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Process fastcat (1) terminated with an error exit status (1) #129

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CWYuan08 opened this issue Nov 12, 2024 · 1 comment
Open

Process fastcat (1) terminated with an error exit status (1) #129

CWYuan08 opened this issue Nov 12, 2024 · 1 comment
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@CWYuan08
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CWYuan08 commented Nov 12, 2024

Ask away!

Hi @SamStudio8 @sarahjeeeze @amblina @cjw85 @nrhorner
I am running nextflow run epi2me-labs/wf-transcriptomes -r v1.2.0
with --transcriptome_source reference-guided --cdna_kit SQK-PCS111 -profile singularity
This code worked before but now I have the issue below when running it for new data.
How could I fix this?
Thank you very much!!

executor > local (5)
[d4/5605be] process > fastcat (1) [100%] 1 of 1, failed: 1 ✘
[ce/cd2c9e] process > pipeline:preprocess_ref_ann... [100%] 1 of 1 ✔
[- ] process > pipeline:collectFastqIngres... -
[c7/900f62] process > pipeline:getVersions [100%] 1 of 1 ✔
[19/c58cf7] process > pipeline:getParams [100%] 1 of 1 ✔
[- ] process > pipeline:preprocess_reads -
[de/7854ba] process > pipeline:build_minimap_inde... [100%] 1 of 1 ✔
[- ] process > pipeline:reference_assembly... -
[- ] process > pipeline:split_bam -
[- ] process > pipeline:assemble_transcripts -
[- ] process > pipeline:merge_gff_bundles -
[- ] process > pipeline:run_gffcompare -
[- ] process > pipeline:get_transcriptome -
[- ] process > pipeline:makeReport -
[- ] process > output -
ERROR ~ Error executing process > 'fastcat (1)'

Caused by:
Process fastcat (1) terminated with an error exit status (1)

Command executed:

mkdir fastcat_stats
mkdir fastq_chunks

Save file as compressed fastq

fastcat -s AC_LA_rep2 -f fastcat_stats/per-file-stats.tsv -i fastcat_stats/per-file-runids.txt --histograms histograms -r >(bgzip -c > fastcat_stats/per-read-stats.tsv.gz) 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

awk 'NR==1{for (i=1; i<=NF; i++) {ix[$i] = i}} NR>1 {print $ix["run_id"]}' fastcat_stats/per-file-runids.txt | sort | uniq > fastcat_stats/run_ids

Command exit status:
1

Command output:
(empty)

Command error:
Processing input_src/PAK81470_pass_5b60d7af_01f1c15d_1912.fastq.gz
Processing input_src/PAK81470_pass_5b60d7af_01f1c15d_2589.fastq.gz
Processing input_src/PAK81470_pass_5b60d7af_01f1c15d_1733.fastq.gz
Processing input_src/PAK81470_pass_5b60d7af_01f1c15d_2711.fastq.gz
Processing input_src/PAK81470_pass_5b60d7af_01f1c15d_1160.fastq.gz
Processing input_src/PAK81470_pass_5b60d7af_01f1c15d_2386.fastq.gz
Processing input_src/PAK81470_pass_5b60d7af_01f1c15d_2933.fastq.gz
Processing input_src/PAK81470_pass_5b60d7af_01f1c15d_131.fastq.gz
Processing input_src/PAK81470_pass_5b60d7af_01f1c15d_454.fastq.gz
Processing input_src/PAK81470_pass_5b60d7af_01f1c15d_2627.fastq.gz
Processing input_src/PAK81470_pass_5b60d7af_01f1c15d_514.fastq.gz
Processing input_src/PAK81470_pass_5b60d7af_01f1c15d_750.fastq.gz
Processing input_src/PAK81470_pass_5b60d7af_01f1c15d_1585.fastq.gz
Processing input_src/PAK81470_pass_5b60d7af_01f1c15d_403.fastq.gz
Processing input_src/PAK81470_pass_5b60d7af_01f1c15d_3012.fastq.gz
Processing input_src/PAK81470_pass_5b60d7af_01f1c15d_239.fastq.gz
Processing input_src/PAK81470_pass_5b60d7af_01f1c15d_2435.fastq.gz
Processing input_src/PAK81470_pass_5b60d7af_01f1c15d_1877.fastq.gz
Processing input_src/PAK81470_pass_5b60d7af_01f1c15d_279.fastq.gz
Processing input_src/PAK81470_pass_5b60d7af_01f1c15d_2396.fastq.gz
Processing input_src/PAK81470_pass_5b60d7af_01f1c15d_1922.fastq.gz
Processing input_src/PAK81470_pass_5b60d7af_01f1c15d_1775.fastq.gz
Processing input_src/PAK81470_pass_5b60d7af_01f1c15d_3085.fastq.gz
Processing input_src/PAK81470_pass_5b60d7af_01f1c15d_1642.fastq.gz
Processing input_src/PAK81470_pass_5b60d7af_01f1c15d_2110.fastq.gz
Processing input_src/PAK81470_pass_5b60d7af_01f1c15d_2714.fastq.gz
Processing input_src/PAK81470_pass_5b60d7af_01f1c15d_2584.fastq.gz
Processing input_src/PAK81470_pass_5b60d7af_01f1c15d_869.fastq.gz
Processing input_src/PAK81470_pass_5b60d7af_01f1c15d_171.fastq.gz
Processing input_src/PAK81470_pass_5b60d7af_01f1c15d_2128.fastq.gz
Processing input_src/PAK81470_pass_5b60d7af_01f1c15d_1582.fastq.gz
Processing input_src/PAK81470_pass_5b60d7af_01f1c15d_887.fastq.gz
Processing input_src/PAK81470_pass_5b60d7af_01f1c15d_1071.fastq.gz
Processing input_src/PAK81470_pass_5b60d7af_01f1c15d_1685.fastq.gz
Processing input_src/PAK81470_pass_5b60d7af_01f1c15d_864.fastq.gz
Processing input_src/PAK81470_pass_5b60d7af_01f1c15d_2816.fastq.gz
Processing input_src/PAK81470_pass_5b60d7af_01f1c15d_865.fastq.gz
Processing input_src/PAK81470_pass_5b60d7af_01f1c15d_2155.fastq.gz
Processing input_src/PAK81470_pass_5b60d7af_01f1c15d_89.fastq.gz
Processing input_src/PAK81470_pass_5b60d7af_01f1c15d_2027.fastq.gz
Processing input_src/PAK81470_pass_5b60d7af_01f1c15d_1028.fastq.gz
Processing input_src/PAK81470_pass_5b60d7af_01f1c15d_2441.fastq.gz
Processing input_src/PAK81470_pass_5b60d7af_01f1c15d_1250.fastq.gz
Processing input_src/PAK81470_pass_5b60d7af_01f1c15d_1232.fastq.gz
Processing input_src/PAK81470_pass_5b60d7af_01f1c15d_1054.fastq.gz
Processing input_src/PAK81470_pass_5b60d7af_01f1c15d_2888.fastq.gz
Processing input_src/PAK81470_pass_5b60d7af_01f1c15d_2563.fastq.gz
Processing input_src/PAK81470_pass_5b60d7af_01f1c15d_1884.fastq.gz
Processing input_src/PAK81470_pass_5b60d7af_01f1c15d_1381.fastq.gz
Completed processing with errors. Outputs may be incomplete.

@CWYuan08 CWYuan08 added the question Further information is requested label Nov 12, 2024
@sarahjeeeze
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hi - could you share the nextflow.log file?

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