Is it possible to detect mutations in Mouse chrM

[HuangRuocheng]

sorry, I am trying mtdna-server-2 in local using docker.

I simply run "nextflow run main.nf -c test_mitohpc_mutserve.config -profile test,development" where config set to bamflies mapping to Mouse mm10. But failed with:

executor > local (4) [56/f770f1] MTDNA_SERVER_2:CALCULATE_STATISTICS (2) [100%] 2 of 2 ✔ [a0/280316] MTDNA_SERVER_2:INPUT_VALIDATION [100%] 1 of 1, failed: 1 [- ] MTDNA_SERVER_2:INDEX_CREATION - [- ] MTDNA_SERVER_2:QUALITY_CONTROL - [- ] MTDNA_SERVER_2:MUTSERVE - [- ] MTDNA_SERVER_2:FILTER_VARIANTS - [- ] MTDNA_SERVER_2:MERGING_VARIANTS - [- ] MTDNA_SERVER_2:VCF_MERGE - [- ] MTDNA_SERVER_2:HAPLOGROUPS_CONTAMINATION - [- ] MTDNA_SERVER_2:COVERAGE_ESTIMATION - [- ] MTDNA_SERVER_2:ANNOTATE - [- ] MTDNA_SERVER_2:REPORT - [- ] MTDNA_SERVER_2:SAMPLE_REPORT - WARN: Undocumented setting docker.userEmulation is not supported any more - please remove it from your config ERROR ~ Error executing process > 'MTDNA_SERVER_2:INPUT_VALIDATION'

Caused by: Process MTDNA_SERVER_2:INPUT_VALIDATION terminated with an error exit status (255)

Command executed:

csvtk concat -t C.summary.txt KO.summary.txt -T -o sample_statistics.txt --num-cpus 1

csvtk concat -t C.mapping.txt KO.mapping.txt -T -o sample_mappings.txt --num-cpus 1

java -jar /opt/mutserve/mutserve.jar stats --input sample_statistics.txt --mapping sample_mappings.txt --detection-limit 0.03 --reference rcrs --baseQ 20 --mapQ 20 --alignQ 30 --output-excluded-samples excluded_samples.txt --output-contig contig.txt --tool mutserve

delete excluded_samples from BAM input channel directly

awk -v q='"' '{print "rm " q $1 q }' excluded_samples.txt | sh

python -m json.tool cloudgene.report.json

Command exit status: 255

Command output:

mtDNA Variant Detection v2.0.1 https://github.com/seppinho/mutserve (c) Sebastian Schoenherr, Hansi Weissensteiner, Lukas Forer [stats, --input, sample_statistics.txt, --mapping, sample_mappings.txt, --detection-limit, 0.03, --reference, rcrs, --baseQ, 20, --mapQ, 20, --alignQ, 30, --output-excluded-samples, excluded_samples.txt, --output-contig, contig.txt, --tool, mutserve]

ERROR: No valid mtDNA contigs detected.

Command error:

mtDNA Variant Detection v2.0.1 https://github.com/seppinho/mutserve (c) Sebastian Schoenherr, Hansi Weissensteiner, Lukas Forer [stats, --input, sample_statistics.txt, --mapping, sample_mappings.txt, --detection-limit, 0.03, --reference, rcrs, --baseQ, 20, --mapQ, 20, --alignQ, 30, --output-excluded-samples, excluded_samples.txt, --output-contig, contig.txt, --tool, mutserve]

ERROR: No valid mtDNA contigs detected.

Work dir: /home/Group/dna/dnapipe_v3/env_gatk4/mtdna-server-2-2.1.12/work/a0/28031637a0f03345fa16cd16486d5a

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named .command.sh

-- Check '.nextflow.log' file for details

I think maybe I should change reference in somewhere...

[HuangRuocheng]

I have changed

files/rcrs_mutserve.fasta content to mm10 chrM sequence modules/local/calculate_statistics.nf 16569 to 16299, which is the length of mm10 chrM sequence

yet still get the following error in MutServe:

java -Xmx1024M -jar /opt/mutserve/mutserve.jar call C.sub.bam --reference rcrs_mutserve.fasta --output zzztest.vcf

mtDNA Variant Detection v2.0.1 https://github.com/seppinho/mutserve (c) Sebastian Schoenherr, Hansi Weissensteiner, Lukas Forer [call, C.sub.bam, --reference, rcrs_mutserve.fasta, --output, zzztest.vcf] ? C.sub.bam[>-------------------------------------][00:00:00] java.lang.IllegalArgumentException: Invalid reference index -1 at htsjdk.samtools.QueryInterval.(QueryInterval.java:24) at htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.query(SamReader.java:555) at genepi.mut.tasks.VariantCallingTask.run(VariantCallingTask.java:130) at lukfor.progress.tasks.Task.call(Task.java:39) at lukfor.progress.tasks.Task.call(Task.java:1) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635) at java.base/java.lang.Thread.run(Thread.java:840) java.lang.Exception: Invalid reference index -1 at genepi.mut.tasks.VariantCallingTask.run(VariantCallingTask.java:134) at lukfor.progress.tasks.Task.call(Task.java:39) at lukfor.progress.tasks.Task.call(Task.java:1) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635) at java.base/java.lang.Thread.run(Thread.java:840) Variant Calling failed. Mutserve terminated.

where shows Invalid reference index -1.

I am trying Mutect2 option in mtdna-server-2 in local using docker now, still running.

I guess if it is because some human chrM length is coded into mutserve.jar

[seppinho]

Hi, correct. We are focusing on human mitochondrial DNA. BUT If you have a valid BAM file you could still run it with your data and add the --contig-name XXoption and the --reference XX.fastato mutserve.

Please keep in mind that all annotations etc are only for human mtDNA.

[HuangRuocheng]

OK, thank you very much! I will try it out.

ps, Mutect2 has completed and as you said the annotations in the final report are linked to human mtDNA.