<div dir="ltr">Hello Dr. Wang,<div><br></div><div>As I don't have your complete sequence file I am not able to reproduce your error. However it does appear to be a known bug. We are tracking this in <a href="https://github.com/ged-lab/khmer/issues/249">https://github.com/ged-lab/khmer/issues/249</a></div>
<div><br></div><div>As a workaround you can disable threading with "-T 1" when you run into this error.</div><div><br></div><div>My apologies for this.</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">
On Wed, Jan 8, 2014 at 11:15 AM, Shaolin Wang <span dir="ltr"><<a href="mailto:sw4ed@eservices.virginia.edu" target="_blank">sw4ed@eservices.virginia.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr"><div>I am new, please help, I got InvalidFASTQFileFormat error, the sequence looks fine, even after I remove that sequence, it still shows the error, and the error always show on line 16181.</div><div><br>
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<div>[17:27:40]sw4ed@hpcserver:~/Meta/SoilMeta> load-into-counting.py -T 4 -k 20 -N 4 -x 4e9 Sample_2024-1F_1.kh Sample_2024-1F_1.trimmed.fastq</div><div><br></div><div>PARAMETERS:</div><div> - kmer size = 20 (-k)</div>
<div> - n hashes = 4 (-N)</div><div> - min hashsize = 4e+09 (-x)</div><div><br></div><div>Estimated memory usage is 1.6e+10 bytes (n_hashes x min_hashsize)</div><div>--------</div><div>Saving hashtable to Sample_2024-1F_1.kh</div>
<div>Loading kmers from sequences in ['Sample_2024-1F_1.trimmed.fastq']</div><div>making hashtable</div><div>consuming input Sample_2024-1F_1.trimmed.fastq</div><div>terminate called after throwing an instance of 'khmer::read_parsers::InvalidFASTQFileFormat'</div>
<div> what(): InvalidFASTQFileFormat: illegal sequence letters: @HISEQ700708:147:D278GACXX:2:1101:6816:3815 2:N:0:ATCACG</div><div>Aborted (core dumped)</div><div><br></div><div><div>[17:44:12]sw4ed@hpcserver:~/Meta/SoilMeta> sed -n '16181,16188p' Sample_2024-1F_1.trimmed.fastq</div>
<div>@HISEQ700708:147:D278GACXX:2:1101:6816:3815 2:N:0:ATCACG</div><div>ATTGTCTGCGCGTTACGATATTATCAAGAATCGCGACTGGTTATGGTCTCTTACTGCTACAACACTGAACACTAAGACCAAATATGCTAACATTGGCAAC</div><div>+</div><div>CCCFFFFFHHHHHIJJJJIJJJJJJJJJJJJJJJJJJJJJIJIIIJIHHHHHFFFFFFFFEEEDDDDDDDDDDCDDDDDDDDDDEEDEDDDDDDDDDDDD</div>
<div>@HISEQ700708:147:D278GACXX:2:1101:6919:3932 1:N:0:ATCACG</div><div>TATTCAGGAAAACCTGCCGCAGACGCTTGGGGTCGCAGGAGATTTCCGGAATGTCTTCGTCATTGTCGATATAGTCCAGTCGAATACCGTCCTGGGCCAG</div><div>+</div><div>@C@FFFDFFHGFHIGIIJIIIJJJJGIJIJJIFEFHIIGGDHFHHHHFF<ACAEDDCDD=?A?DD@CBDDBDDCC@CDCDD@B?C@CCB<@DD>C?BDDB</div>
<span class="HOEnZb"><font color="#888888">
</font></span></div><span class="HOEnZb"><font color="#888888"><div><br></div><div><br></div>-- <br><div dir="ltr">Shaolin Wang, Ph.D<br>Research Scientist<br>Department of Psychiatry & Neurobiology Science<br>University of Virginia<br>
1670 Discovery Drive, Suite 110<br>Charlottesville, VA 22911<br>
<font face="Arial, sans-serif">
</font>Phone: <a href="tel:434-982-0243" value="+14349820243" target="_blank">434-982-0243</a><br>Fax:<a href="tel:434-973-7031" value="+14349737031" target="_blank">434-973-7031</a><br>E-mail: <span><span><a href="mailto:sw4ed@eservices.virginia.edu" target="_blank">swang@virginia.edu</a></span></span><div style="display:inline">
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<br></blockquote></div><br><br clear="all"><div><br></div>-- <br><div dir="ltr"><font face="courier new, monospace">Michael R. Crusoe: Software Engineer and Bioinformatician <a href="mailto:mcrusoe@msu.edu" target="_blank">mcrusoe@msu.edu</a><br>
@ the Genomics, Evolution, and Development lab; Michigan State University<br><a href="http://ged.msu.edu/" target="_blank">http://ged.msu.edu/</a> <a href="http://orcid.org/0000-0002-2961-9670" target="_blank">http://orcid.org/0000-0002-2961-9670</a> <a href="http://twitter.com/biocrusoe" target="_blank">@biocrusoe</a></font><br>
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