Hello! I'm trying to run the

fetchngs

pipeline but it's failing at

NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_PREFETCH

Would someone be able to help me? Here's the error:

ERROR ~ Error executing process > 'NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_PREFETCH (SRR12848126)'

Caused by:
 Missing output file(s) `SRR12848126` expected by process `NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_PREFETCH (SRR12848126)`


Command executed [/stg3/data1/eunice/.nextflow/assets/nf-core/fetchngs/./workflows/sra/../../subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/../../../modules/nf-core/sratools/prefetch/templates/retry_with_backoff.sh]:

 #!/usr/bin/env bash

 set -u

 retry_with_backoff() {
   local max_attempts=${1}
   local delay=${2}
   local max_time=${3}
   local attempt=1
   local output=
   local status=

   # Remove the first three arguments to this function in order to access
   # the 'real' command with `${@}`.
   shift 3

   while [ ${attempt} -le ${max_attempts} ]; do
     output=$("${@}")
     status=${?}

     if [ ${status} -eq 0 ]; then
       break
     fi

     if [ ${attempt} -lt ${max_attempts} ]; then
       echo "Failed attempt ${attempt} of ${max_attempts}. Retrying in ${delay} s." >&2
       sleep ${delay}
     elif [ ${attempt} -eq ${max_attempts} ]; then
       echo "Failed after ${attempt} attempts." >&2
       return ${status}
     fi

     attempt=$(( ${attempt} + 1 ))
     delay=$(( ${delay} * 2 ))
     if [ ${delay} -ge ${max_time} ]; then
       delay=${max_time}
     fi
   done

executor > slurm (44), local (11)
[55/56f319] process > NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO (SRR14709033)                              [100%] 10 of 10 :heavy_check_mark:
[8c/5da6a8] process > NFCORE_FETCHNGS:SRA:SRA_RUNINFO_TO_FTP (1)                                   [100%] 10 of 10 :heavy_check_mark:
[16/f5abb0] process > NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (SRX17709228_SRR21711855)                          [100%] 11 of 11 :heavy_check_mark:
[f4/45c1e6] process > NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:CUSTOM_SRATOOLSNCBISETTINGS (ncbi-settings) [100%] 1 of 1 :heavy_check_mark:
[68/dd56d6] process > NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_PREFETCH (SRR14593545)        [ 91%] 11 of 12, failed: 11, retries: 9
[-    ] process > NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_FASTERQDUMP            -
[-    ] process > NFCORE_FETCHNGS:SRA:ASPERA_CLI                                        -
[fc/294094] process > NFCORE_FETCHNGS:SRA:SRA_TO_SAMPLESHEET (SRX17709228_SRR21711855)                        [100%] 11 of 11
[-    ] process > NFCORE_FETCHNGS:SRA:MULTIQC_MAPPINGS_CONFIG                                 -
ERROR ~ Error executing process > 'NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_PREFETCH (SRR12848126)'

Caused by:
 Missing output file(s) `SRR12848126` expected by process `NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_PREFETCH (SRR12848126)`


Command executed [/stg3/data1/eunice/.nextflow/assets/nf-core/fetchngs/./workflows/sra/../../subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/../../../modules/nf-core/sratools/prefetch/templates/retry_with_backoff.sh]:

 #!/usr/bin/env bash

 set -u

 retry_with_backoff() {
   local max_attempts=${1}
   local delay=${2}
   local max_time=${3}
   local attempt=1
   local output=
   local status=

   # Remove the first three arguments to this function in order to access
   # the 'real' command with `${@}`.
   shift 3

   while [ ${attempt} -le ${max_attempts} ]; do
     output=$("${@}")
     status=${?}

     if [ ${status} -eq 0 ]; then
       break
     fi

     if [ ${attempt} -lt ${max_attempts} ]; then
       echo "Failed attempt ${attempt} of ${max_attempts}. Retrying in ${delay} s." >&2
       sleep ${delay}
     elif [ ${attempt} -eq ${max_attempts} ]; then
       echo "Failed after ${attempt} attempts." >&2
       return ${status}
     fi

     attempt=$(( ${attempt} + 1 ))
     delay=$(( ${delay} * 2 ))
     if [ ${delay} -ge ${max_time} ]; then
       delay=${max_time}
     fi
   done

   echo "${output}"
 }

 export NCBI_SETTINGS="$PWD/user-settings.mkfg"

 retry_with_backoff 5 1 100 \
   prefetch \
    \
   SRR12848126

 [ -f SRR12848126.sralite ] && vdb-validate SRR12848126.sralite || vdb-validate SRR12848126

 cat <<-END_VERSIONS > versions.yml
 "NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_PREFETCH":
   sratools: $(prefetch --version 2>&1 | grep -Eo '[0-9.]+')
 END_VERSIONS

Command exit status:
 0

Command output:
 (empty)

Command error:
 2024-06-13T16:30:54 prefetch.2.8.0 err: path not found while resolving tree within virtual file system module - 'SRR12848126' cannot be found.
 Failed attempt 1 of 5. Retrying in 1 s.
 2024-06-13T16:33:05 prefetch.2.8.0 err: path not found while resolving tree within virtual file system module - 'SRR12848126' cannot be found.
 Failed attempt 2 of 5. Retrying in 2 s.
 2024-06-13T16:35:16 prefetch.2.8.0 err: path not found while resolving tree within virtual file system module - 'SRR12848126' cannot be found.
 Failed attempt 3 of 5. Retrying in 4 s.
 2024-06-13T16:37:31 prefetch.2.8.0 err: path not found while resolving tree within virtual file system module - 'SRR12848126' cannot be found.
 Failed attempt 4 of 5. Retrying in 8 s.
 2024-06-13T16:39:51 prefetch.2.8.0 err: path not found while resolving tree within virtual file system module - 'SRR12848126' cannot be found.
 Failed after 5 attempts.
 2024-06-13T16:39:51 vdb-validate.2.8.0 info: 'SRR12848126' could not be found

Work dir:
 /new-stg/home/eunice_2/Entropy/01_spectral/DATA/BULK_pbmc_aging/work/78/0d91f1772463ba6cbec226b73fb494

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

 -- Check '.nextflow.log' file for details

ERROR ~ Failed to invoke `workflow.onComplete` event handler

 -- Check script '/stg3/data1/eunice/.nextflow/assets/nf-core/fetchngs/./subworkflows/local/utils_nfcore_fetchngs_pipeline/main.nf' at line: 122 or see '.nextflow.log' file for more details
WARN: Killing running tasks (1)

Hello, I don't know if you still need it. But have you checked if the file exist in the output folder? If not maybe something went wrong with the dowload and the pipeline can't find it, and in this case resuming it can be a good idea 🙂