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Issue with RNA-seq data processing(Step-2) #17

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sim3023 opened this issue Feb 29, 2024 · 0 comments
Open

Issue with RNA-seq data processing(Step-2) #17

sim3023 opened this issue Feb 29, 2024 · 0 comments

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@sim3023
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sim3023 commented Feb 29, 2024

I am facing an error during the 2nd step of the pipeline. I suppose the error is related to prefetch and fasterq-dump while fetching data from SRA. Also, I would like to mention that I am using version 22.10.8 of nextflow for running the pipeline as I face errors with the latest version of the same.
It would be great if someone could help with the following error.

sudo ./nextflow run main.nf -profile local --organism mycobacterium_abscessus --metadata mab.tsv --sequence_dir sequence_dir/ --outdir results
N E X T F L O W ~ version 22.10.8
Launching main.nf [reverent_bartik] DSL1 - revision: ef90b5fca3
executor > local (13)
[27/ad4b19] process > bowtie_build [100%] 1 of 1 ✔
[8d/7bec19] process > gff2bed [100%] 1 of 1 ✔
[56/467f86] process > download_fastq (14) [ 1%] 5 of 306, failed: 5, retries: 5
[- ] process > stage_fastq_single -
executor > local (13)
[27/ad4b19] process > bowtie_build [100%] 1 of 1 ✔
[8d/7bec19] process > gff2bed [100%] 1 of 1 ✔
[56/467f86] process > download_fastq (14) [ 1%] 5 of 306, failed: 5, retries: 5
[- ] process > stage_fastq_single -
executor > local (14)
[27/ad4b19] process > bowtie_build [100%] 1 of 1 ✔
[8d/7bec19] process > gff2bed [100%] 1 of 1 ✔
[41/5bd9cd] process > download_fastq (20) [ 1%] 6 of 307, failed: 6, retries: 6
[- ] process > stage_fastq_single -

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