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<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">Hello,
<div>I have recently removed miso and tried to reinstall miso under ubuntu, but here is the problem I have:</div>
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<div>I used easy_install misopy to install miso. All went well. </div>
<div>import misopy and import pysplicing ok.</div>
<div>module_availability checked ok, all modules available.</div>
<div>test_miso failed with errors (see further)</div>
<div>Typing sam_to_bam or miso into the command line<span style="font-size: 10pt;"> </span><span style="font-size: 10pt;">failed</span><span style="font-size: 10pt;"> (command not found)</span></div>
<div>Typing index_gff works (requesting index files etc)</div>
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<div>Does anyone know what I should do please?</div>
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<div>Thanks</div>
<div>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: 15.199999809265137px; line-height: 21.299999237060547px; background-color: rgb(255, 255, 255);">Testing fr-unstranded...</span><br style="line-height: 21.299999237060547px; color: rgb(68, 68, 68); font-family: 'Microsoft YaHei UI', 'Microsoft YaHei', 宋体, Calibri, sans-serif; font-size: 15.199999809265137px; 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: 15.199999809265137px; line-height: 21.299999237060547px; background-color: rgb(255, 255, 255);">Checking read f_read against +</span><br style="line-height: 21.299999237060547px; color: rgb(68, 68, 68); font-family: 'Microsoft YaHei UI', 'Microsoft YaHei', 宋体, Calibri, sans-serif; font-size: 15.199999809265137px; 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: 15.199999809265137px; line-height: 21.299999237060547px; background-color: rgb(255, 255, 255);">Checking read f_read against -</span><br style="line-height: 21.299999237060547px; color: rgb(68, 68, 68); font-family: 'Microsoft YaHei UI', 'Microsoft YaHei', 宋体, Calibri, sans-serif; font-size: 15.199999809265137px; 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: 15.199999809265137px; line-height: 21.299999237060547px; background-color: rgb(255, 255, 255);">Checking read r_read against +</span><br style="line-height: 21.299999237060547px; color: rgb(68, 68, 68); font-family: 'Microsoft YaHei UI', 'Microsoft YaHei', 宋体, Calibri, sans-serif; font-size: 15.199999809265137px; 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: 15.199999809265137px; line-height: 21.299999237060547px; background-color: rgb(255, 255, 255);">Checking read r_read against -</span><br style="line-height: 21.299999237060547px; color: rgb(68, 68, 68); font-family: 'Microsoft YaHei UI', 'Microsoft YaHei', 宋体, Calibri, sans-serif; font-size: 15.199999809265137px; 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: 15.199999809265137px; line-height: 21.299999237060547px; background-color: rgb(255, 255, 255);">Testing fr-firststrand...</span><br style="line-height: 21.299999237060547px; color: rgb(68, 68, 68); font-family: 'Microsoft YaHei UI', 'Microsoft YaHei', 宋体, Calibri, sans-serif; font-size: 15.199999809265137px; 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: 15.199999809265137px; line-height: 21.299999237060547px; background-color: rgb(255, 255, 255);">Testing fr-secondstrand...</span><br style="line-height: 21.299999237060547px; color: rgb(68, 68, 68); font-family: 'Microsoft YaHei UI', 'Microsoft YaHei', 宋体, Calibri, sans-serif; font-size: 15.199999809265137px; 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: 15.199999809265137px; line-height: 21.299999237060547px; background-color: rgb(255, 255, 255);">.Testing conversion of SAM to BAM...</span><br style="line-height: 21.299999237060547px; color: rgb(68, 68, 68); font-family: 'Microsoft YaHei UI', 'Microsoft YaHei', 宋体, Calibri, sans-serif; font-size: 15.199999809265137px; 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: 15.199999809265137px; line-height: 21.299999237060547px; background-color: rgb(255, 255, 255);">Executing: sam_to_bam --convert /home/delong/misopy-0.5.2/misopy/test-data/sam-data/c2c12.Atp2b1.sam
/home/delong/misopy-0.5.2/misopy/test-output/sam-output</span><br style="line-height: 21.299999237060547px; color: rgb(68, 68, 68); font-family: 'Microsoft YaHei UI', 'Microsoft YaHei', 宋体, Calibri, sans-serif; font-size: 15.199999809265137px; 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: 15.199999809265137px; line-height: 21.299999237060547px; background-color: rgb(255, 255, 255);">sh: 1: sam_to_bam: not found</span><br style="line-height: 21.299999237060547px; color: rgb(68, 68, 68); font-family: 'Microsoft YaHei UI', 'Microsoft YaHei', 宋体, Calibri, sans-serif; font-size: 15.199999809265137px; 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: 15.199999809265137px; line-height: 21.299999237060547px; background-color: rgb(255, 255, 255);">FTesting gene-level Psi...</span><br style="line-height: 21.299999237060547px; color: rgb(68, 68, 68); font-family: 'Microsoft YaHei UI', 'Microsoft YaHei', 宋体, Calibri, sans-serif; font-size: 15.199999809265137px; 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: 15.199999809265137px; line-height: 21.299999237060547px; background-color: rgb(255, 255, 255);">Testing GFF indexing of: /home/delong/misopy-0.5.2/misopy/gff-events/mm9/genes/Atp2b1.mm9.gff</span><br style="line-height: 21.299999237060547px; color: rgb(68, 68, 68); font-family: 'Microsoft YaHei UI', 'Microsoft YaHei', 宋体, Calibri, sans-serif; font-size: 15.199999809265137px; 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: 15.199999809265137px; line-height: 21.299999237060547px; background-color: rgb(255, 255, 255);">Executing: index_gff --index /home/delong/misopy-0.5.2/misopy/gff-events/mm9/genes/Atp2b1.mm9.gff
/home/delong/misopy-0.5.2/misopy/gff-events/mm9/genes/Atp2b1/indexed</span><br style="line-height: 21.299999237060547px; color: rgb(68, 68, 68); font-family: 'Microsoft YaHei UI', 'Microsoft YaHei', 宋体, Calibri, sans-serif; font-size: 15.199999809265137px; 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: 15.199999809265137px; line-height: 21.299999237060547px; background-color: rgb(255, 255, 255);">sh: 1: index_gff: not found</span><br style="line-height: 21.299999237060547px; color: rgb(68, 68, 68); font-family: 'Microsoft YaHei UI', 'Microsoft YaHei', 宋体, Calibri, sans-serif; font-size: 15.199999809265137px; 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: 15.199999809265137px; line-height: 21.299999237060547px; background-color: rgb(255, 255, 255);">Executing: miso --run /home/delong/misopy-0.5.2/misopy/gff-events/mm9/genes/Atp2b1/indexed
/home/delong/misopy-0.5.2/misopy/test-output/sam-output/c2c12.Atp2b1.sorted.bam --output-dir /home/delong/misopy-0.5.2/misopy/test-output/gene-psi-output --read-len 36 </span><br style="line-height: 21.299999237060547px; color: rgb(68, 68, 68); font-family: 'Microsoft YaHei UI', 'Microsoft YaHei', 宋体, Calibri, sans-serif; font-size: 15.199999809265137px; 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: 15.199999809265137px; line-height: 21.299999237060547px; background-color: rgb(255, 255, 255);">sh: 1: miso: not found</span><br style="line-height: 21.299999237060547px; color: rgb(68, 68, 68); font-family: 'Microsoft YaHei UI', 'Microsoft YaHei', 宋体, Calibri, sans-serif; font-size: 15.199999809265137px; 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: 15.199999809265137px; line-height: 21.299999237060547px; background-color: rgb(255, 255, 255);">.</span><br style="line-height: 21.299999237060547px; color: rgb(68, 68, 68); font-family: 'Microsoft YaHei UI', 'Microsoft YaHei', 宋体, Calibri, sans-serif; font-size: 15.199999809265137px; 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: 15.199999809265137px; line-height: 21.299999237060547px; background-color: rgb(255, 255, 255);">======================================================================</span><br style="line-height: 21.299999237060547px; color: rgb(68, 68, 68); font-family: 'Microsoft YaHei UI', 'Microsoft YaHei', 宋体, Calibri, sans-serif; font-size: 15.199999809265137px; 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: 15.199999809265137px; line-height: 21.299999237060547px; background-color: rgb(255, 255, 255);">FAIL: test_a_sam_to_bam (__main__.TestMISO)</span><br style="line-height: 21.299999237060547px; color: rgb(68, 68, 68); font-family: 'Microsoft YaHei UI', 'Microsoft YaHei', 宋体, Calibri, sans-serif; font-size: 15.199999809265137px; 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: 15.199999809265137px; line-height: 21.299999237060547px; background-color: rgb(255, 255, 255);">----------------------------------------------------------------------</span><br style="line-height: 21.299999237060547px; color: rgb(68, 68, 68); font-family: 'Microsoft YaHei UI', 'Microsoft YaHei', 宋体, Calibri, sans-serif; font-size: 15.199999809265137px; 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: 15.199999809265137px; line-height: 21.299999237060547px; background-color: rgb(255, 255, 255);">Traceback (most recent call last):</span><br style="line-height: 21.299999237060547px; color: rgb(68, 68, 68); font-family: 'Microsoft YaHei UI', 'Microsoft YaHei', 宋体, Calibri, sans-serif; font-size: 15.199999809265137px; 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: 15.199999809265137px; line-height: 21.299999237060547px; background-color: rgb(255, 255, 255);"> File "misopy-0.5.2/misopy/test_miso.py",
line 51, in test_a_sam_to_bam</span><br style="line-height: 21.299999237060547px; color: rgb(68, 68, 68); font-family: 'Microsoft YaHei UI', 'Microsoft YaHei', 宋体, Calibri, sans-serif; font-size: 15.199999809265137px; 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: 15.199999809265137px; line-height: 21.299999237060547px; background-color: rgb(255, 255, 255);"> "c2c12.Atp2b1.sorted.bam")))</span><br style="line-height: 21.299999237060547px; color: rgb(68, 68, 68); font-family: 'Microsoft YaHei UI', 'Microsoft YaHei', 宋体, Calibri, sans-serif; font-size: 15.199999809265137px; 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: 15.199999809265137px; line-height: 21.299999237060547px; background-color: rgb(255, 255, 255);">AssertionError</span></div>
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