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I am trying to run DEXSeq_count.py script and am running into problems. Here is the output. I had no problems before running HTseq. The alignments were done using Tophat 2.0.4 and samtools was used to convert to sam file format. Sort was used to sort the file and these are paired end reads. The sorted sam files were feed into dexseq_count.py. Few lines from the sam file as well are added.
python dexseq_count.py -p yes -s no Gallus_gallus.WASHUC2.67.gff /home/sudeep/work/6-20-12/layers/all_infected_bams/1_4I_accepted_hits_RG_sorted.sam /home/sudeep/work/6-20-12/layers/all_infected_bams/1_4I_count.txt
Traceback (most recent call last):
File "dexseq_count.py", line 132, in <module>
for af, ar in HTSeq.pair_SAM_alignments( HTSeq.SAM_Reader( sam_file ) ):
File "/usr/local/lib/python2.6/dist-packages/HTSeq-0.5.3p3-py2.6-linux-x86_64.egg/HTSeq/__init__.py", line 604, in pair_SAM_alignments
for almnt in alignments:
File "/usr/local/lib/python2.6/dist-packages/HTSeq-0.5.3p3-py2.6-linux-x86_64.egg/HTSeq/__init__.py", line 543, in __iter__
algnt = SAM_Alignment.from_SAM_line( line )
File "_HTSeq.pyx", line 1247, in HTSeq._HTSeq.SAM_Alignment.from_SAM_line (src/_HTSeq.c:21146)
File "_HTSeq.pyx", line 765, in HTSeq._HTSeq.SequenceWithQualities.__init__ (src/_HTSeq.c:13133)
ValueError: ("'seq' and 'qualstr' do not have the same length.", 'line 2 of file /home/sudeep/work/6-20-12/layers/all_infected_bams/1_4I_accepted_hits_RG_sorted.sam')
HWI-ST913:105:C0EYJACXX:5:1101:10000:100418 99 13 13229153 50 100M = 13229168 115 GATGTGAGCTGCAACACTGGCACAGTGTGAAGGATACCACCTGGTTCCCAGCCTTCTCCTGTCCCCGAAGACACCTCTCCCAGCACCCGCAGCAGCGATG CCCFFFFFHHHHHJJJJIJIJJJJJJIIJJJJJIJIIIIJJJJJIJJJJJJJJJJJJJJJJIJIJJIHHHFFFFDCDEDDDDDDDDDDDDDDDDDDDBD< MD:Z:100 RG:Z:1 XG:i:0 NH:i:1 NM:i:0 XM:i:0 XN:i:0 XO:i:0 AS:i:0 XS:A:+ YT:Z:UU
HWI-ST913:105:C0EYJACXX:5:1101:10000:100418 147 13 13229168 50 100M = 13229153 -115 ACTGGCACAGTGTGAAGGATACCACCTGGTTCCCAGCCTTCTCCTGTCCCCGAAGACACCTCTCCCAGCACCCGCAGCAGCGATGCAGAGACCACCCCTG * MD:Z:100 RG:Z:1 XG:i:0 NH:i:1 NM:i:0 XM:i:0 XN:i:0 XO:i:0 AS:i:0 XS:A:+ YT:Z:UU
HWI-ST913:105:C0EYJACXX:5:1101:10000:105912 99 5 13576179 50 52M241N48M = 13576221 383 GTCCTCCGCGCCTCTGCCGCTCACGCTGCTCTGCCAGCCCTCCCGGGCATCGCTGATCACTTTGGCTGCCCAAGCACCTCCAGGTCCTCTCCGAGCAGCA @@CDFFFFHDDFHGIIJJJGIIGIIIIEIIJIGHIGGFHIIIIJIHGFFFEBCBBDDDDCDDDCCCCD@18>A8<<CBDDDCC<:>CCCCCDBD>BDDBD MD:Z:24C75 RG:Z:1 XG:i:0 NH:i:1 NM:i:1 XM:i:1 XO:i:0 AS:i:-4 XS:A:-
HWI-ST913:105:C0EYJACXX:5:1101:10000:105912 147 5 13576221 50 10M241N90M = 13576179 -383 CCGGGCATCGCTGATCACTTTGGCTGCCCAAGCACCTCCAGGTCCTCTCCGAGCAGCATCGTAATTGCCACGAGCATGGAAATACTTGTCAGCACCAATG B>CC?5@DDDCC@EDC@DDDDDDDDDBDCECEBBFFHHHHGIHJIHHHJHJIHGGJIJJIIJJJIIJJIHIJJJJJJIJJJJGFJJIHHHDGFDFDF@<B MD:Z:100 RG:Z:1 XG:i:0 NH:i:1 NM:i:0 XM:i:0 XN:i:0 XO:i:0 AS:i:0 XS:A:- YT:Z:UU
HWI-ST913:105:C0EYJACXX:5:1101:10000:108641 99 14 4187451 50 100M = 4187485 134 CAGCCCGCTTGCTTGACAAACCAAAAAGGATCAAGTGTGTTTTGTTTTTAAGGCGGAAGATACAAAAAGACACTTGTTGGGTTACATAATTTACAGACAA CCCFFFFFHHHHHJJJJIJJJJJIJJJJIJIJIJJFGFHDGIIJGIJJJIFIIJIFFDDDDDDDDDDDDDDDCDDCCCDDD?BBCDEEDDEEDDCCDDDC MD:Z:100 RG:Z:1 XG:i:0 NH:i:1 NM:i:0 XM:i:0 XN:i:0 XO:i:0 AS:i:0 YT:Z:UU
HWI-ST913:105:C0EYJACXX:5:1101:10000:108641 147 14 4187485 50 100M = 4187451 -134 GTGTGTTTTGTTTTTAAGGCGGAAGATACAAAAAGACACTTGTTGGGTTACATAATTTACAGACAAGCAATTATCATCTAACACCAGTAATTGGTACCGG @BDDDDDDDDDEEEECFFFHHGHGHJIGJIIJJJIHHGJIIHCJJIIIIJJIIJJIJIGJIHHJJJJJJJJJJJJJJJJIHHEJJJJGHHHHFFFFFCCC MD:Z:100 RG:Z:1 XG:i:0 NH:i:1 NM:i:0 XM:i:0 XN:i:0 XO:i:0 AS:i:0 YT:Z:UU
HWI-ST913:105:C0EYJACXX:5:1101:10000:112338 83 1 63990590 50 45M1I54M = 63990536 -153 GCAGAGACACCAGGTACTCCTCCTTTCTCATTCAAGGCTGGTATCTTTTTTTCTCTCCAGCAAGCTGCTCTGAAGCCAATGACCACCTTCTTTCTCAAGC BDDDDDDCCDDDDC?ADDDB?DDC@>DCEEECEEEFFFHHHHHHIJJJJIGGHGHFJJJJIJJGJIIIFJJJJJJJJJJJJHHHGIIHGHHHFFFFFCC@ MD:Z:23C75 RG:Z:1 XG:i:1 NH:i:1 NM:i:2 XM:i:1 XN:i:0 XO:i:1 AS:i:-13 XS:A:- YT:Z:UU
HWI-ST913:105:C0EYJACXX:5:1101:10000:112338 163 1 63990536 50 100M = 63990590 153 CCTGAGTCTAAGTCTGTTCAGTGAACCTGAGATGTGAATACAATGTGCTACTGAGCAGAGACACCAGGTACTCCTCCTTTCTCATTCAAGGCTGGTATCT @@CFFFDEHHHHHIIIJJJJJIIIIJJJJJIIJJGGIJJJJIJJJIJJJIGGGIIIIJIJJIJJJJIJCAHGHIJIJHHHHHHFFFFFFFEDEED;@CC@ MD:Z:77C22 RG:Z:1 XG:i:0 NH:i:1 NM:i:1 XM:i:1 XN:i:0 XO:i:0 AS:i:-5 XS:A:- YT:Z:UU
HWI-ST913:105:C0EYJACXX:5:1101:10000:131377 83 6 27265446 50 48M1064N52M = 27265379 -1231 TGGAAGAGTACAAGAAAACAATTGAGCGCAAGCAGCTAGGGCTGGAAGATGCTGAACAGGAATTATTCTCAGATGACGGTTCATCTGTGTCACAAATTCA DDDDDDFEDDDDDDDDEEEECCDEEHHIIIHIJJIIIGJJJJJIJJJJJJJIJIGHJJJJJIJJJJJJJJJJJJHHJIHIJJJJJJJHHHHFFFFFFCCC MD:Z:100 RG:Z:1 XG:i:0 NH:i:1 NM:i:0 XM:i:0 XN:i:0 XO:i:0 AS:i:0 XS:A:+ YT:Z:UU
HWI-ST913:105:C0EYJACXX:5:1101:10000:131377 163 6 27265379 50 100M = 27265446 1231 TTTGAAGATGATGAGCACGCGCCACCAGCACCACCCAACCCATTCAGCCATCTCACAGAAAAGGAACTGGAAGAGTACAAGAAAACAATTGAGCGCAAGC * MD:Z:100 RG:Z:1 XG:i:0 NH:i:1 NM:i:0 XM:i:0 XN:i:0 XO:i:0 AS:i:0 XS:A:+ YT:Z:UU
Thanks in advance
I am trying to run DEXSeq_count.py script and am running into problems. Here is the output. I had no problems before running HTseq. The alignments were done using Tophat 2.0.4 and samtools was used to convert to sam file format. Sort was used to sort the file and these are paired end reads. The sorted sam files were feed into dexseq_count.py. Few lines from the sam file as well are added.
python dexseq_count.py -p yes -s no Gallus_gallus.WASHUC2.67.gff /home/sudeep/work/6-20-12/layers/all_infected_bams/1_4I_accepted_hits_RG_sorted.sam /home/sudeep/work/6-20-12/layers/all_infected_bams/1_4I_count.txt
Traceback (most recent call last):
File "dexseq_count.py", line 132, in <module>
for af, ar in HTSeq.pair_SAM_alignments( HTSeq.SAM_Reader( sam_file ) ):
File "/usr/local/lib/python2.6/dist-packages/HTSeq-0.5.3p3-py2.6-linux-x86_64.egg/HTSeq/__init__.py", line 604, in pair_SAM_alignments
for almnt in alignments:
File "/usr/local/lib/python2.6/dist-packages/HTSeq-0.5.3p3-py2.6-linux-x86_64.egg/HTSeq/__init__.py", line 543, in __iter__
algnt = SAM_Alignment.from_SAM_line( line )
File "_HTSeq.pyx", line 1247, in HTSeq._HTSeq.SAM_Alignment.from_SAM_line (src/_HTSeq.c:21146)
File "_HTSeq.pyx", line 765, in HTSeq._HTSeq.SequenceWithQualities.__init__ (src/_HTSeq.c:13133)
ValueError: ("'seq' and 'qualstr' do not have the same length.", 'line 2 of file /home/sudeep/work/6-20-12/layers/all_infected_bams/1_4I_accepted_hits_RG_sorted.sam')
HWI-ST913:105:C0EYJACXX:5:1101:10000:100418 99 13 13229153 50 100M = 13229168 115 GATGTGAGCTGCAACACTGGCACAGTGTGAAGGATACCACCTGGTTCCCAGCCTTCTCCTGTCCCCGAAGACACCTCTCCCAGCACCCGCAGCAGCGATG CCCFFFFFHHHHHJJJJIJIJJJJJJIIJJJJJIJIIIIJJJJJIJJJJJJJJJJJJJJJJIJIJJIHHHFFFFDCDEDDDDDDDDDDDDDDDDDDDBD< MD:Z:100 RG:Z:1 XG:i:0 NH:i:1 NM:i:0 XM:i:0 XN:i:0 XO:i:0 AS:i:0 XS:A:+ YT:Z:UU
HWI-ST913:105:C0EYJACXX:5:1101:10000:100418 147 13 13229168 50 100M = 13229153 -115 ACTGGCACAGTGTGAAGGATACCACCTGGTTCCCAGCCTTCTCCTGTCCCCGAAGACACCTCTCCCAGCACCCGCAGCAGCGATGCAGAGACCACCCCTG * MD:Z:100 RG:Z:1 XG:i:0 NH:i:1 NM:i:0 XM:i:0 XN:i:0 XO:i:0 AS:i:0 XS:A:+ YT:Z:UU
HWI-ST913:105:C0EYJACXX:5:1101:10000:105912 99 5 13576179 50 52M241N48M = 13576221 383 GTCCTCCGCGCCTCTGCCGCTCACGCTGCTCTGCCAGCCCTCCCGGGCATCGCTGATCACTTTGGCTGCCCAAGCACCTCCAGGTCCTCTCCGAGCAGCA @@CDFFFFHDDFHGIIJJJGIIGIIIIEIIJIGHIGGFHIIIIJIHGFFFEBCBBDDDDCDDDCCCCD@18>A8<<CBDDDCC<:>CCCCCDBD>BDDBD MD:Z:24C75 RG:Z:1 XG:i:0 NH:i:1 NM:i:1 XM:i:1 XO:i:0 AS:i:-4 XS:A:-
HWI-ST913:105:C0EYJACXX:5:1101:10000:105912 147 5 13576221 50 10M241N90M = 13576179 -383 CCGGGCATCGCTGATCACTTTGGCTGCCCAAGCACCTCCAGGTCCTCTCCGAGCAGCATCGTAATTGCCACGAGCATGGAAATACTTGTCAGCACCAATG B>CC?5@DDDCC@EDC@DDDDDDDDDBDCECEBBFFHHHHGIHJIHHHJHJIHGGJIJJIIJJJIIJJIHIJJJJJJIJJJJGFJJIHHHDGFDFDF@<B MD:Z:100 RG:Z:1 XG:i:0 NH:i:1 NM:i:0 XM:i:0 XN:i:0 XO:i:0 AS:i:0 XS:A:- YT:Z:UU
HWI-ST913:105:C0EYJACXX:5:1101:10000:108641 99 14 4187451 50 100M = 4187485 134 CAGCCCGCTTGCTTGACAAACCAAAAAGGATCAAGTGTGTTTTGTTTTTAAGGCGGAAGATACAAAAAGACACTTGTTGGGTTACATAATTTACAGACAA CCCFFFFFHHHHHJJJJIJJJJJIJJJJIJIJIJJFGFHDGIIJGIJJJIFIIJIFFDDDDDDDDDDDDDDDCDDCCCDDD?BBCDEEDDEEDDCCDDDC MD:Z:100 RG:Z:1 XG:i:0 NH:i:1 NM:i:0 XM:i:0 XN:i:0 XO:i:0 AS:i:0 YT:Z:UU
HWI-ST913:105:C0EYJACXX:5:1101:10000:108641 147 14 4187485 50 100M = 4187451 -134 GTGTGTTTTGTTTTTAAGGCGGAAGATACAAAAAGACACTTGTTGGGTTACATAATTTACAGACAAGCAATTATCATCTAACACCAGTAATTGGTACCGG @BDDDDDDDDDEEEECFFFHHGHGHJIGJIIJJJIHHGJIIHCJJIIIIJJIIJJIJIGJIHHJJJJJJJJJJJJJJJJIHHEJJJJGHHHHFFFFFCCC MD:Z:100 RG:Z:1 XG:i:0 NH:i:1 NM:i:0 XM:i:0 XN:i:0 XO:i:0 AS:i:0 YT:Z:UU
HWI-ST913:105:C0EYJACXX:5:1101:10000:112338 83 1 63990590 50 45M1I54M = 63990536 -153 GCAGAGACACCAGGTACTCCTCCTTTCTCATTCAAGGCTGGTATCTTTTTTTCTCTCCAGCAAGCTGCTCTGAAGCCAATGACCACCTTCTTTCTCAAGC BDDDDDDCCDDDDC?ADDDB?DDC@>DCEEECEEEFFFHHHHHHIJJJJIGGHGHFJJJJIJJGJIIIFJJJJJJJJJJJJHHHGIIHGHHHFFFFFCC@ MD:Z:23C75 RG:Z:1 XG:i:1 NH:i:1 NM:i:2 XM:i:1 XN:i:0 XO:i:1 AS:i:-13 XS:A:- YT:Z:UU
HWI-ST913:105:C0EYJACXX:5:1101:10000:112338 163 1 63990536 50 100M = 63990590 153 CCTGAGTCTAAGTCTGTTCAGTGAACCTGAGATGTGAATACAATGTGCTACTGAGCAGAGACACCAGGTACTCCTCCTTTCTCATTCAAGGCTGGTATCT @@CFFFDEHHHHHIIIJJJJJIIIIJJJJJIIJJGGIJJJJIJJJIJJJIGGGIIIIJIJJIJJJJIJCAHGHIJIJHHHHHHFFFFFFFEDEED;@CC@ MD:Z:77C22 RG:Z:1 XG:i:0 NH:i:1 NM:i:1 XM:i:1 XN:i:0 XO:i:0 AS:i:-5 XS:A:- YT:Z:UU
HWI-ST913:105:C0EYJACXX:5:1101:10000:131377 83 6 27265446 50 48M1064N52M = 27265379 -1231 TGGAAGAGTACAAGAAAACAATTGAGCGCAAGCAGCTAGGGCTGGAAGATGCTGAACAGGAATTATTCTCAGATGACGGTTCATCTGTGTCACAAATTCA DDDDDDFEDDDDDDDDEEEECCDEEHHIIIHIJJIIIGJJJJJIJJJJJJJIJIGHJJJJJIJJJJJJJJJJJJHHJIHIJJJJJJJHHHHFFFFFFCCC MD:Z:100 RG:Z:1 XG:i:0 NH:i:1 NM:i:0 XM:i:0 XN:i:0 XO:i:0 AS:i:0 XS:A:+ YT:Z:UU
HWI-ST913:105:C0EYJACXX:5:1101:10000:131377 163 6 27265379 50 100M = 27265446 1231 TTTGAAGATGATGAGCACGCGCCACCAGCACCACCCAACCCATTCAGCCATCTCACAGAAAAGGAACTGGAAGAGTACAAGAAAACAATTGAGCGCAAGC * MD:Z:100 RG:Z:1 XG:i:0 NH:i:1 NM:i:0 XM:i:0 XN:i:0 XO:i:0 AS:i:0 XS:A:+ YT:Z:UU
Thanks in advance
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