3
$\begingroup$

I have two GSM ID as test case where both of them are having data when I checked through sra explorer tool but when I try to fetch through a script only one of them returns output where the other one fails.

GSM ID GSM3603268 GSM2683458

Output For GSM3603268

$ cat GSM3603268.test.fastq
@GSM3603268.1 1 length=100
TTTTTTAAAGAAAACTTGAGCTTTTGGAGCATGGCAACCTAGCCTGCAGACACCGTATCCCCTTGTCCACTTCCCCCTGCAAACCATAAGTCCATTCCTA
+GSM3603268.1 1 length=100
=@@DDDDA++2CDABCEG@GEHHEHGA9EDFHGHD3::B??<DBFFBFB===)5;CA;(7=?;?CE;7)7;>C((583;<9>(,89@@@@CCCCDD:BC:
@GSM3603268.1 1 length=100
AGTTCCACGAGTTTTCTTTTTTTTAAGTGGTAGGAATGGACTTATGGGTTGCAGGGGGAAGTGGACAAGGGGCTACGGTGTCTGCAGGCTTGGTTGCCAT
+GSM3603268.1 1 length=100
:?=BD:D?C)<CDGH4+<CCCGHI)??D<D?00?D*?39C<CG4BFE28;4(.7AB############################################

$ cat GSM3603268.test.log
2023-09-26T21:18:46 fastq-dump.3.0.1 int: string unexpected while executing query within virtual file system module - multiple response SRR URLs for the same service 's3'
2023-09-26T21:18:46 fastq-dump.3.0.1 int: string unexpected while executing query within virtual file system module - multiple response SRR URLs for the same service 's3'
2023-09-26T21:18:46 fastq-dump.3.0.1 int: string unexpected while executing query within virtual file system module - multiple response SRR URLs for the same service 's3'
Read 1 spots for GSM3603268
Written 1 spots for GSM3603268

Output for GSM2683458

$ cat GSM2683458.test.fastq
    bash-5.1#

$ cat GSM2683458.test.log
2023-09-26T21:16:55 fastq-dump.3.0.1 int: string unexpected while executing query within virtual file system module - multiple response SRR URLs for the same service 's3'
2023-09-26T21:16:55 fastq-dump.3.0.1 int: string unexpected while executing query within virtual file system module - multiple response SRR URLs for the same service 's3'
2023-09-26T21:16:55 fastq-dump.3.0.1 int: string unexpected while executing query within virtual file system module - multiple response SRR URLs for the same service 's3'
2023-09-26T21:17:11 fastq-dump.3.0.1 warn: directory not found while opening manager within virtual file system module - can't open NC_000076.5 as a RefSeq or as a WGS
2023-09-26T21:17:11 fastq-dump.3.0.1 err: directory not found while opening manager within virtual file system module - failed GSM2683458

=============================================================
An error occurred during processing.
A report was generated into the file '/root/ncbi_error_report.txt'.
If the problem persists, you may consider sending the file
to '[email protected]' for assistance.
=============================================================

fastq-dump quit with error code 3

The script

#!/bin/sh

set -x
PS4='[\\d \\t] '

# Check parameter for error
check=0
# Print fastq-dump executable path
echo $(which fastq-dump)

# Function to download FastQ with retries
download_with_retry() {
    local id="$1"
local retries=5
for attempt in $(seq "$retries"); do
    # Download start of fastq
    fastq-dump $(get_ngc) -X 1 -Z --split-spot "$id" > "${id}.test.fastq" 2> "${id}.test.log"
    numLines=$(cat "${id}.test.fastq" | wc -l)
    if [ $numLines -gt 0 ]; then
            echo "${id} has data... OK"
        return 0
    else
        echo "${id} does not have data on attempt $attempt... Retrying in 5 seconds..."
        sleep 5
    fi
done
echo "${id} could not be downloaded after $retries attempts... ERROR"
    check=1
    return 1
}

# Loop through all parameters to check validity
for file in "$@"; do
cp "${file}" .
    # Extract filename for sampleID
    file_basename=$(basename "${file}")
    id="${file_basename%".id"}"
# Start validation with retries
echo "Checking ${id}..."
    download_with_retry "$id"
done

# Exit with error if some FastQs are not accessible
if [ $check -gt 0 ]; then
    echo "ERROR: One or more samples have inaccessible FastQs.. exiting"
    exit 1
fi

What exactly is going wrong in the case of the other ID? No matter how many retries I give, it fails.

Any suggestion or help would be really appreciated.

The error log:

$ cat ncbi_error_report.txt
<Report>
 <Run>
  <Date>
   <Start value="Tue Sep 26 2023 9:16:55 PM"/>
   <End value="Tue Sep 26 2023 9:17:11 PM"/>
  </Date>
  <Home name="HOME" value="/root"/>
  <Cwd>/tmp</Cwd>
  <CommandLine argc="6">
   <Arg index="0" value="fastq-dump"/>
   <Arg index="1" value="-X"/>
   <Arg index="2" value="1"/>
   <Arg index="3" value="-Z"/>
   <Arg index="4" value="--split-spot"/>
   <Arg index="5" value="GSM2683458"/>
  </CommandLine>
  <Result rc="RC(rcVFS,rcMgr,rcOpening,rcDirectory,rcNotFound)"/>
  <User admin="true"/>
 </Run>
 <Configuration>
  <Files count="2">
   <File name="/etc/ncbi/settings.kfg"/>
   <File name="/root/.ncbi/user-settings.mkfg"/>
  </Files>
  <refseq state="not found"/>
  <krypto state="pwfile: not found"/>
  <sra>
   <quality_type>raw_scores</quality_type>
  </sra>
  <Config>
  <ConfigurationFiles>
/etc/ncbi/settings.kfg
/root/.ncbi/user-settings.mkfg
    </ConfigurationFiles>
    <APPNAME>"fastq-dump"</APPNAME>
    <APPPATH>"/tmp/"</APPPATH>
    <BUILD>"RELEASE"</BUILD>
    <HOME>"/root"</HOME>
    <HOST></HOST>
    <LIBS>
      <GUID>"119c217a-7b81-47e8-91d6-56d19c8c9f15"</GUID>
      <IMAGE_GUID>"119c217a-7b81-47e8-91d6-62229c64ee59"</IMAGE_GUID>
    </LIBS>
    <NCBI_HOME>"/root/.ncbi"</NCBI_HOME>
    <NCBI_SETTINGS>"/root/.ncbi/user-settings.mkfg"</NCBI_SETTINGS>
    <OS>"linux"</OS>
    <PWD>"/tmp"</PWD>
    <USER></USER>
    <VDB_CONFIG></VDB_CONFIG>
    <VDB_ROOT></VDB_ROOT>
    <kfg>
      <arch>
        <bits>"64"</bits>
        <name>"56d19c8c9f15"</name>
      </arch>
      <dir>"/root/.ncbi"</dir>
      <name>"user-settings.mkfg"</name>
    </kfg>
    <libs>
      <cloud>
        <report_instance_identity>"true"</report_instance_identity>
      </cloud>
    </libs>
    <repository>
      <user>
        <ad>
          <public>
            <apps>
              <file>
                <volumes>
                  <flat></flat>
                  <flatAd>"."</flatAd>
                </volumes>
              </file>
              <refseq>
                <volumes>
                  <refseqAd>"."</refseqAd>
                </volumes>
              </refseq>
              <sra>
                <volumes>
                  <sraAd>"."</sraAd>
                </volumes>
              </sra>
              <sraPileup>
                <volumes>
                  <ad>"."</ad>
                </volumes>
              </sraPileup>
              <sraRealign>
                <volumes>
                  <ad>"."</ad>
                </volumes>
              </sraRealign>
              <wgs>
                <volumes>
                  <wgsAd>"."</wgsAd>
                </volumes>
              </wgs>
            </apps>
            <root>"."</root>
          </public>
        </ad>
      </user>
    </repository>
    <sra>
      <quality_type>"raw_scores"</quality_type>
    </sra>
    <vdb>
      <lib>
        <paths>
          <kfg>"/usr/local/bin"</kfg>
        </paths>
      </lib>
    </vdb>
  </Config>
  <RemoteAccess available="false"/>
  <CurrentProtectedRepository found="false"/>
 </Configuration>
 <Object path="https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR5755657/SRR5755657" type="database" fs_type="unexpected">
  <Dependencies>
   <List count="22" missing="22">
    <Dependency index="0" seq_id="NC_000067.5" local="false" path=""/>
    <Dependency index="1" seq_id="NC_000068.6" local="false" path=""/>
    <Dependency index="2" seq_id="NC_000069.5" local="false" path=""/>
    <Dependency index="3" seq_id="NC_000070.5" local="false" path=""/>
    <Dependency index="4" seq_id="NC_000071.5" local="false" path=""/>
    <Dependency index="5" seq_id="NC_000072.5" local="false" path=""/>
    <Dependency index="6" seq_id="NC_000073.5" local="false" path=""/>
    <Dependency index="7" seq_id="NC_000074.5" local="false" path=""/>
    <Dependency index="8" seq_id="NC_000075.5" local="false" path=""/>
    <Dependency index="9" seq_id="NC_000076.5" local="false" path=""/>
    <Dependency index="10" seq_id="NC_000077.5" local="false" path=""/>
    <Dependency index="11" seq_id="NC_000078.5" local="false" path=""/>
    <Dependency index="12" seq_id="NC_000079.5" local="false" path=""/>
    <Dependency index="13" seq_id="NC_000080.5" local="false" path=""/>
    <Dependency index="14" seq_id="NC_000081.5" local="false" path=""/>
    <Dependency index="15" seq_id="NC_000082.5" local="false" path=""/>
    <Dependency index="16" seq_id="NC_000083.5" local="false" path=""/>
    <Dependency index="17" seq_id="NC_000084.5" local="false" path=""/>
    <Dependency index="18" seq_id="NC_000085.5" local="false" path=""/>
    <Dependency index="19" seq_id="NC_000086.6" local="false" path=""/>
    <Dependency index="20" seq_id="NC_000087.6" local="false" path=""/>
    <Dependency index="21" seq_id="NC_005089.1" local="false" path=""/>
   </List>
  </Dependencies>
 </Object>
 <SOFTWARE>
  <VDBLibrary vers="2.7.47"/>
  <Build static="true">
   <Module name=""/>
  </Build>
  <Tool date="Nov 18 2022" name="fastq-dump" vers="3.0.1">
   <Binary path="/usr/local/bin/fastq-dump" type="alias" md5="c461c39bfa514aff3c4f7c0416ced617">
    <Alias resolved="fastq-dump.3">
     <Alias resolved="fastq-dump.3.0.1">
      <Alias resolved="sratools.3.0.1"/>
     </Alias>
    </Alias>
   </Binary>
  </Tool>
 </SOFTWARE>
 <Env>
 </Env>
</Report>
$\endgroup$
3
  • $\begingroup$ How are you running the script? What arguments are you giving it? What is get_ngc? What are the files you are copying (cp "${file}" .), what do they contain? And why are you running this as root!? Never run things as root unless it is absolutely necessary. Any minor error or bug could result in destroying your system if you run the wrong command as root! $\endgroup$
    – terdon
    Sep 27 at 8:05
  • $\begingroup$ to test it locally I i first start the container and then I copy the script inside the container and run using a single GSM id as input here the issue is for this particular series of GSM id none of them works $\endgroup$
    – kcm
    Sep 27 at 12:01
  • $\begingroup$ 'and why are you running this as root!? Never run things as root unless it is absolutely necessary' im running it in a container $\endgroup$
    – kcm
    Sep 27 at 12:02

1 Answer 1

2
$\begingroup$

Use the SRR accessions, not the sample-IDs you are using.

With entrez e-utils, I found the SRR of GSM2683458:

esearch -db sra -query GSM2683458 | efetch -format xml | xtract -pattern IDENTIFIERS -if PRIMARY_ID -contains SRR -element PRIMARY_ID is SRR5755657.

For GSM3603268, using esearch -db sra -query GSM3603268 | efetch -format xml | xtract -pattern IDENTIFIERS -if PRIMARY_ID -contains SRR -element PRIMARY_ID, the SRR is: SRR8571942

Then just do fasterq-dump SRR5755657; fasterq-dump SRR8571942.

$\endgroup$
1
  • $\begingroup$ well the pipeline is already made to use GSE id so i have no option but to use it $\endgroup$
    – kcm
    Oct 5 at 8:20

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