Multilane sequencing not handled correctly

[riederd]

Description of the bug

When using a sample sheet in which multiple fastq files per sample are present (multiple lanes sequenced), the fastq files are not concatenated to a single one before processing but they are handled separately, which leads to situations in which bam index files and bam files are mixed up, e.g. index coming from one sequencing lane and bam file from another sequencing lane in ASCAT_SC.

Command used and terminal output

[.....]
Command output:                                                                                                                                                                                
  [1] "checking arguments"                                                                                                                                                                     
  [1] "## load Bins for Genome Build: hg38"                                                                                                                                                    
  [1] "## calculate Target Bin size"                                                                                                                                                           
  [1] "## get Tracks from Tumour bams"                                                                                                                                                         
  [1] "## smooth Tracks"                                                                                                                                                                       
  [1] "   ## correct for GC content"                                                                                                                                                           
  [1] "   ## segment Tracks"                                                                                                                                                                   
  [1] "## fit Purity/Ploidy"                                                                                                                                                                   
  Solution found.                                                                                                                                                                              
  [1] "## get Fitted Cna Profiles"                                                                                                                                                             
  [1] "## compile Results"                                                                                                                                                                     
  [1] "## predict Refit"                                                                                                                                                                       
  [1] "## print Results"                                                                                                                                                                       
                                                                                                                                                                                               
Command error:                                                                                                                                                                                 
  [E::bgzf_read] Read block operation failed with error 3 after 0 of 4 bytes                                                                                                                   
  [E::bgzf_read_block] Invalid BGZF header at offset 6759679475                                                                                                                                
  [E::bgzf_read] Read block operation failed with error 3 after 0 of 4 bytes  
[.....]

Relevant files

sample,fastq_1,fastq_2
sample_1,sample_1_L001_R1.fastq.gz,sample_1_L001_R2.fastq.gz
sample_1,sample_1_L002_R1.fastq.gz,sample_1_L002_R2.fastq.gz

System information

No response

[riederd]

Here are the SAM PG headers from the bam and bai file that were been symlinked to the ASCAT_SC work dir:

bam:

@PG     ID:bwa  PN:bwa  VN:0.7.17-r1188 CL:bwa mem -t 10 ./bwa/GRCh38.d1.vd1.fa sample_1_L001_R1.fastq.gz sample_1_L001_R2.fastq.gz

bai:

@PG     ID:bwa  PN:bwa  VN:0.7.17-r1188 CL:bwa mem -t 10 ./bwa/GRCh38.d1.vd1.fa sample_1_L002_R1.fastq.gz sample_1_L002_R2.fastq.gz

[lbeltrame]

Thanks for your report. To make sure I understand: you'd like SAMURAI to concatenate the same sample from multiple lanes before doing anything, am I right?

This is a valid use case (I admit we don't split by lane normally), but more than a bug, I'd say it's entirely new functionality that is missing. If you don't mind, I'll convert this into a feature request (because it requires changes to the way sample sheets are handled) and add a note to README.md pointing to this issue.

EDIT: I added a note to the README warning about this potential problem.

[riederd]

Thanks for looking into it. I was thinking it already should concatenate lanes from the same sample as I read the following from the samplesheet description in usage.md:

https://github.com/DIncalciLab/samurai/blob/master/docs/usage.md

.... This entry will be identical for multiple sequencing libraries/runs from the same sample. ...

I was used to that from the nf-core/rnaseq pipeline which uses the cat_fastq [1] module and thought samurai is doing the same.

Anyway, I'm looking forward to see this enhancement.

[1] https://nf-co.re/modules/cat_fastq/

[lbeltrame]

Fine point, sorry about this, and thanks for pointing to the module (I wasn't even aware it existed!)