Closed DarianHole closed 4 years ago
Hi @DarianHole - this should be fixed by https://github.com/connor-lab/ncov2019-artic-nf/commit/8b0f5ea06f94a8f7235613c20fc371c886f695b9.
Oh thanks @m-bull ! I'll test it out! Great workflow
Works now, thanks again!
Hi, I'm getting a similar error:
Error executing process > 'articNcovNanopore:sequenceAnalysisNanopolish:articMinIONNanopolish (guppy3.6_110520_barcode03)'
Caused by:
Process `articNcovNanopore:sequenceAnalysisNanopolish:articMinIONNanopolish (guppy3.6_110520_barcode03)` terminated with an error exit status (20)
Command executed:
artic minion --normalise 500 --minimap2 --threads 1 --scheme-directory scheme/primer_schemes --read-file guppy3.6_110520_barcode03.fastq --fast5-directory fast5_pass --sequencing-sum
mary sequencing_summary.txt nCoV-2019/V2 guppy3.6_110520_barcode03
Command exit status:
20
Command output:
(empty)
Command error:
[readdb] indexing fast5_pass
[readdb] num reads: 140498, num reads with path to fast5: 140498
[M::mm_idx_gen::0.003*2.51] collected minimizers
[M::mm_idx_gen::0.005*1.92] sorted minimizers
[M::main::0.005*1.92] loaded/built the index for 1 target sequence(s)
[M::mm_mapopt_update::0.006*1.86] mid_occ = 3
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1
[M::mm_idx_stat::0.006*1.82] distinct minimizers: 5587 (99.93% are singletons); average occurrences: 1.004; average spacing: 5.332
[M::worker_pipeline::40.111*0.91] mapped 140498 sequences
[M::main] Version: 2.17-r941
[M::main] CMD: minimap2 -a -x map-ont -t 1 scheme/primer_schemes/nCoV-2019/V2/nCoV-2019.reference.fasta guppy3.6_110520_barcode03.fastq
[M::main] Real time: 40.250 sec; CPU: 36.441 sec; Peak RSS: 0.189 GB
[post-run summary] total reads: 73910, unparseable: 0, qc fail: 31, could not calibrate: 2, no alignment: 109, bad fast5: 0
[post-run summary] total reads: 71208, unparseable: 0, qc fail: 24, could not calibrate: 3, no alignment: 109, bad fast5: 0
Traceback (most recent call last):
File "/opt/conda/bin/artic_plot_amplicon_depth", line 10, in <module>
sys.exit(main())
File "/opt/conda/lib/python3.6/site-packages/artic/plot_amplicon_depth.py", line 143, in main
go(args)
File "/opt/conda/lib/python3.6/site-packages/artic/plot_amplicon_depth.py", line 84, in go
x=df['position'], bins=starts, labels=amplicons)
File "/opt/conda/lib/python3.6/site-packages/pandas/core/reshape/tile.py", line 260, in cut
raise ValueError("bins must increase monotonically.")
ValueError: bins must increase monotonically.
Running: nanopolish index -s sequencing_summary.txt -d fast5_pass guppy3.6_110520_barcode03.fastq
Running: minimap2 -a -x map-ont -t 1 scheme/primer_schemes/nCoV-2019/V2/nCoV-2019.reference.fasta guppy3.6_110520_barcode03.fastq | samtools view -bS -F 4 - | samtools sort -o guppy3.6_110520_barcode03.sorted.bam -
Running: samtools index guppy3.6_110520_barcode03.sorted.bam
Running: align_trim --start --normalise 500 scheme/primer_schemes/nCoV-2019/V2/nCoV-2019.scheme.bed --report guppy3.6_110520_barcode03.alignreport.txt < guppy3.6_110520_barcode03.sorted.bam 2> guppy3.6_110520_barcode03.alignreport.er | samtools sort -T guppy3.6_110520_barcode03 - -o guppy3.6_110520_barcode03.trimmed.rg.sorted.bam
Running: align_trim --normalise 500 scheme/primer_schemes/nCoV-2019/V2/nCoV-2019.scheme.bed --remove-incorrect-pairs --report guppy3.6_110520_barcode03.alignreport.txt < guppy3.6_110520_barcode03.sorted.bam 2> guppy3.6_110520_barcode03.alignreport.er | samtools sort -T guppy3.6_110520_barcode03 - -o guppy3.6_110520_barcode03.primertrimmed.rg.sorted.bam
Running: samtools index guppy3.6_110520_barcode03.trimmed.rg.sorted.bam
Running: samtools index guppy3.6_110520_barcode03.primertrimmed.rg.sorted.bam
Running: nanopolish variants --min-flanking-sequence 10 -x 1000000 --progress -t 1 --reads guppy3.6_110520_barcode03.fastq -o guppy3.6_110520_barcode03.nCoV-2019_2.vcf -b guppy3.6_110520_barcode03.trimmed.rg.sorted.bam -g scheme/primer_schemes/nCoV-2019/V2/nCoV-2019.reference.fasta -w "MN908947.3:1-29904" --ploidy 1 -m 0.15 --read-group nCoV-2019_2
Running: nanopolish variants --min-flanking-sequence 10 -x 1000000 --progress -t 1 --reads guppy3.6_110520_barcode03.fastq -o guppy3.6_110520_barcode03.nCoV-2019_1.vcf -b guppy3.6_110520_barcode03.trimmed.rg.sorted.bam -g scheme/primer_schemes/nCoV-2019/V2/nCoV-2019.reference.fasta -w "MN908947.3:1-29904" --ploidy 1 -m 0.15 --read-group nCoV-2019_1
Running: artic_vcf_merge guppy3.6_110520_barcode03 scheme/primer_schemes/nCoV-2019/V2/nCoV-2019.scheme.bed nCoV-2019_2:guppy3.6_110520_barcode03.nCoV-2019_2.vcf nCoV-2019_1:guppy3.6_110520_barcode03.nCoV-2019_1.vcf
Running: artic_vcf_filter --nanopolish guppy3.6_110520_barcode03.merged.vcf guppy3.6_110520_barcode03.pass.vcf guppy3.6_110520_barcode03.fail.vcf
Running: artic_make_depth_mask --store-rg-depths scheme/primer_schemes/nCoV-2019/V2/nCoV-2019.reference.fasta guppy3.6_110520_barcode03.primertrimmed.rg.sorted.bam guppy3.6_110520_barcode03.coverage_mask.txt
Running: artic_plot_amplicon_depth --primerScheme scheme/primer_schemes/nCoV-2019/V2/nCoV-2019.scheme.bed --sampleID guppy3.6_110520_barcode03 --outFilePrefix guppy3.6_110520_barcode03 guppy3.6_110520_barcode03*.depths
Command failed:artic_plot_amplicon_depth --primerScheme scheme/primer_schemes/nCoV-2019/V2/nCoV-2019.scheme.bed --sampleID guppy3.6_110520_barcode03 --outFilePrefix guppy3.6_110520_barcode03 guppy3.6_110520_barcode03*.depths
Work dir:
/mnt/ubi/iferres/covid19/prueba/work2/75/4c0c76414f294aa76e95002e9adebb
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`
[iferres@nagual prueba]$ [1;2CDD
I have updated the nextflow pipeline, but still getting that error. Any advice? Thanks
Mine started failing again in the same spot yesterday after working on Wednesday so I'm not sure what happened. Potentially the conda env update had an issue
It must be something with the pandas. It's throwing an error as if a file doesn't exists, but it actually does.
singularity exec /mnt/ubi/iferres/covid19/artic.sif artic_plot_amplicon_depth --primerScheme scheme/primer_schemes/nCoV-2019/V2/nCoV-2019.scheme.bed --sampleID guppy3.6_110520_barcode03 --outFilePrefix guppy3.6_110520_barcode03 guppy3.6_110520_barcode03*.depths
Traceback (most recent call last):
File "/opt/conda/bin/artic_plot_amplicon_depth", line 10, in <module>
sys.exit(main())
File "/opt/conda/lib/python3.6/site-packages/artic/plot_amplicon_depth.py", line 143, in main
go(args)
File "/opt/conda/lib/python3.6/site-packages/artic/plot_amplicon_depth.py", line 29, in go
primerScheme = read_bed_file(args.primerScheme)
File "/opt/conda/lib/python3.6/site-packages/artic/vcftagprimersites.py", line 88, in read_bed_file
skiprows=0)
File "/opt/conda/lib/python3.6/site-packages/pandas/io/parsers.py", line 685, in parser_f
return _read(filepath_or_buffer, kwds)
File "/opt/conda/lib/python3.6/site-packages/pandas/io/parsers.py", line 457, in _read
parser = TextFileReader(fp_or_buf, **kwds)
File "/opt/conda/lib/python3.6/site-packages/pandas/io/parsers.py", line 895, in __init__
self._make_engine(self.engine)
File "/opt/conda/lib/python3.6/site-packages/pandas/io/parsers.py", line 1135, in _make_engine
self._engine = CParserWrapper(self.f, **self.options)
File "/opt/conda/lib/python3.6/site-packages/pandas/io/parsers.py", line 1917, in __init__
self._reader = parsers.TextReader(src, **kwds)
File "pandas/_libs/parsers.pyx", line 382, in pandas._libs.parsers.TextReader.__cinit__
File "pandas/_libs/parsers.pyx", line 689, in pandas._libs.parsers.TextReader._setup_parser_source
FileNotFoundError: [Errno 2] File b'scheme/primer_schemes/nCoV-2019/V2/nCoV-2019.scheme.bed' does not exist: b'scheme/primer_schemes/nCoV-2019/V2/nCoV-2019.scheme.bed'
The singularity image was built today.
Hi @iferres , @DarianHole - I've chased this error and this error to the way that the recently released artic v1.1.1
parses the V2 primer scheme, which is the one that this workflow uses by default. There is a fix incoming from the ARTIC project for this, hopefully within the next few days. I'll update here when this happens.
This, I can't reproduce, but am happy to investigate further when ARTIC patch fieldbioinformatics.
I think the last one is the same error. From the nextflow log I understand that the artic_plot_amplicon_depth
command is the one that is failing. I just called the command that failed from the singularity container directly.
Thanks a lot!
After playing around with it it also seems that specifying artic=1.1.0 in the conda config or installing that version of artic works too for the moment if you need to run data
Hi all - sorry about this issue. New patch version is up in conda (1.1.2) and should fix this
The artic nCov repo has now had the version bumped too.
Thanks again both of you, that fixes the issue!
Hi,
I feel like there is something wrong with my input data but I cannot seem to figure out what it is after searching and looking through the logs. Currently I keep getting the following:
Exit code is 20 and the exact command it is failing on it
artic minion --normalise 500 --minimap2 --threads 1 --scheme-directory scheme/primer_schemes --read-file output_prefix_barcode13.fastq --fast5-directory fast5_pass --sequencing-summary sequencing_summary_FAK48225_b6fcf7e3.txt nCoV-2019/V2 output_prefix_barcode13
My guess is I've done something wrong with the
guppy_barcoder
command so I'll look into it that wayThanks for any help or advice you can give me! Darian