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<p><span lang="EN-US">Hello,<o:p></o:p></span></p>
<p><span lang="EN-US">I’ve been trying to make InParanoid work using de novo transcriptomes of two non-model species (birds) I assembled with Trinity. They were 'translated' to protein sequences using Transdecoder. The resulting fasta file I'm trying to use
in InParanoid looks like this (~30 000 seqs):<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";mso-fareast-language:FR-CA">>comp100291_c0_seq1<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";mso-fareast-language:FR-CA">LPKKILLPIQQVLGHLLLALSYRGKVMQVKALKSKHEHNGPETLDAFLSSKLVVVKQPRE<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";mso-fareast-language:FR-CA">QAGFPLSIVFIPGEGRQERFLLHGEYNQSFCKEPVMELPRQ<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";mso-fareast-language:FR-CA">>comp102162_c0_seq1<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";mso-fareast-language:FR-CA">PNMTLHFLKSSPGSWRLSGLVLIPYVTETISGSCETLTRLQMPAHIQQSRWKAKHGPRIL<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";mso-fareast-language:FR-CA">LLGLLQNLRSLFPLKVLPPGANSQLKRNCSFTSVCLIGTFYVESS<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";mso-fareast-language:FR-CA">>comp102206_c0_seq1<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";mso-fareast-language:FR-CA">CQEQKWQKGNREEKGWAGVTVWGAYFPYLLIRCPNHQTSTPLSIHSQQHFMLCIIICPFS<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";mso-fareast-language:FR-CA">WLKPPVKTTQMFKGFFFKSGLKKFLALFLISWAAFATDRPLLGKQQSR<o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif";mso-fareast-language:FR-CA">I tried the example fasta files supplied with the program (called SC
and EC) and it works, but when I use my files, it's stuck at the first step and it does not create any file (nor disk usage) after days. Here is what I get with my fasta files:<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";mso-fareast-language:FR-CA">Loading module bio/ncbi-blast-2.2.22.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";mso-fareast-language:FR-CA">Formatting BLAST databases<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";mso-fareast-language:FR-CA">Done formatting<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";mso-fareast-language:FR-CA">Starting BLAST searches...<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";mso-fareast-language:FR-CA"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";mso-fareast-language:FR-CA">Starting first BLAST pass for bf - bf on [blastall] WARNING: the -C 3 argument is currently experimental<o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif";mso-fareast-language:FR-CA">It then stays like this forever (I tried up to 6 days with 24 CPUs and
256G).<o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif";mso-fareast-language:FR-CA">I also tried supplying my Blast results (inter-sample) generated myself
that I parsed with their supplied parser but then it still stays forever at the same state, again without generating any file:<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";mso-fareast-language:FR-CA">Done BLAST searches. Starting ortholog detection...<o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif";mso-fareast-language:FR-CA">I tried with and without bootstraping, multitreading (-a16 option) or
not, as I said with or without supplied blast results and I also cleaned my fasta files for any weird characters (removed annotations, all ' * ', spaces, empty lines and dots. Now I'm running out of ideas... I'm using a Unix cluster. I tried these jobs using
up to 4 to 24 CPUs with 8 to 256G memory.<o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif";mso-fareast-language:FR-CA">Finally, since it was working with SC and EC, I tried with a small subset
of my transcriptomes (a few thousands sequences) and it worked. Thus it seems to me that the problem could be that InParanoid cannot take more than, say, 10000 sequences. I could split my transcriptomes into several smaller files of specified sequence ranges
but then the orthologs that do not have the exact same length will have a chance to be missed if they are in two different split files.<o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif";mso-fareast-language:FR-CA">Thanks in advance for your help,<o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif";mso-fareast-language:FR-CA">Jean-Nicolas</span><span lang="EN-US"><o:p></o:p></span></p>
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