<div dir="ltr">Hi Carson,<div><br></div><div>Great— the full temporary directory was indeed the issue! On amazon the AMI images are so small that a couple of big files will fill this up, and of course because the script cleans up after itself, I was never the wiser. Thanks for the insight. I was missing about 1GB of data! Doh!</div><div><br></div><div>Mike, I was able to regenerate my GFF file with this in mind, and no more complaining. It was indeed the truncated file that was the culprit. Thanks for your insights as well.</div><div><br></div><div>Best,</div><div>Jason Gallant</div><div><br></div><div><br></div><br><div class="gmail_quote"><div dir="ltr">On Wed, Nov 4, 2015 at 11:10 AM Carson Holt <<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word">If you have a truncated result, then you should look for truncation in one of the pre-merged files (usually indicates a broken file lock if you started multiple instances of MAKER simultaneously). Also make sure your /tmp or whatever your system default TMPDIR is has not become full. gff3_merge uses that directory to store temporary files.</div><div style="word-wrap:break-word"><div><br></div><div>—Carson</div></div><div style="word-wrap:break-word"><div><br></div><div><br><div><blockquote type="cite"><div>On Nov 3, 2015, at 8:20 PM, Jason Gallant <<a href="mailto:jgallant@msu.edu" target="_blank">jgallant@msu.edu</a>> wrote:</div><br><div><div dir="ltr">Hi Mike,<div><br></div><div>I’ve done a little digging on my own, and I think I have traced the issue… it appears that the script is being thrown for the first time when it encounters the line containing the first FASTA sequence header in the GFF file. For example:</div><div><br></div><div><div>Scaffold435<span style="white-space:pre-wrap"> </span>blastx<span style="white-space:pre-wrap"> </span>match_part<span style="white-space:pre-wrap"> </span>102606<span style="white-space:pre-wrap"> </span>102851<span style="white-space:pre-wrap"> </span>201<span style="white-space:pre-wrap"> </span>-<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>ID=Scaffold435:hsp:71210:3.10.1.2;Parent=Scaffold435:hit:24267:3.10.1.2;Target=gi|37594442|ref|NP_003431.2| 161 242;Gap=M82</div><div>Scaffold435<span style="white-space:pre-wrap"> </span>blastx<span style="white-space:pre-wrap"> </span>match_part<span style="white-space:pre-wrap"> </span>102528<span style="white-space:pre-wrap"> </span>102851<span style="white-space:pre-wrap"> </span>173<span style="white-space:pre-wrap"> </span>-<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>ID=Scaffold435:hsp:71211:3.10.1.2;Pare##FASTA</div><div>>Scaffold3579</div><div>GCAGTAGGCTGTGATACGTTTGCACCCGGGGACTAAGGGGAGATGTGTACAGGATGGGGA</div><div>GATGTGTACAGGATGGGGAGATGTGTACAGGATGGAGGGGTCCGTGCGAGAGCGTACCAC</div><div>GTGTCTCCCGTGCAGTGGTGCGGCGTGTACTTGATGCGATAAGCCACAGGGTCCTGCTTC</div><div>CCATCCTCCATGATCATTTTCATCCGCAGCGTGACCTCCCCCTCAGAAAAGACCCCCTTC</div><div>CTCATCCTCTCAAAGAGCACCAGAGATTCCTCAATCGGCCGATCCCTCCAAGGGGACAGG</div><div>GGAGGGCTGTGGCCCTTCAGCTCCTCCACACGCTGGTGACACACATAGGCGAGGCCCCTG</div><div>GATGCAGAACAGTGCAGACAGTGACATACCATTCACATGACACTGATCCGGTTAAGCCAC</div><div>ACGCGATACAATACAGTGTCATCATCAGGAAGAAGGGGAAACAGAGGCGTCAAAACGCCC</div><div>TATGAAGAGAGGAGTCTGCTTGCACTCACCGGCGAATAAGATCCACTGCGAGGTCGTACA</div><div>GCTTTTGGAAGTGGTCAGACGCGTGGGTCACTGCATAGGGCGTGTACCCTGTTTTACAGA</div></div><div><br></div><div>Perl complains when it encounters the line containing >Scaffold3579 and pretty much every line thereafter. Intriguingly, it would appear that the preceding line appears to be truncated compared to those before it. I can trace this all the way back to the output of gff3_merge for several files. Not sure what to do here (or if you can help!).</div><div><br></div><div>Best,</div><div>Jason</div><div><br></div><div><br></div><div><br></div><br><div class="gmail_quote"><div dir="ltr">On Tue, Nov 3, 2015 at 4:06 PM Michael Campbell <<a href="mailto:michael.s.campbell1@gmail.com" target="_blank">michael.s.campbell1@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word">Hi Jason,<div><br></div><div>It could be a couple of things. If you have a cut down version of your gff3 that I can use to recreate the error I can debug it. The <a href="http://quality_filter.pl/" target="_blank">quality_filter.pl</a> script is still a pretty young accessory script, so you may have something in your file that It wasn’t tested against.</div><div><br></div><div>Thanks,</div><div>Mike</div><div><br></div><div> </div><div><br><div><blockquote type="cite"></blockquote></div></div></div><div style="word-wrap:break-word"><div><div><blockquote type="cite"><div>On Nov 3, 2015, at 2:48 PM, Jason Gallant <<a href="mailto:jgallant@msu.edu" target="_blank">jgallant@msu.edu</a>> wrote:</div><br></blockquote></div></div></div><div style="word-wrap:break-word"><div><div><blockquote type="cite"><div><div dir="ltr">Hi Mike (list copied for future reference),<div><br></div><div>I found your very nice protocols paper on using Maker from 2014. I’ve been following it to the letter as I’m wrapping up my annotation project.</div><div><br></div><div>I’ve located your <a href="http://quality_filter.pl/" target="_blank">quality_filter.pl</a> script and am using it on my GFF files to create maker standard and maker default data sets from my maker-max GFF file. I’m noticing that perl complains a lot while this is running about “use of uninitialized value”. This occurs on two separate passes as far as I can tell. When generating the “maker standard” file, it occurs for many lines in my GFF file as:</div><div><br></div><div>Use of uninitialized value $array[2] in pattern match (m//) at /mnt/home/jgallant/<a href="http://quality_filter.pl/" target="_blank">quality_filter.pl</a> line 50, <GEN0> line Y.<br></div><div><br></div><div>And then later it complains again with a similar message</div><div><br></div><div>Use of uninitialized value $array[2] in string eq at /mnt/home/jgallant/<a href="http://quality_filter.pl/" target="_blank">quality_filter.pl</a> line 92, <GEN1> line X.<br></div><div>Use of uninitialized value $array[2] in string eq at /mnt/home/jgallant/<a href="http://quality_filter.pl/" target="_blank">quality_filter.pl</a> line 96, <GEN1> line X.<br></div><div>Use of uninitialized value $array[2] in string eq at /mnt/home/jgallant/<a href="http://quality_filter.pl/" target="_blank">quality_filter.pl</a> line 100, <GEN1> line X<br></div><div><br></div><div>Any insights as to what causes this? I seem to get a fully formed GFF3 file out the other side, but the command line fills with these messages and makes me nervous that something isn’t right.</div><div><br></div><div>I’d appreciate any thoughts!</div><div><br></div><div>Best,</div><div>Jason Gallant</div></div></div></blockquote></div></div></div><div style="word-wrap:break-word"><div><div><blockquote type="cite"><div>
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