Answers.Body: <p>Use the SRR accessions, not the sample-IDs you are using.</p>
  <p>With entrez e-utils, I found the SRR of GSM2683458:</p>
  <p><code>esearch -db sra -query GSM2683458 | efetch -format xml | xtract -pattern IDENTIFIERS -if PRIMARY_ID -contains SRR -element PRIMARY_ID</code> is <code>SRR5755657</code>.</p>
  <p>For GSM3603268, using <code>esearch -db sra -query GSM3603268 | efetch -format xml | xtract -pattern IDENTIFIERS -if PRIMARY_ID -contains SRR -element PRIMARY_ID</code>, the SRR is: <code>SRR8571942</code></p>
  <p>Then just do <code>fasterq-dump SRR5755657; fasterq-dump SRR8571942</code>.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-10-05T08:20:39.017Z
Answers.Text: well the pipeline is already made to use GSE id so i have no option but to use it
Answers.UserDisplayName: kcm
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-10-05T00:47:56.850Z
Answers.LastActivityDate: 2023-10-05T00:47:56.850Z
Answers.UserDisplayName: user3479780
Body: <p>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.</p>
  <p><strong>GSM ID</strong>
  GSM3603268
  GSM2683458</p>
  <p><strong>Output</strong>
  For GSM3603268</p>
  <pre><code>$ cat GSM3603268.test.fastq
  @GSM3603268.1 1 length=100
  TTTTTTAAAGAAAACTTGAGCTTTTGGAGCATGGCAACCTAGCCTGCAGACACCGTATCCCCTTGTCCACTTCCCCCTGCAAACCATAAGTCCATTCCTA
  +GSM3603268.1 1 length=100
  =@@DDDDA++2CDABCEG@GEHHEHGA9EDFHGHD3::B??&lt;DBFFBFB===)5;CA;(7=?;?CE;7)7;&gt;C((583;&lt;9&gt;(,89@@@@CCCCDD:BC:
  @GSM3603268.1 1 length=100
  AGTTCCACGAGTTTTCTTTTTTTTAAGTGGTAGGAATGGACTTATGGGTTGCAGGGGGAAGTGGACAAGGGGCTACGGTGTCTGCAGGCTTGGTTGCCAT
  +GSM3603268.1 1 length=100
  :?=BD:D?C)&lt;CDGH4+&lt;CCCGHI)??D&lt;D?00?D*?39C&lt;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
  </code></pre>
  <p>Output for GSM2683458</p>
  <pre><code>$ 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 'sra-tools@ncbi.nlm.nih.gov' for assistance.
  =============================================================
  
  fastq-dump quit with error code 3
  </code></pre>
  <p>The script</p>
  <pre class="lang-sh prettyprint-override"><code>#!/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=&quot;<span class="math-container">$1"
  local retries=5
  for attempt in $</span>(seq &quot;<span class="math-container">$retries"); do
      # Download start of fastq
      fastq-dump $</span>(get_ngc) -X 1 -Z --split-spot &quot;<span class="math-container">$id" &gt; "$</span>{id}.test.fastq&quot; 2&gt; &quot;<span class="math-container">${id}.test.log"
      numLines=$</span>(cat &quot;<span class="math-container">${id}.test.fastq" | wc -l)
      if [ $</span>numLines -gt 0 ]; then
              echo &quot;<span class="math-container">${id} has data... OK"
          return 0
      else
          echo "$</span>{id} does not have data on attempt <span class="math-container">$attempt... Retrying in 5 seconds..."
          sleep 5
      fi
  done
  echo "$</span>{id} could not be downloaded after $retries attempts... ERROR&quot;
      check=1
      return 1
  }
  
  # Loop through all parameters to check validity
  for file in &quot;<span class="math-container">$@"; do
  cp "$</span>{file}&quot; .
      # Extract filename for sampleID
      file_basename=<span class="math-container">$(basename "$</span>{file}&quot;)
      id=&quot;<span class="math-container">${file_basename%".id"}"
  # Start validation with retries
  echo "Checking $</span>{id}...&quot;
      download_with_retry &quot;$id&quot;
  done
  
  # Exit with error if some FastQs are not accessible
  if [ $check -gt 0 ]; then
      echo &quot;ERROR: One or more samples have inaccessible FastQs.. exiting&quot;
      exit 1
  fi
  </code></pre>
  <p>What exactly is going wrong in the case of the other ID? No matter how many retries I give, it fails.</p>
  <p>Any suggestion or help would be really appreciated.</p>
  <p>The error log:</p>
  <pre><code>$ cat ncbi_error_report.txt
  &lt;Report&gt;
   &lt;Run&gt;
    &lt;Date&gt;
     &lt;Start value=&quot;Tue Sep 26 2023 9:16:55 PM&quot;/&gt;
     &lt;End value=&quot;Tue Sep 26 2023 9:17:11 PM&quot;/&gt;
    &lt;/Date&gt;
    &lt;Home name=&quot;HOME&quot; value=&quot;/root&quot;/&gt;
    &lt;Cwd&gt;/tmp&lt;/Cwd&gt;
    &lt;CommandLine argc=&quot;6&quot;&gt;
     &lt;Arg index=&quot;0&quot; value=&quot;fastq-dump&quot;/&gt;
     &lt;Arg index=&quot;1&quot; value=&quot;-X&quot;/&gt;
     &lt;Arg index=&quot;2&quot; value=&quot;1&quot;/&gt;
     &lt;Arg index=&quot;3&quot; value=&quot;-Z&quot;/&gt;
     &lt;Arg index=&quot;4&quot; value=&quot;--split-spot&quot;/&gt;
     &lt;Arg index=&quot;5&quot; value=&quot;GSM2683458&quot;/&gt;
    &lt;/CommandLine&gt;
    &lt;Result rc=&quot;RC(rcVFS,rcMgr,rcOpening,rcDirectory,rcNotFound)&quot;/&gt;
    &lt;User admin=&quot;true&quot;/&gt;
   &lt;/Run&gt;
   &lt;Configuration&gt;
    &lt;Files count=&quot;2&quot;&gt;
     &lt;File name=&quot;/etc/ncbi/settings.kfg&quot;/&gt;
     &lt;File name=&quot;/root/.ncbi/user-settings.mkfg&quot;/&gt;
    &lt;/Files&gt;
    &lt;refseq state=&quot;not found&quot;/&gt;
    &lt;krypto state=&quot;pwfile: not found&quot;/&gt;
    &lt;sra&gt;
     &lt;quality_type&gt;raw_scores&lt;/quality_type&gt;
    &lt;/sra&gt;
    &lt;Config&gt;
    &lt;ConfigurationFiles&gt;
  /etc/ncbi/settings.kfg
  /root/.ncbi/user-settings.mkfg
      &lt;/ConfigurationFiles&gt;
      &lt;APPNAME&gt;&quot;fastq-dump&quot;&lt;/APPNAME&gt;
      &lt;APPPATH&gt;&quot;/tmp/&quot;&lt;/APPPATH&gt;
      &lt;BUILD&gt;&quot;RELEASE&quot;&lt;/BUILD&gt;
      &lt;HOME&gt;&quot;/root&quot;&lt;/HOME&gt;
      &lt;HOST&gt;&lt;/HOST&gt;
      &lt;LIBS&gt;
        &lt;GUID&gt;&quot;119c217a-7b81-47e8-91d6-56d19c8c9f15&quot;&lt;/GUID&gt;
        &lt;IMAGE_GUID&gt;&quot;119c217a-7b81-47e8-91d6-62229c64ee59&quot;&lt;/IMAGE_GUID&gt;
      &lt;/LIBS&gt;
      &lt;NCBI_HOME&gt;&quot;/root/.ncbi&quot;&lt;/NCBI_HOME&gt;
      &lt;NCBI_SETTINGS&gt;&quot;/root/.ncbi/user-settings.mkfg&quot;&lt;/NCBI_SETTINGS&gt;
      &lt;OS&gt;&quot;linux&quot;&lt;/OS&gt;
      &lt;PWD&gt;&quot;/tmp&quot;&lt;/PWD&gt;
      &lt;USER&gt;&lt;/USER&gt;
      &lt;VDB_CONFIG&gt;&lt;/VDB_CONFIG&gt;
      &lt;VDB_ROOT&gt;&lt;/VDB_ROOT&gt;
      &lt;kfg&gt;
        &lt;arch&gt;
          &lt;bits&gt;&quot;64&quot;&lt;/bits&gt;
          &lt;name&gt;&quot;56d19c8c9f15&quot;&lt;/name&gt;
        &lt;/arch&gt;
        &lt;dir&gt;&quot;/root/.ncbi&quot;&lt;/dir&gt;
        &lt;name&gt;&quot;user-settings.mkfg&quot;&lt;/name&gt;
      &lt;/kfg&gt;
      &lt;libs&gt;
        &lt;cloud&gt;
          &lt;report_instance_identity&gt;&quot;true&quot;&lt;/report_instance_identity&gt;
        &lt;/cloud&gt;
      &lt;/libs&gt;
      &lt;repository&gt;
        &lt;user&gt;
          &lt;ad&gt;
            &lt;public&gt;
              &lt;apps&gt;
                &lt;file&gt;
                  &lt;volumes&gt;
                    &lt;flat&gt;&lt;/flat&gt;
                    &lt;flatAd&gt;&quot;.&quot;&lt;/flatAd&gt;
                  &lt;/volumes&gt;
                &lt;/file&gt;
                &lt;refseq&gt;
                  &lt;volumes&gt;
                    &lt;refseqAd&gt;&quot;.&quot;&lt;/refseqAd&gt;
                  &lt;/volumes&gt;
                &lt;/refseq&gt;
                &lt;sra&gt;
                  &lt;volumes&gt;
                    &lt;sraAd&gt;&quot;.&quot;&lt;/sraAd&gt;
                  &lt;/volumes&gt;
                &lt;/sra&gt;
                &lt;sraPileup&gt;
                  &lt;volumes&gt;
                    &lt;ad&gt;&quot;.&quot;&lt;/ad&gt;
                  &lt;/volumes&gt;
                &lt;/sraPileup&gt;
                &lt;sraRealign&gt;
                  &lt;volumes&gt;
                    &lt;ad&gt;&quot;.&quot;&lt;/ad&gt;
                  &lt;/volumes&gt;
                &lt;/sraRealign&gt;
                &lt;wgs&gt;
                  &lt;volumes&gt;
                    &lt;wgsAd&gt;&quot;.&quot;&lt;/wgsAd&gt;
                  &lt;/volumes&gt;
                &lt;/wgs&gt;
              &lt;/apps&gt;
              &lt;root&gt;&quot;.&quot;&lt;/root&gt;
            &lt;/public&gt;
          &lt;/ad&gt;
        &lt;/user&gt;
      &lt;/repository&gt;
      &lt;sra&gt;
        &lt;quality_type&gt;&quot;raw_scores&quot;&lt;/quality_type&gt;
      &lt;/sra&gt;
      &lt;vdb&gt;
        &lt;lib&gt;
          &lt;paths&gt;
            &lt;kfg&gt;&quot;/usr/local/bin&quot;&lt;/kfg&gt;
          &lt;/paths&gt;
        &lt;/lib&gt;
      &lt;/vdb&gt;
    &lt;/Config&gt;
    &lt;RemoteAccess available=&quot;false&quot;/&gt;
    &lt;CurrentProtectedRepository found=&quot;false&quot;/&gt;
   &lt;/Configuration&gt;
   &lt;Object path=&quot;https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR5755657/SRR5755657&quot; type=&quot;database&quot; fs_type=&quot;unexpected&quot;&gt;
    &lt;Dependencies&gt;
     &lt;List count=&quot;22&quot; missing=&quot;22&quot;&gt;
      &lt;Dependency index=&quot;0&quot; seq_id=&quot;NC_000067.5&quot; local=&quot;false&quot; path=&quot;&quot;/&gt;
      &lt;Dependency index=&quot;1&quot; seq_id=&quot;NC_000068.6&quot; local=&quot;false&quot; path=&quot;&quot;/&gt;
      &lt;Dependency index=&quot;2&quot; seq_id=&quot;NC_000069.5&quot; local=&quot;false&quot; path=&quot;&quot;/&gt;
      &lt;Dependency index=&quot;3&quot; seq_id=&quot;NC_000070.5&quot; local=&quot;false&quot; path=&quot;&quot;/&gt;
      &lt;Dependency index=&quot;4&quot; seq_id=&quot;NC_000071.5&quot; local=&quot;false&quot; path=&quot;&quot;/&gt;
      &lt;Dependency index=&quot;5&quot; seq_id=&quot;NC_000072.5&quot; local=&quot;false&quot; path=&quot;&quot;/&gt;
      &lt;Dependency index=&quot;6&quot; seq_id=&quot;NC_000073.5&quot; local=&quot;false&quot; path=&quot;&quot;/&gt;
      &lt;Dependency index=&quot;7&quot; seq_id=&quot;NC_000074.5&quot; local=&quot;false&quot; path=&quot;&quot;/&gt;
      &lt;Dependency index=&quot;8&quot; seq_id=&quot;NC_000075.5&quot; local=&quot;false&quot; path=&quot;&quot;/&gt;
      &lt;Dependency index=&quot;9&quot; seq_id=&quot;NC_000076.5&quot; local=&quot;false&quot; path=&quot;&quot;/&gt;
      &lt;Dependency index=&quot;10&quot; seq_id=&quot;NC_000077.5&quot; local=&quot;false&quot; path=&quot;&quot;/&gt;
      &lt;Dependency index=&quot;11&quot; seq_id=&quot;NC_000078.5&quot; local=&quot;false&quot; path=&quot;&quot;/&gt;
      &lt;Dependency index=&quot;12&quot; seq_id=&quot;NC_000079.5&quot; local=&quot;false&quot; path=&quot;&quot;/&gt;
      &lt;Dependency index=&quot;13&quot; seq_id=&quot;NC_000080.5&quot; local=&quot;false&quot; path=&quot;&quot;/&gt;
      &lt;Dependency index=&quot;14&quot; seq_id=&quot;NC_000081.5&quot; local=&quot;false&quot; path=&quot;&quot;/&gt;
      &lt;Dependency index=&quot;15&quot; seq_id=&quot;NC_000082.5&quot; local=&quot;false&quot; path=&quot;&quot;/&gt;
      &lt;Dependency index=&quot;16&quot; seq_id=&quot;NC_000083.5&quot; local=&quot;false&quot; path=&quot;&quot;/&gt;
      &lt;Dependency index=&quot;17&quot; seq_id=&quot;NC_000084.5&quot; local=&quot;false&quot; path=&quot;&quot;/&gt;
      &lt;Dependency index=&quot;18&quot; seq_id=&quot;NC_000085.5&quot; local=&quot;false&quot; path=&quot;&quot;/&gt;
      &lt;Dependency index=&quot;19&quot; seq_id=&quot;NC_000086.6&quot; local=&quot;false&quot; path=&quot;&quot;/&gt;
      &lt;Dependency index=&quot;20&quot; seq_id=&quot;NC_000087.6&quot; local=&quot;false&quot; path=&quot;&quot;/&gt;
      &lt;Dependency index=&quot;21&quot; seq_id=&quot;NC_005089.1&quot; local=&quot;false&quot; path=&quot;&quot;/&gt;
     &lt;/List&gt;
    &lt;/Dependencies&gt;
   &lt;/Object&gt;
   &lt;SOFTWARE&gt;
    &lt;VDBLibrary vers=&quot;2.7.47&quot;/&gt;
    &lt;Build static=&quot;true&quot;&gt;
     &lt;Module name=&quot;&quot;/&gt;
    &lt;/Build&gt;
    &lt;Tool date=&quot;Nov 18 2022&quot; name=&quot;fastq-dump&quot; vers=&quot;3.0.1&quot;&gt;
     &lt;Binary path=&quot;/usr/local/bin/fastq-dump&quot; type=&quot;alias&quot; md5=&quot;c461c39bfa514aff3c4f7c0416ced617&quot;&gt;
      &lt;Alias resolved=&quot;fastq-dump.3&quot;&gt;
       &lt;Alias resolved=&quot;fastq-dump.3.0.1&quot;&gt;
        &lt;Alias resolved=&quot;sratools.3.0.1&quot;/&gt;
       &lt;/Alias&gt;
      &lt;/Alias&gt;
     &lt;/Binary&gt;
    &lt;/Tool&gt;
   &lt;/SOFTWARE&gt;
   &lt;Env&gt;
   &lt;/Env&gt;
  &lt;/Report&gt;
  </code></pre>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-09-27T08:05:12.093Z
Comments.Text: 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!
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-09-27T12:01:43.193Z
Comments.Text: 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
Comments.UserDisplayName: kcm
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-09-27T12:02:13.343Z
Comments.Text: 'and why are you running this as root!? Never run things as root unless it is absolutely necessary' im running it in a container
Comments.UserDisplayName: kcm
Tags: <fastq><sratoolkit><ncbi>
Title: Shell script to validate fastq issue
ThreadText: # Shell script to validate fastq issue
  
  (Asked by: username_0 on 2023-09-26)
  
  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 'sra-tools@ncbi.nlm.nih.gov' for assistance.
  =============================================================
  
  fastq-dump quit with error code 3
  
  ```
  
  The script
  
  ```sh
  #!/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>
  
  ```
  
  **Tags:** fastq, sratoolkit, ncbi
  
  > **Comments:**
  > **username_1**: 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!  
  > **username_0**: 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  
  > **username_0**: 'and why are you running this as root!? Never run things as root unless it is absolutely necessary' im running it in a container  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2023-10-05. Score: 2
  
  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`.
  
  > **Comments:**
  > **username_0**: well the pipeline is already made to use GSE id so i have no option but to use it  
  
  ---
  
  