Error executing process > 'pangolin (SARS-CoV-2 lineage Determination)'

[SVN-PhD]

This was using the git cloned version of Cecret. Error from NextFlow:

Error executing process > 'pangolin (SARS-CoV-2 lineage Determination)'

Caused by: Process pangolin (SARS-CoV-2 lineage Determination) terminated with an error exit status (2)

Command executed:

mkdir -p pangolin logs/pangolin log_file=logs/pangolin/pangolin.11a368d3-9f2d-4abc-b735-f07ad370a00d.log err_file=logs/pangolin/pangolin.11a368d3-9f2d-4abc-b735-f07ad370a00d.err

date | tee -a $log_file $err_file > /dev/null pangolin --all-versions >> $log_file

for fasta in 2111180087.consensus.fa do cat $fasta >> ultimate_fasta.fasta done

pangolin --threads 4 --outdir pangolin ultimate_fasta.fasta 2>> $err_file >> $log_file cp ultimate_fasta.fasta pangolin/combined.fasta

Command exit status: 2

Command output: (empty)

Command error: WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap. usage: pangolin [options] pangolin: error: unrecognized arguments: --all-versions

Work dir: /home/mdubfx/cecret_test/Cecret/work/be/1e5b21170bcb2897537dc02b9f6f8b

Tip: when you have fixed the problem you can continue the execution adding the option -resume to the run command line

The StaPH-B version of Cecret is also crashing at the pangolin stage. Thanks!

[erinyoung]

This is an alarming issue. I would like to get this resolved fairly soon.

pangolin: error: unrecognized arguments: --all-versions

What pangolin container are you using?

Admittedly I let the StaPH-B version get a little out of date while I was working on bugs (that should be remedied as soon as I clear up all these issues), so would it be possible to share the error message that you observed with the staph-B toolkit?

[SVN-PhD]

Error executing process > 'summary (2111180087)'

Caused by: Process summary (2111180087) terminated with an error exit status (125)

Command executed:

mkdir -p summary logs/summary log_file=logs/summary/2111180087.70a5d324-4c24-4041-8790-69875d9dc92e.log err_file=logs/summary/2111180087.70a5d324-4c24-4041-8790-69875d9dc92e.err

date | tee -a $log_file $err_file > /dev/null

sampleid=($(echo 2111180087 | cut -f 1 -d "" ))

header="sample_id,sample" result="${sample_id},2111180087"

header="$header,pangolin_lineage,pangolin_status,pangolin_scorpio_call" result="$result,AY.25,passed_qc,Delta (B.1.617.2-like)"

header="$header,nextclade_clade" result="$result,21J (Delta)"

header="$header,fastqc_raw_reads_1,fastqc_raw_reads_2" result="$result,327849,327849"

header="$header,seqyclean_pairs_kept_after_cleaning,seqyclean_percent_kept_after_cleaning" result="$result,293714,89.5882"

header="$header,fastp_reads_passed" result="$result,null"

header="$header,depth_after_trimming,1X_coverage_after_trimming" result="$result,2123.65,99.8161"

header="$header,num_pos_100X" result="$result,28275"

header="$header,insert_size_before_trimming,insert_size_after_trimming" result="$result,137.2,137.6"

organism=$(echo "Severe acute respiratory syndrome-related coronavirus" | sed 's/ /_/g') header="$header,%_humanreads,percent${organism}_reads" result="$result,null,null"

header="$header,ivar_num_variants_identified,bcftools_variants_identified" result="$result,40,null"

header="$header,bedtools_num_failed_amplicons,samtools_num_failed_amplicons" result="$result,0,0"

header="$header,vadr_conclusion" result="$result,null"

header="$header,num_N,num_degenerage,num_non-ambiguous,num_total" result="$result,1574,0,28276,29850"

header="$header,pangolin_version,pangolearn_version,constellations_version,scorpio_version" result="$result,3.1.17,2021-11-25,v0.0.28,0.3.15"

header="$header,nextclade_version" result="$result,1.4.5"

header="$header,cleaner_version,aligner_version,trimmer_version,ivar_version" result="$result,seqyclean : Version: 1.10.09 (2018-10-16),bwa : Version: 0.7.17-r1188,ivar : iVar version 1.3.1 Please raise issues and bug reports at https://github.com/andersen-lab/ivar/,iVar version 1.3.1"

echo $header > summary/2111180087.summary.csv echo $result >> summary/2111180087.summary.csv

cat summary/2111180087.summary.csv | tr ',' ' ' > summary/2111180087.summary.txt

Command exit status: 125

Command output: (empty)

Command error: docker: invalid reference format. See 'docker run --help'.

Work dir: /home/mdubfx/cecret_test/Cecret/211203_cecret2/logs/work/54/812388bc2f8231dd324171747b4f3f

Tip: you can replicate the issue by changing to the process work dir and entering the command bash .command.run

[erinyoung]

It looks like for the StaPH-B toolkit that pangolin is working fine, it's the process summary that has run into issues. You have given the error

docker: invalid reference format.

which is one I'm not familiar with. I'm going to google this for a sec and get back with you.

[erinyoung]

I WAS ABLE TO REPLICATE YOUR DOCKER ERROR!!! 🥳

I normally use singularity, so I was worried.

This must be an issue with the container that's being used. Perhaps there's a typo somewhere. I wonder why it works fine with singularity?

[SVN-PhD]

That's great! I was able to get Pangolin to work by docker pull the latest versions of Pangolin. The other docker error still persists.

[erinyoung]

It's because I put docker:// at the beginning of the image name. I think. At least, I got the error to go away on my end.

I've created a new release and will push an update to the staphb toolkit by the end of the day, but you could try updating this repo and trying again.

https://github.com/UPHL-BioNGS/Cecret/releases/tag/2.2.20211213

[SVN-PhD]

Repo updated and it's working properly, thanks!!