Error executing process > 'fastcat (6)' #63
Comments
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This then happened when I tried to run the demo data again, which now looks a lot like the error I am getting with my own data! --fastq 'wf-clone-validation-demo/fastq' \
--primers 'wf-clone-validation-demo/primers.tsv' \
--sample_sheet 'wf-clone-validation-demo/sample_sheet.csv' \
-profile standard
N E X T F L O W ~ version 24.10.3
Launching `https://github.com/epi2me-labs/wf-clone-validation` [happy_mahavira] DSL2 - revision: 5b0d7357de [master]
|||||||||| _____ ____ ___ ____ __ __ _____ _ _
|||||||||| | ____| _ \_ _|___ \| \/ | ____| | | __ _| |__ ___
||||| | _| | |_) | | __) | |\/| | _| _____| |/ _` | '_ \/ __|
||||| | |___| __/| | / __/| | | | |__|_____| | (_| | |_) \__ \
|||||||||| |_____|_| |___|_____|_| |_|_____| |_|\__,_|_.__/|___/
|||||||||| wf-clone-validation v1.7.1-g5b0d735
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Core Nextflow options
revision : master
runName : happy_mahavira
containerEngine: docker
container : [withLabel:wfplasmid:ontresearch/wf-clone-validation:sha55e97540ca3ca4f06310269c2ebd3175e1e9352a, withLabel:canu:ontresearch/canu:shabbdea3813f6fb436ea0cbaa19958ad772db9154c, withLabel:medaka:ontresearch/medaka:sha447c70a639b8bcf17dc49b51e74dfcde6474837b, withLabel:wf_common:ontresearch/wf-common:shaabceef445fb63214073cbf5836fdd33c04be4ac7, withLabel:plannotate:ontresearch/plannotate:shaf7f37f751dd0bc529121b765fb63322502288a03]
launchDir : /Users/jameslloyd/Documents/Main_Work_JPBL/LL/BULLYWUG
workDir : /Users/jameslloyd/Documents/Main_Work_JPBL/LL/BULLYWUG/work
projectDir : /Users/jameslloyd/.nextflow/assets/epi2me-labs/wf-clone-validation
userName : jameslloyd
profile : standard
configFiles : /Users/jameslloyd/.nextflow/assets/epi2me-labs/wf-clone-validation/nextflow.config
Input Options
fastq : wf-clone-validation-demo/fastq
primers : wf-clone-validation-demo/primers.tsv
Sample Options
sample_sheet : wf-clone-validation-demo/sample_sheet.csv
!! Only displaying parameters that differ from the pipeline defaults !!
--------------------------------------------------------------------------------
If you use epi2me-labs/wf-clone-validation for your analysis please cite:
* The nf-core framework
https://doi.org/10.1038/s41587-020-0439-x
--------------------------------------------------------------------------------
This is epi2me-labs/wf-clone-validation v1.7.1-g5b0d735.
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Searching input for [.fastq, .fastq.gz, .fq, .fq.gz] files.
executor > local (5)
[c7/8342a7] validate_sample_sheet [100%] 1 of 1 ✔
[eb/495907] fastcat (4) [ 0%] 0 of 11
[- ] cutsite_qc -
[- ] pipeline:filterHostReads -
[- ] pipeline:checkIfEnoughReads -
[- ] pipeline:assembleCore -
[- ] pipeline:medakaPolishAssembly -
[- ] pipeline:reorientateFastqAndGetFasta -
[- ] pipeline:downsampledStats -
[- ] pipeline:findPrimers -
[7e/f3ead3] pipeline:medakaVersion [ 0%] 0 of 1
[- ] pipeline:flyeVersion -
[- ] pipeline:getVersions -
[22/b7564e] pipeline:getParams [100%] 1 of 1 ✔
[- ] pipeline:assembly_qc -
[- ] pipeline:inserts -
[- ] pipeline:insert_qc -
[- ] pipeline:align_assembly -
[- ] pipeline:assembly_comparison -
[- ] pipeline:runPlannotate -
[- ] pipeline:assemblyMafs -
[- ] pipeline:report -
[- ] publish -
WARN: Input directory 'barcode12' was found, but sample sheet 'wf-clone-validation-demo/sample_sheet.csv' has no such entry.
ERROR ~ Error executing process > 'fastcat (7)'
Caused by:
Process `fastcat (7)` terminated with an error exit status (1)
Command executed:
executor > local (5)
[c7/8342a7] validate_sample_sheet [100%] 1 of 1 ✔
[eb/86da80] fastcat (7) [ 9%] 1 of 11, failed: 1
[- ] cutsite_qc -
[- ] pipeline:filterHostReads -
[- ] pipeline:checkIfEnoughReads -
[- ] pipeline:assembleCore -
[- ] pipeline:medakaPolishAssembly -
[- ] pipeline:reorientateFastqAndGetFasta -
[- ] pipeline:downsampledStats -
[- ] pipeline:findPrimers -
[7e/f3ead3] pipeline:medakaVersion [ 0%] 0 of 1
[- ] pipeline:flyeVersion -
[- ] pipeline:getVersions -
[22/b7564e] pipeline:getParams [100%] 1 of 1 ✔
[- ] pipeline:assembly_qc -
[- ] pipeline:inserts -
[- ] pipeline:insert_qc -
[- ] pipeline:align_assembly -
[- ] pipeline:assembly_comparison -
[- ] pipeline:runPlannotate -
[- ] pipeline:assemblyMafs -
[- ] pipeline:report -
[- ] publish -
WARN: Input directory 'barcode12' was found, but sample sheet 'wf-clone-validation-demo/sample_sheet.csv' has no such entry.
ERROR ~ Error executing process > 'fastcat (7)'
Caused by:
Process `fastcat (7)` terminated with an error exit status (1)
Command executed:
executor > local (5)
[c7/8342a7] validate_sample_sheet [100%] 1 of 1 ✔
[eb/86da80] fastcat (7) [ 9%] 1 of 11, failed: 1
[- ] cutsite_qc -
[- ] pipeline:filterHostReads -
[- ] pipeline:checkIfEnoughReads -
[- ] pipeline:assembleCore -
[- ] pipeline:medakaPolishAssembly -
[- ] pipeline:reorientateFastqAndGetFasta -
[- ] pipeline:downsampledStats -
[- ] pipeline:findPrimers -
[7e/f3ead3] pipeline:medakaVersion [ 0%] 0 of 1
[- ] pipeline:flyeVersion -
[- ] pipeline:getVersions -
[22/b7564e] pipeline:getParams [100%] 1 of 1 ✔
[- ] pipeline:assembly_qc -
[- ] pipeline:inserts -
[- ] pipeline:insert_qc -
[- ] pipeline:align_assembly -
[- ] pipeline:assembly_comparison -
[- ] pipeline:runPlannotate -
[- ] pipeline:assemblyMafs -
[- ] pipeline:report -
[- ] publish -
WARN: Input directory 'barcode12' was found, but sample sheet 'wf-clone-validation-demo/sample_sheet.csv' has no such entry.
ERROR ~ Error executing process > 'fastcat (7)'
Caused by:
Process `fastcat (7)` terminated with an error exit status (1)
Command executed:
mkdir fastcat_stats
mkdir fastq_chunks
# Save file as compressed fastq
fastcat -s sample07 -f fastcat_stats/per-file-stats.tsv -i fastcat_stats/per-file-runids.tsv -l fastcat_stats/per-file-basecallers.tsv --histograms histograms input_src | if [ "0" = "0" ]; then
bgzip -@ 4 > fastq_chunks/seqs.fastq.gz
else
split -l null -d --additional-suffix=.fastq.gz --filter='bgzip -@ 4 > $FILE' - fastq_chunks/seqs_;
fi
mv histograms/* fastcat_stats
# get n_seqs from per-file stats - need to sum them up
awk 'NR==1{for (i=1; i<=NF; i++) {ix[$i] = i}} NR>1 {c+=$ix["n_seqs"]} END{print c}' fastcat_stats/per-file-stats.tsv > fastcat_stats/n_seqs
# get unique run IDs (we add `-F '\t'` as `awk` uses any stretch of whitespace
# as field delimiter per default and thus ignores empty columns)
awk -F '\t' '
NR==1 {for (i=1; i<=NF; i++) {ix[$i] = i}}
# only print run_id if present
NR>1 && $ix["run_id"] != "" {print $ix["run_id"]}
' fastcat_stats/per-file-runids.tsv | sort | uniq > fastcat_stats/run_ids
# get unique basecall models
awk -F '\t' '
NR==1 {for (i=1; i<=NF; i++) {ix[$i] = i}}
# only print basecall model if present
NR>1 && $ix["basecaller"] != "" {print $ix["basecaller"]}
' fastcat_stats/per-file-basecallers.tsv | sort | uniq > fastcat_stats/basecallers
Command exit status:
1
Command output:
(empty)
Command error:
Error reading file 'input_src', possibly truncated
Completed processing with errors. Outputs may be incomplete.
Work dir:
/Users/jameslloyd/Documents/Main_Work_JPBL/LL/BULLYWUG/work/eb/86da80c815366d946fc8c0819f3fff
Container:
ontresearch/wf-common:shaabceef445fb63214073cbf5836fdd33c04be4ac7
Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`
-- Check '.nextflow.log' file for details
WARN: Killing running tasks (2) |
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Can you still run hello-world? eg. |
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Thanks for getting back to me When I run N E X T F L O W ~ version 24.10.3
Pulling nextflow-io/hello ...
downloaded from https://github.com/nextflow-io/hello.git
Launching `https://github.com/nextflow-io/hello` [clever_heyrovsky] DSL2 - revision: afff16a9b4 [master]
executor > local (4)
[75/0155c8] sayHello (1) [100%] 4 of 4 ✔
Hola world!
Hello world!
Ciao world!
Bonjour world!I have not run this before, but it looks ok to me. As for where the data is, I have one storage disk in my MacBook and it is the same as where EPI2ME is installed and where the data was when I ran it successfully at the start of the week. I have included the commands and output from nextflow for them for you to compare to the failed runs above (and how they are almost identical). I also tried running it from the GUI (EPI2ME desktop) and I had an issue as well, so I have attached the issue export to this. Please let me know if you have any other thoughts or suggestions. I do not think that the issue is related not EPI2ME not being able to find the input files as I could manually find and select the fastq in the GUI without issue. |
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What I did was to nuke everything (nextflow, docker, the downloaded EPI2ME code), and then I re-installed everything (nextflow, epi2me and docker) and it is now running beautifully again on demo and real data. Such an odd bug but at least it is behaving again. |
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Operating System
macOS
Other Linux
Sequoia 15.2
Workflow Version
version 24.10.3
Workflow Execution
Command line (Local)
Other workflow execution
version 24.10.3
EPI2ME Version
wf-clone-validation v1.7.1-g5b0d735
CLI command run
nextflow run epi2me-labs/wf-clone-validation
--fastq /Users/jameslloyd/Documents/Main_Work_JPBL/LL/BULLYWUG/2024-12-19_James_plasmids/fastq_pass_cat/BigTest01
--sample_sheet /Users/jameslloyd/Documents/Main_Work_JPBL/LL/BULLYWUG/2024-12-19_James_plasmids/fastq_pass_cat/BigTest01/sample_sheet_BigTest01.csv
--out_dir /Users/jameslloyd/Documents/Main_Work_JPBL/LL/BULLYWUG/2024-12-19_James_plasmids/fastq_pass_cat/BigTest05_debugging_output
Workflow Execution - CLI Execution Profile
standard (default)
What happened?
Yesterday I was running commands without issue. Today I attempted to re-run the same commands and kept getting errors on every run. See output of my runs below and the trace file.
I have uninstalled and reinstalled Docker Desktop but that did not solve the issue. I have considered doing the same for Nextflow but I have not tried that yet. Please advise.
`nextflow info
Version: 24.10.3 build 5933
Created: 16-12-2024 15:34 UTC (23:34 AWDT)
System: Mac OS X 15.2
Runtime: Groovy 4.0.23 on OpenJDK 64-Bit Server VM 17.0.10+7
Encoding: UTF-8 (UTF-8)
`
trace.txt
Relevant log output
Application activity log entry
Were you able to successfully run the latest version of the workflow with the demo data?
other (please describe below)
Other demo data information
The text was updated successfully, but these errors were encountered: