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<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;"><span style="font-size: 10pt;">Hello,</span><br>
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<div style="color: rgb(0, 0, 0); font-family: Tahoma; font-size: 10pt;">I have successfully used miso on one of my dataset without paired-end option, when I try to use the paired end option, it fails with the warings "thread batch-0 might have failed" etc.
Then I retry this dataset without paired-end option, fails with the same massege. But it goes well with other datasets.</div>
<div style="color: rgb(0, 0, 0); font-family: Tahoma; font-size: 10pt;">Complete log can be found below, I deleted the loading gene parts so that the message does not exeed size limite.</div>
<div style="color: rgb(0, 0, 0); font-family: Tahoma; font-size: 10pt;">Could someone please explain the problem?</div>
<div style="color: rgb(0, 0, 0); font-family: Tahoma; font-size: 10pt;">Thanks,</div>
<div style="color: rgb(0, 0, 0); font-family: Tahoma; font-size: 10pt;">Delong</div>
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<div><span style="color: rgb(68, 68, 68); font-family: 'Microsoft YaHei UI', 'Microsoft YaHei', 宋体, Calibri, sans-serif; font-size: 15px; line-height: 21px; background-color: rgb(255, 255, 255);">Probabilistic analysis of RNA-Seq data to detect differential
isoforms</span><br style="line-height:21px; color:rgb(68,68,68); font-family:'Microsoft YaHei UI','Microsoft YaHei',宋体,Calibri,sans-serif; font-size:15px; background-color:rgb(255,255,255)">
<span style="color: rgb(68, 68, 68); font-family: 'Microsoft YaHei UI', 'Microsoft YaHei', 宋体, Calibri, sans-serif; font-size: 15px; line-height: 21px; background-color: rgb(255, 255, 255);">Use --help argument to view options.</span><br style="line-height:21px; color:rgb(68,68,68); font-family:'Microsoft YaHei UI','Microsoft YaHei',宋体,Calibri,sans-serif; font-size:15px; background-color:rgb(255,255,255)">
<br style="line-height:21px; color:rgb(68,68,68); font-family:'Microsoft YaHei UI','Microsoft YaHei',宋体,Calibri,sans-serif; font-size:15px; background-color:rgb(255,255,255)">
<span style="color: rgb(68, 68, 68); font-family: 'Microsoft YaHei UI', 'Microsoft YaHei', 宋体, Calibri, sans-serif; font-size: 15px; line-height: 21px; background-color: rgb(255, 255, 255);">Loading settings from: /usr/local/lib/python2.7/dist-packages/misopy-0.4.9-py2.7-linux-x86_64.egg/misopy/settings/miso_settings.txt</span><br style="line-height:21px; color:rgb(68,68,68); font-family:'Microsoft YaHei UI','Microsoft YaHei',宋体,Calibri,sans-serif; font-size:15px; background-color:rgb(255,255,255)">
<span style="color: rgb(68, 68, 68); font-family: 'Microsoft YaHei UI', 'Microsoft YaHei', 宋体, Calibri, sans-serif; font-size: 15px; line-height: 21px; background-color: rgb(255, 255, 255);">Computing Psi values...</span><br style="line-height:21px; color:rgb(68,68,68); font-family:'Microsoft YaHei UI','Microsoft YaHei',宋体,Calibri,sans-serif; font-size:15px; background-color:rgb(255,255,255)">
<span style="color: rgb(68, 68, 68); font-family: 'Microsoft YaHei UI', 'Microsoft YaHei', 宋体, Calibri, sans-serif; font-size: 15px; line-height: 21px; background-color: rgb(255, 255, 255);"> - GFF index: /home/delong/hg19/indexed_SE_events</span><br style="line-height:21px; color:rgb(68,68,68); font-family:'Microsoft YaHei UI','Microsoft YaHei',宋体,Calibri,sans-serif; font-size:15px; background-color:rgb(255,255,255)">
<span style="color: rgb(68, 68, 68); font-family: 'Microsoft YaHei UI', 'Microsoft YaHei', 宋体, Calibri, sans-serif; font-size: 15px; line-height: 21px; background-color: rgb(255, 255, 255);"> - BAM: /home/delong/s4_50_ accepted_hits].bam</span><br style="line-height:21px; color:rgb(68,68,68); font-family:'Microsoft YaHei UI','Microsoft YaHei',宋体,Calibri,sans-serif; font-size:15px; background-color:rgb(255,255,255)">
<span style="color: rgb(68, 68, 68); font-family: 'Microsoft YaHei UI', 'Microsoft YaHei', 宋体, Calibri, sans-serif; font-size: 15px; line-height: 21px; background-color: rgb(255, 255, 255);"> - Read length: 50</span><br style="line-height:21px; color:rgb(68,68,68); font-family:'Microsoft YaHei UI','Microsoft YaHei',宋体,Calibri,sans-serif; font-size:15px; background-color:rgb(255,255,255)">
<span style="color: rgb(68, 68, 68); font-family: 'Microsoft YaHei UI', 'Microsoft YaHei', 宋体, Calibri, sans-serif; font-size: 15px; line-height: 21px; background-color: rgb(255, 255, 255);"> - Output directory: /home/delong/s4-50-paired-end</span><br style="line-height:21px; color:rgb(68,68,68); font-family:'Microsoft YaHei UI','Microsoft YaHei',宋体,Calibri,sans-serif; font-size:15px; background-color:rgb(255,255,255)">
<span style="color: rgb(68, 68, 68); font-family: 'Microsoft YaHei UI', 'Microsoft YaHei', 宋体, Calibri, sans-serif; font-size: 15px; line-height: 21px; background-color: rgb(255, 255, 255);">Checking your GFF annotation and BAM for mismatches...</span><br style="line-height:21px; color:rgb(68,68,68); font-family:'Microsoft YaHei UI','Microsoft YaHei',宋体,Calibri,sans-serif; font-size:15px; background-color:rgb(255,255,255)">
<span style="color: rgb(68, 68, 68); font-family: 'Microsoft YaHei UI', 'Microsoft YaHei', 宋体, Calibri, sans-serif; font-size: 15px; line-height: 21px; background-color: rgb(255, 255, 255);">Checking if BAM has mixed read lengths...</span><br style="line-height:21px; color:rgb(68,68,68); font-family:'Microsoft YaHei UI','Microsoft YaHei',宋体,Calibri,sans-serif; font-size:15px; background-color:rgb(255,255,255)">
<span style="color: rgb(68, 68, 68); font-family: 'Microsoft YaHei UI', 'Microsoft YaHei', 宋体, Calibri, sans-serif; font-size: 15px; line-height: 21px; background-color: rgb(255, 255, 255);">Found reads of length 50 in BAM.</span><br style="line-height:21px; color:rgb(68,68,68); font-family:'Microsoft YaHei UI','Microsoft YaHei',宋体,Calibri,sans-serif; font-size:15px; background-color:rgb(255,255,255)">
<span style="color: rgb(68, 68, 68); font-family: 'Microsoft YaHei UI', 'Microsoft YaHei', 宋体, Calibri, sans-serif; font-size: 15px; line-height: 21px; background-color: rgb(255, 255, 255);">Mapping genes to their indexed GFF representation, using /home/delong/hg19/indexed_SE_events</span><br style="line-height:21px; color:rgb(68,68,68); font-family:'Microsoft YaHei UI','Microsoft YaHei',宋体,Calibri,sans-serif; font-size:15px; background-color:rgb(255,255,255)">
<span style="color: rgb(68, 68, 68); font-family: 'Microsoft YaHei UI', 'Microsoft YaHei', 宋体, Calibri, sans-serif; font-size: 15px; line-height: 21px; background-color: rgb(255, 255, 255);">Loading indexed gene filenames from: /home/delong/hg19/indexed_SE_events/chrUn_gl000223</span><br style="line-height:21px; color:rgb(68,68,68); font-family:'Microsoft YaHei UI','Microsoft YaHei',宋体,Calibri,sans-serif; font-size:15px; background-color:rgb(255,255,255)">
<span style="color: rgb(68, 68, 68); font-family: 'Microsoft YaHei UI', 'Microsoft YaHei', 宋体, Calibri, sans-serif; font-size: 15px; line-height: 21px; background-color: rgb(255, 255, 255);"> - Loading 3 genes</span><br style="line-height:21px; color:rgb(68,68,68); font-family:'Microsoft YaHei UI','Microsoft YaHei',宋体,Calibri,sans-serif; font-size:15px; background-color:rgb(255,255,255)">
<font color="#444444" face="Microsoft YaHei UI, Microsoft YaHei, 宋体, Calibri, sans-serif"><span style="font-size: 15px; line-height: 21px;">...</span></font><br style="line-height:21px; color:rgb(68,68,68); font-family:'Microsoft YaHei UI','Microsoft YaHei',宋体,Calibri,sans-serif; font-size:15px; background-color:rgb(255,255,255)">
<span style="color: rgb(68, 68, 68); font-family: 'Microsoft YaHei UI', 'Microsoft YaHei', 宋体, Calibri, sans-serif; font-size: 15px; line-height: 21px; background-color: rgb(255, 255, 255);"> - Loading 278 genes</span><br style="line-height:21px; color:rgb(68,68,68); font-family:'Microsoft YaHei UI','Microsoft YaHei',宋体,Calibri,sans-serif; font-size:15px; background-color:rgb(255,255,255)">
<span style="color: rgb(68, 68, 68); font-family: 'Microsoft YaHei UI', 'Microsoft YaHei', 宋体, Calibri, sans-serif; font-size: 15px; line-height: 21px; background-color: rgb(255, 255, 255);">Preparing to run 4 batches of jobs...</span><br style="line-height:21px; color:rgb(68,68,68); font-family:'Microsoft YaHei UI','Microsoft YaHei',宋体,Calibri,sans-serif; font-size:15px; background-color:rgb(255,255,255)">
<span style="color: rgb(68, 68, 68); font-family: 'Microsoft YaHei UI', 'Microsoft YaHei', 宋体, Calibri, sans-serif; font-size: 15px; line-height: 21px; background-color: rgb(255, 255, 255);">Running batch of 10621 genes..</span><br style="line-height:21px; color:rgb(68,68,68); font-family:'Microsoft YaHei UI','Microsoft YaHei',宋体,Calibri,sans-serif; font-size:15px; background-color:rgb(255,255,255)">
<span style="color: rgb(68, 68, 68); font-family: 'Microsoft YaHei UI', 'Microsoft YaHei', 宋体, Calibri, sans-serif; font-size: 15px; line-height: 21px; background-color: rgb(255, 255, 255);"> - Executing: python /usr/local/lib/python2.7/dist-packages/misopy-0.4.9-py2.7-linux-x86_64.egg/EGG-INFO/scripts/run_miso.py
--compute-genes-from-file "/home/delong/s4-50-paired-end/batch-genes/batch-0_genes.txt" /home/delong/s4_50_ accepted_hits].bam /home/delong/s4-50-paired-end --read-len 50 --paired-end 50.0 50.0 --settings-filename /usr/local/lib/python2.7/dist-packages/misopy-0.4.9-py2.7-linux-x86_64.egg/misopy/settings/miso_settings.txt</span><br style="line-height:21px; color:rgb(68,68,68); font-family:'Microsoft YaHei UI','Microsoft YaHei',宋体,Calibri,sans-serif; font-size:15px; background-color:rgb(255,255,255)">
<span style="color: rgb(68, 68, 68); font-family: 'Microsoft YaHei UI', 'Microsoft YaHei', 宋体, Calibri, sans-serif; font-size: 15px; line-height: 21px; background-color: rgb(255, 255, 255);"> - Submitted thread batch-0</span><br style="line-height:21px; color:rgb(68,68,68); font-family:'Microsoft YaHei UI','Microsoft YaHei',宋体,Calibri,sans-serif; font-size:15px; background-color:rgb(255,255,255)">
<span style="color: rgb(68, 68, 68); font-family: 'Microsoft YaHei UI', 'Microsoft YaHei', 宋体, Calibri, sans-serif; font-size: 15px; line-height: 21px; background-color: rgb(255, 255, 255);">Running batch of 10621 genes..</span><br style="line-height:21px; color:rgb(68,68,68); font-family:'Microsoft YaHei UI','Microsoft YaHei',宋体,Calibri,sans-serif; font-size:15px; background-color:rgb(255,255,255)">
<span style="color: rgb(68, 68, 68); font-family: 'Microsoft YaHei UI', 'Microsoft YaHei', 宋体, Calibri, sans-serif; font-size: 15px; line-height: 21px; background-color: rgb(255, 255, 255);"> - Executing: python /usr/local/lib/python2.7/dist-packages/misopy-0.4.9-py2.7-linux-x86_64.egg/EGG-INFO/scripts/run_miso.py
--compute-genes-from-file "/home/delong/s4-50-paired-end/batch-genes/batch-1_genes.txt" /home/delong/s4_50_ accepted_hits].bam /home/delong/s4-50-paired-end --read-len 50 --paired-end 50.0 50.0 --settings-filename /usr/local/lib/python2.7/dist-packages/misopy-0.4.9-py2.7-linux-x86_64.egg/misopy/settings/miso_settings.txt</span><br style="line-height:21px; color:rgb(68,68,68); font-family:'Microsoft YaHei UI','Microsoft YaHei',宋体,Calibri,sans-serif; font-size:15px; background-color:rgb(255,255,255)">
<span style="color: rgb(68, 68, 68); font-family: 'Microsoft YaHei UI', 'Microsoft YaHei', 宋体, Calibri, sans-serif; font-size: 15px; line-height: 21px; background-color: rgb(255, 255, 255);"> - Submitted thread batch-1</span><br style="line-height:21px; color:rgb(68,68,68); font-family:'Microsoft YaHei UI','Microsoft YaHei',宋体,Calibri,sans-serif; font-size:15px; background-color:rgb(255,255,255)">
<span style="color: rgb(68, 68, 68); font-family: 'Microsoft YaHei UI', 'Microsoft YaHei', 宋体, Calibri, sans-serif; font-size: 15px; line-height: 21px; background-color: rgb(255, 255, 255);">Running batch of 10621 genes..</span><br style="line-height:21px; color:rgb(68,68,68); font-family:'Microsoft YaHei UI','Microsoft YaHei',宋体,Calibri,sans-serif; font-size:15px; background-color:rgb(255,255,255)">
<span style="color: rgb(68, 68, 68); font-family: 'Microsoft YaHei UI', 'Microsoft YaHei', 宋体, Calibri, sans-serif; font-size: 15px; line-height: 21px; background-color: rgb(255, 255, 255);"> - Executing: python /usr/local/lib/python2.7/dist-packages/misopy-0.4.9-py2.7-linux-x86_64.egg/EGG-INFO/scripts/run_miso.py
--compute-genes-from-file "/home/delong/s4-50-paired-end/batch-genes/batch-2_genes.txt" /home/delong/s4_50_ accepted_hits].bam /home/delong/s4-50-paired-end --read-len 50 --paired-end 50.0 50.0 --settings-filename /usr/local/lib/python2.7/dist-packages/misopy-0.4.9-py2.7-linux-x86_64.egg/misopy/settings/miso_settings.txt</span><br style="line-height:21px; color:rgb(68,68,68); font-family:'Microsoft YaHei UI','Microsoft YaHei',宋体,Calibri,sans-serif; font-size:15px; background-color:rgb(255,255,255)">
<span style="color: rgb(68, 68, 68); font-family: 'Microsoft YaHei UI', 'Microsoft YaHei', 宋体, Calibri, sans-serif; font-size: 15px; line-height: 21px; background-color: rgb(255, 255, 255);"> - Submitted thread batch-2</span><br style="line-height:21px; color:rgb(68,68,68); font-family:'Microsoft YaHei UI','Microsoft YaHei',宋体,Calibri,sans-serif; font-size:15px; background-color:rgb(255,255,255)">
<span style="color: rgb(68, 68, 68); font-family: 'Microsoft YaHei UI', 'Microsoft YaHei', 宋体, Calibri, sans-serif; font-size: 15px; line-height: 21px; background-color: rgb(255, 255, 255);">Running batch of 10622 genes..</span><br style="line-height:21px; color:rgb(68,68,68); font-family:'Microsoft YaHei UI','Microsoft YaHei',宋体,Calibri,sans-serif; font-size:15px; background-color:rgb(255,255,255)">
<span style="color: rgb(68, 68, 68); font-family: 'Microsoft YaHei UI', 'Microsoft YaHei', 宋体, Calibri, sans-serif; font-size: 15px; line-height: 21px; background-color: rgb(255, 255, 255);"> - Executing: python /usr/local/lib/python2.7/dist-packages/misopy-0.4.9-py2.7-linux-x86_64.egg/EGG-INFO/scripts/run_miso.py
--compute-genes-from-file "/home/delong/s4-50-paired-end/batch-genes/batch-3_genes.txt" /home/delong/s4_50_ accepted_hits].bam /home/delong/s4-50-paired-end --read-len 50 --paired-end 50.0 50.0 --settings-filename /usr/local/lib/python2.7/dist-packages/misopy-0.4.9-py2.7-linux-x86_64.egg/misopy/settings/miso_settings.txt</span><br style="line-height:21px; color:rgb(68,68,68); font-family:'Microsoft YaHei UI','Microsoft YaHei',宋体,Calibri,sans-serif; font-size:15px; background-color:rgb(255,255,255)">
<span style="color: rgb(68, 68, 68); font-family: 'Microsoft YaHei UI', 'Microsoft YaHei', 宋体, Calibri, sans-serif; font-size: 15px; line-height: 21px; background-color: rgb(255, 255, 255);"> - Submitted thread batch-3</span><br style="line-height:21px; color:rgb(68,68,68); font-family:'Microsoft YaHei UI','Microsoft YaHei',宋体,Calibri,sans-serif; font-size:15px; background-color:rgb(255,255,255)">
<span style="color: rgb(68, 68, 68); font-family: 'Microsoft YaHei UI', 'Microsoft YaHei', 宋体, Calibri, sans-serif; font-size: 15px; line-height: 21px; background-color: rgb(255, 255, 255);">Waiting on 4 threads...</span><br style="line-height:21px; color:rgb(68,68,68); font-family:'Microsoft YaHei UI','Microsoft YaHei',宋体,Calibri,sans-serif; font-size:15px; background-color:rgb(255,255,255)">
<span style="color: rgb(68, 68, 68); font-family: 'Microsoft YaHei UI', 'Microsoft YaHei', 宋体, Calibri, sans-serif; font-size: 15px; line-height: 21px; background-color: rgb(255, 255, 255);">WARNING: Thread batch-0 might have failed...</span><br style="line-height:21px; color:rgb(68,68,68); font-family:'Microsoft YaHei UI','Microsoft YaHei',宋体,Calibri,sans-serif; font-size:15px; background-color:rgb(255,255,255)">
<span style="color: rgb(68, 68, 68); font-family: 'Microsoft YaHei UI', 'Microsoft YaHei', 宋体, Calibri, sans-serif; font-size: 15px; line-height: 21px; background-color: rgb(255, 255, 255);">WARNING: Thread batch-1 might have failed...</span><br style="line-height:21px; color:rgb(68,68,68); font-family:'Microsoft YaHei UI','Microsoft YaHei',宋体,Calibri,sans-serif; font-size:15px; background-color:rgb(255,255,255)">
<span style="color: rgb(68, 68, 68); font-family: 'Microsoft YaHei UI', 'Microsoft YaHei', 宋体, Calibri, sans-serif; font-size: 15px; line-height: 21px; background-color: rgb(255, 255, 255);">WARNING: Thread batch-2 might have failed...</span><br style="line-height:21px; color:rgb(68,68,68); font-family:'Microsoft YaHei UI','Microsoft YaHei',宋体,Calibri,sans-serif; font-size:15px; background-color:rgb(255,255,255)">
<span style="color: rgb(68, 68, 68); font-family: 'Microsoft YaHei UI', 'Microsoft YaHei', 宋体, Calibri, sans-serif; font-size: 15px; line-height: 21px; background-color: rgb(255, 255, 255);">WARNING: Thread batch-3 might have failed...</span><br style="line-height:21px; color:rgb(68,68,68); font-family:'Microsoft YaHei UI','Microsoft YaHei',宋体,Calibri,sans-serif; font-size:15px; background-color:rgb(255,255,255)">
<span style="color: rgb(68, 68, 68); font-family: 'Microsoft YaHei UI', 'Microsoft YaHei', 宋体, Calibri, sans-serif; font-size: 15px; line-height: 21px; background-color: rgb(255, 255, 255);"> - Threads completed in 0.00 hours.</span></div>
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