error message from var2vcf_paired.pl

[parlar]

Hi!

I spotted an error message in the flowing by text output while running a paired tumor-normal analysis:

Use of uninitialized value $sample in concatenation (.) or string at /usr/local/bin/var2vcf_paired.pl line 35.

Seems to be related to varscan.

The following settings were used:

details: files: [/home/parlar/Projects/akut_lymfatisk_leukemi/combined_fastqs_new/bam_calls/G290-10/G290-10_1.fq.gz, /home/parlar/Projects/akut_lymfatisk_leukemi/combined_fastqs _new/bam_calls/G290-10/G290-10_2.fq.gz] description: G290-10 metadata: batch: batch1 sex: male phenotype: normal analysis: variant2 genome_build: hg19 algorithm: aligner: bwa mark_duplicates: false variantcaller: [mutect, varscan, freebayes, vardict] quality_format: Standard coverage_interval: regional recalibrate: false realign: gatk merge_bamprep: true variant_regions: /home/parlar/Projects/akut_lymfatisk_leukemi/combined_fastqs_new/design_cat_12_13_sorted_merged.bed ensemble: numpass: 2 files: [/home/parlar/Projects/akut_lymfatisk_leukemi/combined_fastqs_new/bam_calls/G67-11/G67-11_1.fq.gz, /home/parlar/Projects/akut_lymfatisk_leukemi/combined_fastqs_new/bam_calls/G67-11/G67-11_2.fq.gz] description: G67-11 metadata: batch: batch1 sex: male phenotype: tumor analysis: variant2 genome_build: hg19 algorithm: aligner: bwa mark_duplicates: false variantcaller: [mutect, varscan, freebayes, vardict] quality_format: Standard coverage_interval: regional recalibrate: false realign: gatk merge_bamprep: true variant_regions: /home/parlar/Projects/akut_lymfatisk_leukemi/combined_fastqs_new/design_cat_12_13_sorted_merged.bed ensemble: numpass: 2

The error in context:

[2015-02-12T12:45Z] bgzip batch1-chr1_185060700_224102810-raw.indel.vcf [2015-02-12T12:45Z] [mpileup] 1 samples in 1 input files [2015-02-12T12:45Z] Set max per-file depth to 8000 [2015-02-12T12:45Z] INFO 13:45:17,319 ProgressMeter - done 0.0 0.0 s 17.9 h 100.0% 0.0 s 0.0 s [2015-02-12T12:45Z] INFO 13:45:17,320 ProgressMeter - Total runtime 0.07 secs, 0.00 min, 0.00 hours [2015-02-12T12:45Z] tabix index batch1-chr1_185060700_224102810-raw.indel.vcf.gz [2015-02-12T12:45Z] Combine variant files [2015-02-12T12:45Z] bgzip batch1-chr1_52840471_93545098-raw.vcf [2015-02-12T12:45Z] tabix index batch1-chr1_52840471_93545098-raw.vcf.gz [2015-02-12T12:45Z] bgzip batch1-chr1_52840471_93545098-raw-rejectfix.vcf

[2015-02-12T12:45Z] Use of uninitialized value $sample in concatenation (.) or string at /usr/local/bin/var2vcf_paired.pl line 35.

[2015-02-12T12:45Z] tabix index batch1-chr1_52840471_93545098-raw-rejectfix.vcf.gz [2015-02-12T12:45Z] Genotyping with varscan: ('chr2', 74732455, 152266557) G290-10-sort-chr2_74732455_152266557-prep.bam [2015-02-12T12:45Z] GATK: VariantAnnotator [2015-02-12T12:45Z] samtools mpileup [2015-02-12T12:45Z] [mpileup] 1 samples in 1 input files [2015-02-12T12:45Z] Set max per-file depth to 8000 [2015-02-12T12:45Z] Varscan

[mjafin]

Hi @parlar, the warning you're seeing is coming from VarDict I reckon, but if it's not causing a fail in the pipeline and it's just one-off, I wouldn't bee too worried. If you run this in single thread mode you might be able to spot which region it's in and I can help debug.

[parlar]

Thanks,

there were actually bunch of these errors when I saved and checked stderr. I'll try to run in single thread mode to check if there is more info.

[parlar]

In the run I checked there were 29 of these errors.

After running in single thread mode the error context looks like as enclosed below. Does the verdict remain that it is nothing to worry about?

[2015-02-12T13:40Z] INFO 14:40:15,018 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime [2015-02-12T13:40Z] INFO 14:40:15,022 SAMDataSource$SAMReaders - Initializing SAMRecords in serial [2015-02-12T13:40Z] INFO 14:40:15,054 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.03 [2015-02-12T13:40Z] INFO 14:40:15,061 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250 [2015-02-12T13:40Z] Genotyping with VarDict: Inference [2015-02-12T13:40Z] INFO 14:40:15,077 SAMDataSource$SAMReaders - Initializing SAMRecords in serial

[2015-02-12T13:40Z] Use of uninitialized value $sample in concatenation (.) or string at /usr/local/bin/var2vcf_paired.pl line 35.

[2015-02-12T13:40Z] INFO 14:40:15,090 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values. [2015-02-12T13:40Z] Genotyping with VarDict: Inference [2015-02-12T13:40Z] INFO 14:40:15,123 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04 [2015-02-12T13:40Z] Genotyping with VarDict: Inference [2015-02-12T13:40Z] INFO 14:40:15,163 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250

[mjafin]

Looking at https://github.com/AstraZeneca-NGS/VarDict/blob/master/var2vcf_paired.pl#L35 I think the line of code should be in an else-if statement on line 40 rather than standalone. It's essentially complaining about a missing sample name but the sample names are pulled from the command line on line 38. Shouldn't affect any results.

[parlar]

Okay, thanks alot!

[lpantano]

Hi

I am closing this because it seems an old issue. Come back if you find other issues.

cheers