly the same as in the bamlist, so I really can't figure out why it doesn't work.

Here is an exemple of my log file :

2019-07-29 10:14:28,745 - INFO - Beginning variant calling

2019-07-29 10:14:28,745 - INFO - Output will go to FastGBS_platypus.vcf

2019-07-29 10:14:28,752 - DEBUG - Loaded regions from BAM header, SQ tags

2019-07-29 10:14:28,753 - DEBUG - 461 regions will be searched

2019-07-29 10:14:28,783 - DEBUG - Treating --bamFiles argument, ['../results/List_bam'] as a text file containing a list of BAM file names

2019-07-29 10:14:28,790 - DEBUG - Adding sample name H3T5WBBXX_1_P18324_RG.sort.bam, using BAM RG:SM tag in file /home/soblanc/sciences_so/GBS_PN/ALT/data/H3T5WBBXX_1_P18324_RG.sort.bam

2019-07-29 10:14:28,796 - DEBUG - Adding sample name H3T5WBBXX_1_P18325_RG.sort.bam, using BAM RG:SM tag in file /home/soblanc/sciences_so/GBS_PN/ALT/data/H3T5WBBXX_1_P18325_RG.sort.bam

2019-07-29 10:14:28,802 - DEBUG - Adding sample name H3T5WBBXX_1_P18326_RG.sort.bam, using BAM RG:SM tag in file /home/soblanc/sciences_so/GBS_PN/ALT/data/H3T5WBBXX_1_P18326_RG.sort.bam

2019-07-29 10:14:28,808 - DEBUG - Adding sample name H3T5WBBXX_1_P18327_RG.sort.bam, using BAM RG:SM tag in file /home/soblanc/sciences_so/GBS_PN/ALT/data/H3T5WBBXX_1_P18327_RG.sort.bam

2019-07-29 10:14:28,815 - DEBUG - Adding sample name H3T5WBBXX_1_P18328_RG.sort.bam, using BAM RG:SM tag in file /home/soblanc/sciences_so/GBS_PN/ALT/data/H3T5WBBXX_1_P18328_RG.sort.bam

2019-07-29 10:14:28,821 - DEBUG - Adding sample name H3T5WBBXX_1_P18329_RG.sort.bam, using BAM RG:SM tag in file /home/soblanc/sciences_so/GBS_PN/ALT/data/H3T5WBBXX_1_P18329_RG.sort.bam

I tested the Platypus last version of the Git, an older one of oct. 2017, I tested the pipeline fastgbs using samtools, htslib and bcftools version 1.2 and 1.6, and still doesn't work.

Would you have any suggestions? Maybe could you tell me which versions of the tools should we use to make Platypus work properly?

Thank you very much in advance,

Sophie