Answers.Body: <p>So, we figured it out. If you delete everything until the <code>[Data]</code> tag in the sample sheet, leaving the <code>[Data]</code> tag, it starts working. Here is the full <code>sample_sheet.csv</code> that is working:</p>
  
  <pre><code>[Data]
  Lane,Sample_ID,Sample_Name,index,Sample_Project
  1,SI-GA-B4_1,17R,ACTTCATA,Chromium_20180409
  1,SI-GA-B4_2,17R,GAGATGAC,Chromium_20180409
  1,SI-GA-B4_3,17R,TGCCGTGG,Chromium_20180409
  1,SI-GA-B4_4,17R,CTAGACCT,Chromium_20180409
  1,SI-GA-B5_1,19RL,AATAATGG,Chromium_20180409
  1,SI-GA-B5_2,19RL,CCAGGGCA,Chromium_20180409
  1,SI-GA-B5_3,19RL,TGCCTCAT,Chromium_20180409
  1,SI-GA-B5_4,19RL,GTGTCATC,Chromium_20180409
  2,SI-GA-B4_1,17R,ACTTCATA,Chromium_20180409
  2,SI-GA-B4_2,17R,GAGATGAC,Chromium_20180409
  2,SI-GA-B4_3,17R,TGCCGTGG,Chromium_20180409
  2,SI-GA-B4_4,17R,CTAGACCT,Chromium_20180409
  2,SI-GA-B5_1,19RL,AATAATGG,Chromium_20180409
  2,SI-GA-B5_2,19RL,CCAGGGCA,Chromium_20180409
  2,SI-GA-B5_3,19RL,TGCCTCAT,Chromium_20180409
  2,SI-GA-B5_4,19RL,GTGTCATC,Chromium_20180409
  3,SI-GA-B4_1,17R,ACTTCATA,Chromium_20180409
  3,SI-GA-B4_2,17R,GAGATGAC,Chromium_20180409
  3,SI-GA-B4_3,17R,TGCCGTGG,Chromium_20180409
  3,SI-GA-B4_4,17R,CTAGACCT,Chromium_20180409
  3,SI-GA-B5_1,19RL,AATAATGG,Chromium_20180409
  3,SI-GA-B5_2,19RL,CCAGGGCA,Chromium_20180409
  3,SI-GA-B5_3,19RL,TGCCTCAT,Chromium_20180409
  3,SI-GA-B5_4,19RL,GTGTCATC,Chromium_20180409
  4,SI-GA-B4_1,17R,ACTTCATA,Chromium_20180409
  4,SI-GA-B4_2,17R,GAGATGAC,Chromium_20180409
  4,SI-GA-B4_3,17R,TGCCGTGG,Chromium_20180409
  4,SI-GA-B4_4,17R,CTAGACCT,Chromium_20180409
  4,SI-GA-B5_1,19RL,AATAATGG,Chromium_20180409
  4,SI-GA-B5_2,19RL,CCAGGGCA,Chromium_20180409
  4,SI-GA-B5_3,19RL,TGCCTCAT,Chromium_20180409
  4,SI-GA-B5_4,19RL,GTGTCATC,Chromium_20180409
  </code></pre>
  
  <p>It is very unfortunate and disappointing that <code>10X</code> website is generating wrong sample sheet. Still we got very low mapping rates and trying to figure out what went wrong.</p>
  
  <blockquote>
    <p>Update</p>
  </blockquote>
  
  <p>I was supplying <code>--sample-sheet=</code> property, but it should be <code>--samplesheet=</code>. Now it is running fine (except for very low mapping rates) with all the headers on.</p>
  
  <blockquote>
    <p>Update</p>
  </blockquote>
  
  <p>It turned out that we were given the wrong indexes, so we made a sample sheet using sample sheet generator again and even with <code>--samplesheet=</code> correct parameter it was not running. Convertion of <code>CLRF</code> with <code>perl</code> or <code>tr</code> did not help. However, concise format of the sample sheet worked out well which looks like the following:</p>
  
  <pre><code>Lane,Sample,Index
  1-4,17R,SI-GA-B8
  1-4,19RL,SI-GA-B9
  </code></pre>
  
  <p>It needs to be supplied with <code>--csv=</code> parameter.</p>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2018-04-11T20:55:49.967Z
Answers.Text: I found that if you copy and paste the 10X sheet directly from their website it inserts some odd characters on some of the blank lines.  I usually edit the file in vim and delete them.
Answers.UserDisplayName: GWW
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2018-04-12T06:37:28.967Z
Answers.Text: Related to @GWW, I suspect it was the ` ^M` lines (the ones with a space and then line end). Either way, I suggest that you email 10x support and report this issue. It should be easy for them to fix.
Answers.UserDisplayName: Devon Ryan
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2018-04-12T17:08:12.637Z
Answers.Text: It looks like it's a weird unicode character "U+00A0" / NO-BREAK SPACE.
Answers.UserDisplayName: GWW
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2018-04-13T00:33:49.790Z
Answers.Text: That's weird. I copied and pasted from their website and never had issues. But I also run `mac2unix`/`dos2unix` on every sample sheet, so maybe that is a sufficient fix.
Answers.UserDisplayName: burger
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2018-04-11T20:38:44.463Z
Answers.LastActivityDate: 2018-04-18T21:41:18.510Z
Answers.LastEditDate: 2018-04-18T21:41:18.510Z
Answers.UserDisplayName: Nikita Vlasenko
Answers.Body: <p>Apart from supporting only Windows-style and Linux-style line endings and a restricted character set as mentioned above, the sample sheet <a href="https://www.illumina.com/content/dam/illumina-marketing/documents/products/technotes/sequencing-sheet-format-specifications-technical-note-970-2017-004.pdf" rel="nofollow noreferrer">has to be in the correct encoding which is UTF-8</a> (or its subset US-ASCII).
  Many command lines support these <a href="https://stackoverflow.com/questions/805418/how-to-find-encoding-of-a-file-via-script-on-linux">lookup</a> and <a href="https://stackoverflow.com/questions/64860/best-way-to-convert-text-files-between-character-sets">conversion</a> commands:</p>
  <pre class="lang-bash prettyprint-override"><code># lookup
  file -i my_sample_sheet.csv
  
  # conversion
  iconv -f ISO-8859-15 -t UTF-8 in.csv &gt; out.csv
  </code></pre>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-08-26T21:45:26.303Z
Answers.LastActivityDate: 2020-08-26T21:45:26.303Z
Answers.UserDisplayName: Tapper
Body: <p>Also posted <a href="https://www.biostars.org/p/308123/" rel="nofollow noreferrer">on biostars</a>.</p>
  
  <p>I am trying to use <code>cellranger</code> or <code>bcl2fastq</code> to convert the <code>.bcl</code> files that I got from single cell analysis run into <code>fastq</code> files for further analysis. I needed to generate <code>sample_sheet.csv</code> and so I used the following tool:</p>
  
  <p><a href="https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/bcl2fastq-direct" rel="nofollow noreferrer">https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/bcl2fastq-direct</a></p>
  
  <p>which I copy-pasted into a text file using <code>vim</code>. <code>sample_sheet.csv</code> looks like that:</p>
  
  <pre><code>[Header]
  EMFileVersion,4
  
  
  [Reads]
  26
  8
  98
  
  [Data]
  Lane,Sample_ID,Sample_Name,index,Sample_Project
  1,SI-GA-B4_1,17R,ACTTCATA,Chromium_20180406
  1,SI-GA-B4_2,17R,GAGATGAC,Chromium_20180406
  1,SI-GA-B4_3,17R,TGCCGTGG,Chromium_20180406
  1,SI-GA-B4_4,17R,CTAGACCT,Chromium_20180406
  1,SI-GA-B5_1,19RL,AATAATGG,Chromium_20180406 
  1,SI-GA-B5_2,19RL,CCAGGGCA,Chromium_20180406
  1,SI-GA-B5_3,19RL,TGCCTCAT,Chromium_20180406
  1,SI-GA-B5_4,19RL,GTGTCATC,Chromium_20180406
  2,SI-GA-B4_1,17R,ACTTCATA,Chromium_20180406
  2,SI-GA-B4_2,17R,GAGATGAC,Chromium_20180406
  2,SI-GA-B4_3,17R,TGCCGTGG,Chromium_20180406
  2,SI-GA-B4_4,17R,CTAGACCT,Chromium_20180406
  2,SI-GA-B5_1,19RL,AATAATGG,Chromium_20180406
  2,SI-GA-B5_2,19RL,CCAGGGCA,Chromium_20180406
  2,SI-GA-B5_3,19RL,TGCCTCAT,Chromium_20180406
  2,SI-GA-B5_4,19RL,GTGTCATC,Chromium_20180406
  3,SI-GA-B4_1,17R,ACTTCATA,Chromium_20180406
  3,SI-GA-B4_2,17R,GAGATGAC,Chromium_20180406
  3,SI-GA-B4_3,17R,TGCCGTGG,Chromium_20180406
  3,SI-GA-B4_4,17R,CTAGACCT,Chromium_20180406
  3,SI-GA-B5_1,19RL,AATAATGG,Chromium_20180406
  3,SI-GA-B5_2,19RL,CCAGGGCA,Chromium_20180406
  3,SI-GA-B5_3,19RL,TGCCTCAT,Chromium_20180406
  3,SI-GA-B5_4,19RL,GTGTCATC,Chromium_20180406
  4,SI-GA-B4_1,17R,ACTTCATA,Chromium_20180406
  4,SI-GA-B4_2,17R,GAGATGAC,Chromium_20180406
  4,SI-GA-B4_3,17R,TGCCGTGG,Chromium_20180406
  4,SI-GA-B4_4,17R,CTAGACCT,Chromium_20180406
  4,SI-GA-B5_1,19RL,AATAATGG,Chromium_20180406
  4,SI-GA-B5_2,19RL,CCAGGGCA,Chromium_20180406
  4,SI-GA-B5_3,19RL,TGCCTCAT,Chromium_20180406
  </code></pre>
  
  <p>Then I ran <code>cellranger</code> using <code>bash</code> script:</p>
  
  <pre><code>#!/bin/bash
  
   FLOWCELL_DIR="/scratch/nv4e/kipnis/180403_NB501830_0158_AHN3LLBGX5"
   OUTPUT_DIR="/scratch/nv4e/kipnis/fastq"
   SAMPLE_SHEET_PATH="/scratch/nv4e/kipnis/sample_sheet_2.csv"
  
  cellranger mkfastq --id="AHN3LLBGX5" --run=${FLOWCELL_DIR} --csv=${SAMPLE_SHEET_PATH} --output-dir=${OUTPUT_DIR}
  </code></pre>
  
  <p>It fails with the following output:</p>
  
  <p><a href="https://i.sstatic.net/coXGs.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/coXGs.png" alt="enter image description here"></a></p>
  
  <p><code>_stderr</code> file shows:</p>
  
  <p><a href="https://i.sstatic.net/ECDVI.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/ECDVI.png" alt="enter image description here"></a></p>
  
  <p>and that my <code>sample_sheet.csv</code> can not be parsed:</p>
  
  <p><a href="https://i.sstatic.net/NVNW6.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/NVNW6.png" alt="enter image description here"></a></p>
  
  <p>It could be because <code>CLRF</code> needs to be converted into <code>LF</code>, but I tried two commands to do this unsuccessfully:</p>
  
  <p><code>tr -d '\r' &lt; input &gt; output</code> and <code>perl -pi -e 's/\r\n/\n/g' input</code></p>
  
  <p>From the following thread:</p>
  
  <p><a href="https://unix.stackexchange.com/questions/277217/how-to-install-dos2unix-on-linux-without-root-access">https://unix.stackexchange.com/questions/277217/how-to-install-dos2unix-on-linux-without-root-access</a></p>
  
  <p>The above commands successfully strip the <code>\r</code> from the line endings, but the error from bcl2fastq remains.</p>
  
  <p>What am I doing wrong? Any suggestions would be greatly appreciated.</p>
  
  <blockquote>
    <p>Update</p>
  </blockquote>
  
  <p>I looked into the folder that is generated when the <code>cellranger</code> runs and found two <code>.csv</code> files generated by the <code>cellranger</code>. One of them, <code>samplesheet.csv</code>, contains these <code>^M</code> characters that are shown in the error:</p>
  
  <p><a href="https://i.sstatic.net/1FYBP.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/1FYBP.png" alt="enter image description here"></a></p>
  
  <blockquote>
    <p>Update</p>
  </blockquote>
  
  <p>Maybe one of the issues was that I was submitting regular <code>.sh</code> file on the <code>SLURM</code> cluster. However, I wrote the right <code>.slurm</code> file and submitted it yesterday with <code>sbatch</code> command:</p>
  
  <p><a href="https://i.sstatic.net/zjDEy.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/zjDEy.png" alt="enter image description here"></a></p>
  
  <p>However, today I got the message in my email:</p>
  
  <p><a href="https://i.sstatic.net/npZzE.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/npZzE.png" alt="enter image description here"></a></p>
  
  <p>And neither <code>_stderr</code>, nor <code>generate_fastq_id.err</code> or <code>generate_fastq_id.out</code> files contain anything. I thought initially that I set not enough time and it timed out, however, it is not true: I set the time to <code>24h</code> and it has been running for just <code>13h</code> before failing. </p>
  
  <blockquote>
    <p>Update</p>
  </blockquote>
  
  <p>I searched over all of the files in the generated folder with the <code>find</code> linux command and actually found the error files that show the same error as before: issue with the <code>sample_sheet.csv</code> file. This error file is <code>AHN3LLBGX5/MAKE_FASTQS_CS/MAKE_FASTQS/BCL2FASTQ_WITH_SAMPLESHEET/fork0/chnk0-u179acba3d8/_stderr</code>.</p>
  
  <p>So, right now the issue seems to be the following: I am feeding in the right <code>sample_sheet.csv</code> without the <code>^M</code> symbols, but <code>cellranger</code> transforms it into one that contains <code>^M</code> and then uses it giving the error. Above I see also <code>which: no configureBclToFastq.pl</code> and <code>ERROR: bcl2fastq::common::Exception: 2018-Apr-09 13:33:14: Inappropriate ioctl for device</code>, so maybe my input parameters are just wrong to <code>cellranger</code> and it has nothing to do with the <code>sample_sheet.csv</code>? </p>
  
  <blockquote>
    <p>Update</p>
  </blockquote>
  
  <p>I tried to use <code>--sample-sheet</code> instead of <code>--csv</code> since I am feeding in complex sample sheet. No luck.</p>
  
  <blockquote>
    <p>Update</p>
  </blockquote>
  
  <p>Here you can find all the error document in text:</p>
  
  <blockquote>
    <p>which: no configureBclToFastq.pl in (/sfs/lustre/scratch/nv4e/cellranger/samtools_new/1.6:/sfs/lustre/scratch/nv4e/cellranger/cellranger-tiny-fastq/1.2.0:/sfs/lustre/scratch/nv4e/cellranger/cellranger-tiny-ref/1.2.0:/sfs/lustre/scratch/nv4e/cellranger/miniconda-cr-cs/4.3.21-miniconda-cr-cs-c9/bin:/sfs/lustre/scratch/nv4e/cellranger/cellranger-cs/2.1.1/lib/bin:/sfs/lustre/scratch/nv4e/cellranger/cellranger-cs/2.1.1/tenkit/lib/bin:/sfs/lustre/scratch/nv4e/cellranger/cellranger-cs/2.1.1/tenkit/bin:/sfs/lustre/scratch/nv4e/cellranger/cellranger-cs/2.1.1/bin:/sfs/lustre/scratch/nv4e/cellranger/lz4/v1.8.0:/sfs/lustre/scratch/nv4e/cellranger/martian-cs/2.3.2/bin:/sfs/lustre/scratch/nv4e/cellranger/STAR/5dda596:/sfs/lustre/scratch/nv4e/cellranger/samtools_new/1.6:/sfs/lustre/scratch/nv4e/cellranger/cellranger-tiny-fastq/1.2.0:/sfs/lustre/scratch/nv4e/cellranger/cellranger-tiny-ref/1.2.0:/sfs/lustre/scratch/nv4e/cellranger/miniconda-cr-cs/4.3.21-miniconda-cr-cs-c9/bin:/sfs/lustre/scratch/nv4e/cellranger/cellranger-cs/2.1.1/lib/bin:/sfs/lustre/scratch/nv4e/cellranger/cellranger-cs/2.1.1/tenkit/lib/bin:/sfs/lustre/scratch/nv4e/cellranger/cellranger-cs/2.1.1/tenkit/bin:/sfs/lustre/scratch/nv4e/cellranger/cellranger-cs/2.1.1/bin:/sfs/lustre/scratch/nv4e/cellranger/lz4/v1.8.0:/sfs/lustre/scratch/nv4e/cellranger/martian-cs/2.3.2/bin:/sfs/lustre/scratch/nv4e/cellranger/STAR/5dda596:/scratch/nv4e/cellranger:/scratch/nv4e/bcl2fastq/build/bin:/scratch/nv4e/spark/bin:/scratch/nv4e/scala/bin:/sfs/nfs/blue/nv4e/private/bin:/sfs/nfs/blue/nv4e/anaconda2/bin:/sfs/nfs/blue/nv4e/.local/bin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/slurm/current/bin:/opt/slurm/current/sbin:/opt/singularity/current/bin:/opt/rci/bin:/opt/rci/sbin:/opt/nhc/current/sbin:/share/rci_apps/common/bin:/share/resources/HPCtools/)
    BCL to FASTQ file converter
    bcl2fastq v2.20.0.422
    Copyright (c) 2007-2017 Illumina, Inc.
    2018-04-09 18:31:29 [7fcdb39f37c0] Command-line invocation: bcl2fastq --minimum-trimmed-read-length 8 --mask-short-adapter-reads 8 --create-fastq-for-index-reads --ignore-missing-positions --ignore-missing-filter --ignore-missing-bcls --use-bases-mask=Y26,I8,Y98 -R /scratch/nv4e/kipnis/180403_NB501830_0158_AHN3LLBGX5 --output-dir=/scratch/nv4e/kipnis/AHN3LLBGX5/MAKE_FASTQS_CS/MAKE_FASTQS/BCL2FASTQ_WITH_SAMPLESHEET/fork0/chnk0-u21f1cbe9bf/files/fastq_path --interop-dir=/scratch/nv4e/kipnis/AHN3LLBGX5/MAKE_FASTQS_CS/MAKE_FASTQS/BCL2FASTQ_WITH_SAMPLESHEET/fork0/chnk0-u21f1cbe9bf/files/interop_path --sample-sheet=/scratch/nv4e/kipnis/AHN3LLBGX5/MAKE_FASTQS_CS/MAKE_FASTQS/PREPARE_SAMPLESHEET/fork0/chnk0-u09e7cbe891/files/samplesheet.csv -p 6 -r 6 -w 6
    2018-04-09 18:31:29 [7fcdb39f37c0] INFO: Minimum log level: INFO
    2018-04-09 18:31:29 [7fcdb39f37c0] INFO: Sample sheet: '/scratch/nv4e/kipnis/AHN3LLBGX5/MAKE_FASTQS_CS/MAKE_FASTQS/PREPARE_SAMPLESHEET/fork0/chnk0-u09e7cbe891/files/samplesheet.csv'
    2018-04-09 18:31:29 [7fcdb39f37c0] ERROR: bcl2fastq::common::Exception: 2018-Apr-09 18:31:29: Inappropriate ioctl for device (25): /scratch/nv4e/bcl2fastq/src/cxx/include/common/CsvGrammar.hpp(92): Throw in function bcl2fastq::common::CsvGrammarAttribute bcl2fastq::common::parseCsvData(Iterator, Iterator) [with Iterator = __gnu_cxx::__normal_iterator >; bcl2fastq::common::CsvGrammarAttribute = std::vector > >]
    Dynamic exception type: boost::exception_detail::clone_impl
    std::exception::what: Could not parse the CSV stream text:
     ^M
    ^M
    [Reads]^M
    26^M
    98^M
     ^M
    ^M
    [Data]^M
    Lane,Sample_ID,Sample_Name,index,Sample_Project,Original_Sample_ID^M
    1,SI-GA-B4_1,17R,ACTTCATA,Chromium_20180409,SI-GA-B4_1^M
    1,SI-GA-B4_2,17R,GAGATGAC,Chromium_20180409,SI-GA-B4_2^M
    1,SI-GA-B4_3,17R,TGCCGTGG,Chromium_20180409,SI-GA-B4_3^M
    1,SI-GA-B4_4,17R,CTAGACCT,Chromium_20180409,SI-GA-B4_4^M
    1,SI-GA-B5_1,19RL,AATAATGG,Chromium_20180409,SI-GA-B5_1^M
    1,SI-GA-B5_2,19RL,CCAGGGCA,Chromium_20180409,SI-GA-B5_2^M
    1,SI-GA-B5_3,19RL,TGCCTCAT,Chromium_20180409,SI-GA-B5_3^M
    1,SI-GA-B5_4,19RL,GTGTCATC,Chromium_20180409,SI-GA-B5_4^M
    2,SI-GA-B4_1,17R,ACTTCATA,Chromium_20180409,SI-GA-B4_1^M
    2,SI-GA-B4_2,17R,GAGATGAC,Chromium_20180409,SI-GA-B4_2^M
    2,SI-GA-B4_3,17R,TGCCGTGG,Chromium_20180409,SI-GA-B4_3^M
    2,SI-GA-B4_4,17R,CTAGACCT,Chromium_20180409,SI-GA-B4_4^M
    2,SI-GA-B5_1,19RL,AATAATGG,Chromium_20180409,SI-GA-B5_1^M
    2,SI-GA-B5_2,19RL,CCAGGGCA,Chromium_20180409,SI-GA-B5_2^M
    2,SI-GA-B5_3,19RL,TGCCTCAT,Chromium_20180409,SI-GA-B5_3^M
    2,SI-GA-B5_4,19RL,GTGTCATC,Chromium_20180409,SI-GA-B5_4^M
    3,SI-GA-B4_1,17R,ACTTCATA,Chromium_20180409,SI-GA-B4_1^M
    3,SI-GA-B4_2,17R,GAGATGAC,Chromium_20180409,SI-GA-B4_2^M
    3,SI-GA-B4_3,17R,TGCCGTGG,Chromium_20180409,SI-GA-B4_3^M
    3,SI-GA-B4_4,17R,CTAGACCT,Chromium_20180409,SI-GA-B4_4^M
    3,SI-GA-B5_1,19RL,AATAATGG,Chromium_20180409,SI-GA-B5_1^M
    3,SI-GA-B5_2,19RL,CCAGGGCA,Chromium_20180409,SI-GA-B5_2^M
    3,SI-GA-B5_3,19RL,TGCCTCAT,Chromium_20180409,SI-GA-B5_3^M
    3,SI-GA-B5_4,19RL,GTGTCATC,Chromium_20180409,SI-GA-B5_4^M
    4,SI-GA-B4_1,17R,ACTTCATA,Chromium_20180409,SI-GA-B4_1^M
    4,SI-GA-B4_2,17R,GAGATGAC,Chromium_20180409,SI-GA-B4_2^M
    4,SI-GA-B4_3,17R,TGCCGTGG,Chromium_20180409,SI-GA-B4_3^M
    4,SI-GA-B4_4,17R,CTAGACCT,Chromium_20180409,SI-GA-B4_4^M
    4,SI-GA-B5_1,19RL,AATAATGG,Chromium_20180409,SI-GA-B5_1^M
    4,SI-GA-B5_2,19RL,CCAGGGCA,Chromium_20180409,SI-GA-B5_2^M
    4,SI-GA-B5_3,19RL,TGCCTCAT,Chromium_20180409,SI-GA-B5_3^M
    4,SI-GA-B5_4,19RL,GTGTCATC,Chromium_20180409,SI-GA-B5_4^M</p>
  </blockquote>
  
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-04-08T22:28:45.723Z
Comments.Text: What happens if you remove the duplicate emtpy lines (just keep one before each section)?
Comments.UserDisplayName: Devon Ryan
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-04-08T23:45:25.330Z
Comments.Text: There are no duplicate lines in the input file, but inside the generated `_stderr` file they are somehow present
Comments.UserDisplayName: Nikita Vlasenko
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-04-09T09:00:26.293Z
Comments.Text: Is that the output from `_stderr` after removing `\r`? Because the `^M` characters indicate a line break problem. If they go away after running the `tr`/`perl` command, then there's probably an additional problem
Comments.UserDisplayName: heathobrien
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-04-09T17:49:14.977Z
Comments.Text: Yes, it is after fixing the sample sheet.
Comments.UserDisplayName: Nikita Vlasenko
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-04-10T09:58:11.990Z
Comments.Text: Did you manage to install the configureBclToFastq.pl in the path as reported in the _stderr? BTW, if you make your error message as text it would be easier for us to search and quote specific parts of the error: CTRL+SHIFT+C and CTRL+SHIFT+V in terminal
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-04-10T17:44:16.917Z
Comments.Text: No, I have not yet tried installing it because I do not know how. Could you give any links of how to do that and where to get the file?
Comments.UserDisplayName: Nikita Vlasenko
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-04-10T19:17:35.440Z
Comments.Text: There's no reason to install the old bcl2fastq (the configureBclToFastq.pl that's mentioned). Can you directly run `bcl2fastq` with your sample sheet (i.e., without using cellranger)?
Comments.UserDisplayName: Devon Ryan
Tags: <scrnaseq><10x-genomics>
Title: 10X Illumina demultiplexing sample sheet issue
ThreadText: # 10X Illumina demultiplexing sample sheet issue
  
  (Asked by: username_0 on 2018-04-08)
  
  Also posted [on biostars](https://www.biostars.org/p/308123/).
  
  I am trying to use `cellranger` or `bcl2fastq` to convert the `.bcl` files that I got from single cell analysis run into `fastq` files for further analysis. I needed to generate `sample_sheet.csv` and so I used the following tool:
  
  <https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/bcl2fastq-direct>
  
  which I copy-pasted into a text file using `vim`. `sample_sheet.csv` looks like that:
  
  ```
  [Header]
  EMFileVersion,4
  
  [Reads]
  26
  8
  98
  
  [Data]
  Lane,Sample_ID,Sample_Name,index,Sample_Project
  1,SI-GA-B4_1,17R,ACTTCATA,Chromium_20180406
  1,SI-GA-B4_2,17R,GAGATGAC,Chromium_20180406
  1,SI-GA-B4_3,17R,TGCCGTGG,Chromium_20180406
  1,SI-GA-B4_4,17R,CTAGACCT,Chromium_20180406
  1,SI-GA-B5_1,19RL,AATAATGG,Chromium_20180406 
  1,SI-GA-B5_2,19RL,CCAGGGCA,Chromium_20180406
  1,SI-GA-B5_3,19RL,TGCCTCAT,Chromium_20180406
  1,SI-GA-B5_4,19RL,GTGTCATC,Chromium_20180406
  2,SI-GA-B4_1,17R,ACTTCATA,Chromium_20180406
  2,SI-GA-B4_2,17R,GAGATGAC,Chromium_20180406
  2,SI-GA-B4_3,17R,TGCCGTGG,Chromium_20180406
  2,SI-GA-B4_4,17R,CTAGACCT,Chromium_20180406
  2,SI-GA-B5_1,19RL,AATAATGG,Chromium_20180406
  2,SI-GA-B5_2,19RL,CCAGGGCA,Chromium_20180406
  2,SI-GA-B5_3,19RL,TGCCTCAT,Chromium_20180406
  2,SI-GA-B5_4,19RL,GTGTCATC,Chromium_20180406
  3,SI-GA-B4_1,17R,ACTTCATA,Chromium_20180406
  3,SI-GA-B4_2,17R,GAGATGAC,Chromium_20180406
  3,SI-GA-B4_3,17R,TGCCGTGG,Chromium_20180406
  3,SI-GA-B4_4,17R,CTAGACCT,Chromium_20180406
  3,SI-GA-B5_1,19RL,AATAATGG,Chromium_20180406
  3,SI-GA-B5_2,19RL,CCAGGGCA,Chromium_20180406
  3,SI-GA-B5_3,19RL,TGCCTCAT,Chromium_20180406
  3,SI-GA-B5_4,19RL,GTGTCATC,Chromium_20180406
  4,SI-GA-B4_1,17R,ACTTCATA,Chromium_20180406
  4,SI-GA-B4_2,17R,GAGATGAC,Chromium_20180406
  4,SI-GA-B4_3,17R,TGCCGTGG,Chromium_20180406
  4,SI-GA-B4_4,17R,CTAGACCT,Chromium_20180406
  4,SI-GA-B5_1,19RL,AATAATGG,Chromium_20180406
  4,SI-GA-B5_2,19RL,CCAGGGCA,Chromium_20180406
  4,SI-GA-B5_3,19RL,TGCCTCAT,Chromium_20180406
  
  ```
  
  Then I ran `cellranger` using `bash` script:
  
  ```
  #!/bin/bash
  
   FLOWCELL_DIR="/scratch/nv4e/kipnis/180403_NB501830_0158_AHN3LLBGX5"
   OUTPUT_DIR="/scratch/nv4e/kipnis/fastq"
   SAMPLE_SHEET_PATH="/scratch/nv4e/kipnis/sample_sheet_2.csv"
  
  cellranger mkfastq --id="AHN3LLBGX5" --run=${FLOWCELL_DIR} --csv=${SAMPLE_SHEET_PATH} --output-dir=${OUTPUT_DIR}
  
  ```
  
  It fails with the following output:
  
  [![enter image description here](https://i.sstatic.net/coXGs.png)](https://i.sstatic.net/coXGs.png)
  
  `_stderr` file shows:
  
  [![enter image description here](https://i.sstatic.net/ECDVI.png)](https://i.sstatic.net/ECDVI.png)
  
  and that my `sample_sheet.csv` can not be parsed:
  
  [![enter image description here](https://i.sstatic.net/NVNW6.png)](https://i.sstatic.net/NVNW6.png)
  
  It could be because `CLRF` needs to be converted into `LF`, but I tried two commands to do this unsuccessfully:
  
  `tr -d '\r' < input > output` and `perl -pi -e 's/\r\n/\n/g' input`
  
  From the following thread:
  
  <https://unix.stackexchange.com/questions/277217/how-to-install-dos2unix-on-linux-without-root-access>
  
  The above commands successfully strip the `\r` from the line endings, but the error from bcl2fastq remains.
  
  What am I doing wrong? Any suggestions would be greatly appreciated.
  
  > Update
  
  I looked into the folder that is generated when the `cellranger` runs and found two `.csv` files generated by the `cellranger`. One of them, `samplesheet.csv`, contains these `^M` characters that are shown in the error:
  
  [![enter image description here](https://i.sstatic.net/1FYBP.png)](https://i.sstatic.net/1FYBP.png)
  
  > Update
  
  Maybe one of the issues was that I was submitting regular `.sh` file on the `SLURM` cluster. However, I wrote the right `.slurm` file and submitted it yesterday with `sbatch` command:
  
  [![enter image description here](https://i.sstatic.net/zjDEy.png)](https://i.sstatic.net/zjDEy.png)
  
  However, today I got the message in my email:
  
  [![enter image description here](https://i.sstatic.net/npZzE.png)](https://i.sstatic.net/npZzE.png)
  
  And neither `_stderr`, nor `generate_fastq_id.err` or `generate_fastq_id.out` files contain anything. I thought initially that I set not enough time and it timed out, however, it is not true: I set the time to `24h` and it has been running for just `13h` before failing.
  
  > Update
  
  I searched over all of the files in the generated folder with the `find` linux command and actually found the error files that show the same error as before: issue with the `sample_sheet.csv` file. This error file is `AHN3LLBGX5/MAKE_FASTQS_CS/MAKE_FASTQS/BCL2FASTQ_WITH_SAMPLESHEET/fork0/chnk0-u179acba3d8/_stderr`.
  
  So, right now the issue seems to be the following: I am feeding in the right `sample_sheet.csv` without the `^M` symbols, but `cellranger` transforms it into one that contains `^M` and then uses it giving the error. Above I see also `which: no configureBclToFastq.pl` and `ERROR: bcl2fastq::common::Exception: 2018-Apr-09 13:33:14: Inappropriate ioctl for device`, so maybe my input parameters are just wrong to `cellranger` and it has nothing to do with the `sample_sheet.csv`?
  
  > Update
  
  I tried to use `--sample-sheet` instead of `--csv` since I am feeding in complex sample sheet. No luck.
  
  > Update
  
  Here you can find all the error document in text:
  
  > which: no configureBclToFastq.pl in (/sfs/lustre/scratch/nv4e/cellranger/samtools\_new/1.6:/sfs/lustre/scratch/nv4e/cellranger/cellranger-tiny-fastq/1.2.0:/sfs/lustre/scratch/nv4e/cellranger/cellranger-tiny-ref/1.2.0:/sfs/lustre/scratch/nv4e/cellranger/miniconda-cr-cs/4.3.21-miniconda-cr-cs-c9/bin:/sfs/lustre/scratch/nv4e/cellranger/cellranger-cs/2.1.1/lib/bin:/sfs/lustre/scratch/nv4e/cellranger/cellranger-cs/2.1.1/tenkit/lib/bin:/sfs/lustre/scratch/nv4e/cellranger/cellranger-cs/2.1.1/tenkit/bin:/sfs/lustre/scratch/nv4e/cellranger/cellranger-cs/2.1.1/bin:/sfs/lustre/scratch/nv4e/cellranger/lz4/v1.8.0:/sfs/lustre/scratch/nv4e/cellranger/martian-cs/2.3.2/bin:/sfs/lustre/scratch/nv4e/cellranger/STAR/5dda596:/sfs/lustre/scratch/nv4e/cellranger/samtools\_new/1.6:/sfs/lustre/scratch/nv4e/cellranger/cellranger-tiny-fastq/1.2.0:/sfs/lustre/scratch/nv4e/cellranger/cellranger-tiny-ref/1.2.0:/sfs/lustre/scratch/nv4e/cellranger/miniconda-cr-cs/4.3.21-miniconda-cr-cs-c9/bin:/sfs/lustre/scratch/nv4e/cellranger/cellranger-cs/2.1.1/lib/bin:/sfs/lustre/scratch/nv4e/cellranger/cellranger-cs/2.1.1/tenkit/lib/bin:/sfs/lustre/scratch/nv4e/cellranger/cellranger-cs/2.1.1/tenkit/bin:/sfs/lustre/scratch/nv4e/cellranger/cellranger-cs/2.1.1/bin:/sfs/lustre/scratch/nv4e/cellranger/lz4/v1.8.0:/sfs/lustre/scratch/nv4e/cellranger/martian-cs/2.3.2/bin:/sfs/lustre/scratch/nv4e/cellranger/STAR/5dda596:/scratch/nv4e/cellranger:/scratch/nv4e/bcl2fastq/build/bin:/scratch/nv4e/spark/bin:/scratch/nv4e/scala/bin:/sfs/nfs/blue/nv4e/private/bin:/sfs/nfs/blue/nv4e/anaconda2/bin:/sfs/nfs/blue/nv4e/.local/bin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/slurm/current/bin:/opt/slurm/current/sbin:/opt/singularity/current/bin:/opt/rci/bin:/opt/rci/sbin:/opt/nhc/current/sbin:/share/rci\_apps/common/bin:/share/resources/HPCtools/)
  > BCL to FASTQ file converter
  > bcl2fastq v2.20.0.422
  > Copyright (c) 2007-2017 Illumina, Inc.
  > 2018-04-09 18:31:29 [7fcdb39f37c0] Command-line invocation: bcl2fastq --minimum-trimmed-read-length 8 --mask-short-adapter-reads 8 --create-fastq-for-index-reads --ignore-missing-positions --ignore-missing-filter --ignore-missing-bcls --use-bases-mask=Y26,I8,Y98 -R /scratch/nv4e/kipnis/180403\_NB501830\_0158\_AHN3LLBGX5 --output-dir=/scratch/nv4e/kipnis/AHN3LLBGX5/MAKE\_FASTQS\_CS/MAKE\_FASTQS/BCL2FASTQ\_WITH\_SAMPLESHEET/fork0/chnk0-u21f1cbe9bf/files/fastq\_path --interop-dir=/scratch/nv4e/kipnis/AHN3LLBGX5/MAKE\_FASTQS\_CS/MAKE\_FASTQS/BCL2FASTQ\_WITH\_SAMPLESHEET/fork0/chnk0-u21f1cbe9bf/files/interop\_path --sample-sheet=/scratch/nv4e/kipnis/AHN3LLBGX5/MAKE\_FASTQS\_CS/MAKE\_FASTQS/PREPARE\_SAMPLESHEET/fork0/chnk0-u09e7cbe891/files/samplesheet.csv -p 6 -r 6 -w 6
  > 2018-04-09 18:31:29 [7fcdb39f37c0] INFO: Minimum log level: INFO
  > 2018-04-09 18:31:29 [7fcdb39f37c0] INFO: Sample sheet: '/scratch/nv4e/kipnis/AHN3LLBGX5/MAKE\_FASTQS\_CS/MAKE\_FASTQS/PREPARE\_SAMPLESHEET/fork0/chnk0-u09e7cbe891/files/samplesheet.csv'
  > 2018-04-09 18:31:29 [7fcdb39f37c0] ERROR: bcl2fastq::common::Exception: 2018-Apr-09 18:31:29: Inappropriate ioctl for device (25): /scratch/nv4e/bcl2fastq/src/cxx/include/common/CsvGrammar.hpp(92): Throw in function bcl2fastq::common::CsvGrammarAttribute bcl2fastq::common::parseCsvData(Iterator, Iterator) [with Iterator = \_\_gnu\_cxx::\_\_normal\_iterator >; bcl2fastq::common::CsvGrammarAttribute = std::vector > >]
  > Dynamic exception type: boost::exception\_detail::clone\_impl
  > std::exception::what: Could not parse the CSV stream text:
  >  ^M
  > ^M
  > [Reads]^M
  > 26^M
  > 98^M
  >  ^M
  > ^M
  > [Data]^M
  > Lane,Sample\_ID,Sample\_Name,index,Sample\_Project,Original\_Sample\_ID^M
  > 1,SI-GA-B4\_1,17R,ACTTCATA,Chromium\_20180409,SI-GA-B4\_1^M
  > 1,SI-GA-B4\_2,17R,GAGATGAC,Chromium\_20180409,SI-GA-B4\_2^M
  > 1,SI-GA-B4\_3,17R,TGCCGTGG,Chromium\_20180409,SI-GA-B4\_3^M
  > 1,SI-GA-B4\_4,17R,CTAGACCT,Chromium\_20180409,SI-GA-B4\_4^M
  > 1,SI-GA-B5\_1,19RL,AATAATGG,Chromium\_20180409,SI-GA-B5\_1^M
  > 1,SI-GA-B5\_2,19RL,CCAGGGCA,Chromium\_20180409,SI-GA-B5\_2^M
  > 1,SI-GA-B5\_3,19RL,TGCCTCAT,Chromium\_20180409,SI-GA-B5\_3^M
  > 1,SI-GA-B5\_4,19RL,GTGTCATC,Chromium\_20180409,SI-GA-B5\_4^M
  > 2,SI-GA-B4\_1,17R,ACTTCATA,Chromium\_20180409,SI-GA-B4\_1^M
  > 2,SI-GA-B4\_2,17R,GAGATGAC,Chromium\_20180409,SI-GA-B4\_2^M
  > 2,SI-GA-B4\_3,17R,TGCCGTGG,Chromium\_20180409,SI-GA-B4\_3^M
  > 2,SI-GA-B4\_4,17R,CTAGACCT,Chromium\_20180409,SI-GA-B4\_4^M
  > 2,SI-GA-B5\_1,19RL,AATAATGG,Chromium\_20180409,SI-GA-B5\_1^M
  > 2,SI-GA-B5\_2,19RL,CCAGGGCA,Chromium\_20180409,SI-GA-B5\_2^M
  > 2,SI-GA-B5\_3,19RL,TGCCTCAT,Chromium\_20180409,SI-GA-B5\_3^M
  > 2,SI-GA-B5\_4,19RL,GTGTCATC,Chromium\_20180409,SI-GA-B5\_4^M
  > 3,SI-GA-B4\_1,17R,ACTTCATA,Chromium\_20180409,SI-GA-B4\_1^M
  > 3,SI-GA-B4\_2,17R,GAGATGAC,Chromium\_20180409,SI-GA-B4\_2^M
  > 3,SI-GA-B4\_3,17R,TGCCGTGG,Chromium\_20180409,SI-GA-B4\_3^M
  > 3,SI-GA-B4\_4,17R,CTAGACCT,Chromium\_20180409,SI-GA-B4\_4^M
  > 3,SI-GA-B5\_1,19RL,AATAATGG,Chromium\_20180409,SI-GA-B5\_1^M
  > 3,SI-GA-B5\_2,19RL,CCAGGGCA,Chromium\_20180409,SI-GA-B5\_2^M
  > 3,SI-GA-B5\_3,19RL,TGCCTCAT,Chromium\_20180409,SI-GA-B5\_3^M
  > 3,SI-GA-B5\_4,19RL,GTGTCATC,Chromium\_20180409,SI-GA-B5\_4^M
  > 4,SI-GA-B4\_1,17R,ACTTCATA,Chromium\_20180409,SI-GA-B4\_1^M
  > 4,SI-GA-B4\_2,17R,GAGATGAC,Chromium\_20180409,SI-GA-B4\_2^M
  > 4,SI-GA-B4\_3,17R,TGCCGTGG,Chromium\_20180409,SI-GA-B4\_3^M
  > 4,SI-GA-B4\_4,17R,CTAGACCT,Chromium\_20180409,SI-GA-B4\_4^M
  > 4,SI-GA-B5\_1,19RL,AATAATGG,Chromium\_20180409,SI-GA-B5\_1^M
  > 4,SI-GA-B5\_2,19RL,CCAGGGCA,Chromium\_20180409,SI-GA-B5\_2^M
  > 4,SI-GA-B5\_3,19RL,TGCCTCAT,Chromium\_20180409,SI-GA-B5\_3^M
  > 4,SI-GA-B5\_4,19RL,GTGTCATC,Chromium\_20180409,SI-GA-B5\_4^M
  
  **Tags:** scrnaseq, 10x-genomics
  
  > **Comments:**
  > **username_1**: What happens if you remove the duplicate emtpy lines (just keep one before each section)?  
  > **username_0**: There are no duplicate lines in the input file, but inside the generated `_stderr` file they are somehow present  
  > **username_2**: Is that the output from `_stderr` after removing `\r`? Because the `^M` characters indicate a line break problem. If they go away after running the `tr`/`perl` command, then there's probably an additional problem  
  > **username_0**: Yes, it is after fixing the sample sheet.  
  > **username_3**: Did you manage to install the configureBclToFastq.pl in the path as reported in the _stderr? BTW, if you make your error message as text it would be easier for us to search and quote specific parts of the error: CTRL+SHIFT+C and CTRL+SHIFT+V in terminal  
  > **username_0**: No, I have not yet tried installing it because I do not know how. Could you give any links of how to do that and where to get the file?  
  > **username_1**: There's no reason to install the old bcl2fastq (the configureBclToFastq.pl that's mentioned). Can you directly run `bcl2fastq` with your sample sheet (i.e., without using cellranger)?  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_0 on 2018-04-11. Score: 3 | Accepted answer
  
  So, we figured it out. If you delete everything until the `[Data]` tag in the sample sheet, leaving the `[Data]` tag, it starts working. Here is the full `sample_sheet.csv` that is working:
  
  ```
  [Data]
  Lane,Sample_ID,Sample_Name,index,Sample_Project
  1,SI-GA-B4_1,17R,ACTTCATA,Chromium_20180409
  1,SI-GA-B4_2,17R,GAGATGAC,Chromium_20180409
  1,SI-GA-B4_3,17R,TGCCGTGG,Chromium_20180409
  1,SI-GA-B4_4,17R,CTAGACCT,Chromium_20180409
  1,SI-GA-B5_1,19RL,AATAATGG,Chromium_20180409
  1,SI-GA-B5_2,19RL,CCAGGGCA,Chromium_20180409
  1,SI-GA-B5_3,19RL,TGCCTCAT,Chromium_20180409
  1,SI-GA-B5_4,19RL,GTGTCATC,Chromium_20180409
  2,SI-GA-B4_1,17R,ACTTCATA,Chromium_20180409
  2,SI-GA-B4_2,17R,GAGATGAC,Chromium_20180409
  2,SI-GA-B4_3,17R,TGCCGTGG,Chromium_20180409
  2,SI-GA-B4_4,17R,CTAGACCT,Chromium_20180409
  2,SI-GA-B5_1,19RL,AATAATGG,Chromium_20180409
  2,SI-GA-B5_2,19RL,CCAGGGCA,Chromium_20180409
  2,SI-GA-B5_3,19RL,TGCCTCAT,Chromium_20180409
  2,SI-GA-B5_4,19RL,GTGTCATC,Chromium_20180409
  3,SI-GA-B4_1,17R,ACTTCATA,Chromium_20180409
  3,SI-GA-B4_2,17R,GAGATGAC,Chromium_20180409
  3,SI-GA-B4_3,17R,TGCCGTGG,Chromium_20180409
  3,SI-GA-B4_4,17R,CTAGACCT,Chromium_20180409
  3,SI-GA-B5_1,19RL,AATAATGG,Chromium_20180409
  3,SI-GA-B5_2,19RL,CCAGGGCA,Chromium_20180409
  3,SI-GA-B5_3,19RL,TGCCTCAT,Chromium_20180409
  3,SI-GA-B5_4,19RL,GTGTCATC,Chromium_20180409
  4,SI-GA-B4_1,17R,ACTTCATA,Chromium_20180409
  4,SI-GA-B4_2,17R,GAGATGAC,Chromium_20180409
  4,SI-GA-B4_3,17R,TGCCGTGG,Chromium_20180409
  4,SI-GA-B4_4,17R,CTAGACCT,Chromium_20180409
  4,SI-GA-B5_1,19RL,AATAATGG,Chromium_20180409
  4,SI-GA-B5_2,19RL,CCAGGGCA,Chromium_20180409
  4,SI-GA-B5_3,19RL,TGCCTCAT,Chromium_20180409
  4,SI-GA-B5_4,19RL,GTGTCATC,Chromium_20180409
  
  ```
  
  It is very unfortunate and disappointing that `10X` website is generating wrong sample sheet. Still we got very low mapping rates and trying to figure out what went wrong.
  
  > Update
  
  I was supplying `--sample-sheet=` property, but it should be `--samplesheet=`. Now it is running fine (except for very low mapping rates) with all the headers on.
  
  > Update
  
  It turned out that we were given the wrong indexes, so we made a sample sheet using sample sheet generator again and even with `--samplesheet=` correct parameter it was not running. Convertion of `CLRF` with `perl` or `tr` did not help. However, concise format of the sample sheet worked out well which looks like the following:
  
  ```
  Lane,Sample,Index
  1-4,17R,SI-GA-B8
  1-4,19RL,SI-GA-B9
  
  ```
  
  It needs to be supplied with `--csv=` parameter.
  
  > **Comments:**
  > **username_4**: I found that if you copy and paste the 10X sheet directly from their website it inserts some odd characters on some of the blank lines.  I usually edit the file in vim and delete them.  
  > **username_1**: Related to @username_4, I suspect it was the ` ^M` lines (the ones with a space and then line end). Either way, I suggest that you email 10x support and report this issue. It should be easy for them to fix.  
  > **username_4**: It looks like it's a weird unicode character "U+00A0" / NO-BREAK SPACE.  
  > **username_5**: That's weird. I copied and pasted from their website and never had issues. But I also run `mac2unix`/`dos2unix` on every sample sheet, so maybe that is a sufficient fix.  
  
  ---
  
  ### Answer by username_6 on 2020-08-26. Score: 0
  
  Apart from supporting only Windows-style and Linux-style line endings and a restricted character set as mentioned above, the sample sheet [has to be in the correct encoding which is UTF-8](https://www.illumina.com/content/dam/illumina-marketing/documents/products/technotes/sequencing-sheet-format-specifications-technical-note-970-2017-004.pdf) (or its subset US-ASCII).
  Many command lines support these [lookup](https://stackoverflow.com/questions/805418/how-to-find-encoding-of-a-file-via-script-on-linux) and [conversion](https://stackoverflow.com/questions/64860/best-way-to-convert-text-files-between-character-sets) commands:
  
  ```bash
  # lookup
  file -i my_sample_sheet.csv
  
  # conversion
  iconv -f ISO-8859-15 -t UTF-8 in.csv > out.csv
  
  ```
  
  
  ---
  
  