<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40"><head><META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=us-ascii"><meta name=Generator content="Microsoft Word 14 (filtered medium)"><style><!--
/* Font Definitions */
@font-face
{font-family:"Cambria Math";
panose-1:2 4 5 3 5 4 6 3 2 4;}
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
@font-face
{font-family:Tahoma;
panose-1:2 11 6 4 3 5 4 4 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0cm;
margin-bottom:.0001pt;
font-size:11.0pt;
font-family:"Calibri","sans-serif";
mso-fareast-language:EN-US;}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:purple;
text-decoration:underline;}
p
{mso-style-priority:99;
mso-margin-top-alt:auto;
margin-right:0cm;
mso-margin-bottom-alt:auto;
margin-left:0cm;
font-size:12.0pt;
font-family:"Times New Roman","serif";}
p.MsoAcetate, li.MsoAcetate, div.MsoAcetate
{mso-style-priority:99;
mso-style-link:"Texte de bulles Car";
margin:0cm;
margin-bottom:.0001pt;
font-size:8.0pt;
font-family:"Tahoma","sans-serif";
mso-fareast-language:EN-US;}
span.EmailStyle17
{mso-style-type:personal-compose;
font-family:"Calibri","sans-serif";
color:windowtext;}
span.TextedebullesCar
{mso-style-name:"Texte de bulles Car";
mso-style-priority:99;
mso-style-link:"Texte de bulles";
font-family:"Tahoma","sans-serif";}
.MsoChpDefault
{mso-style-type:export-only;
font-family:"Calibri","sans-serif";
mso-fareast-language:EN-US;}
@page WordSection1
{size:612.0pt 792.0pt;
margin:72.0pt 90.0pt 72.0pt 90.0pt;}
div.WordSection1
{page:WordSection1;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]--></head><body lang=FR-CA link=blue vlink=purple><div class=WordSection1><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:</span><span lang=EN-US style='font-size:12.0pt;font-family:"Times New Roman","serif";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'>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).</span><span lang=EN-US style='font-size:12.0pt;font-family:"Times New Roman","serif";mso-fareast-language:FR-CA'><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.</span><span lang=EN-US style='font-size:12.0pt;font-family:"Times New Roman","serif";mso-fareast-language:FR-CA'><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></div></body></html>