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find_circ.py show error #14

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aman21392 opened this issue Jun 24, 2020 · 1 comment
Open

find_circ.py show error #14

aman21392 opened this issue Jun 24, 2020 · 1 comment

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@aman21392
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bowtie2 -q -U unmapped.fastq -x /Drive1/find_circ/index/bow2_homo --reorder --mm --very-sensitive --score-min=C,-15,0 | /home/aclab/apps/find_circ/find_circ.py -G /home/aclab/homo.fa -p homo --stats homo_sites.log --reads homo.fa >homo.bed
[E::sam_parse1] query name too long
[W::sam_read1] Parse error at line 643
Traceback (most recent call last):
File "/home/aclab/apps/find_circ/find_circ.py", line 705, in
sam_line = pair_num * 2
NameError: name 'pair_num' is not defined

""I used single read fastq file and it varies in length and the unmapped fastq file look like::
bf0c7879-f557-4fd4-bbfa-2e789855dc27_A__TTTGACCAAGAAGAGATACGGTGCTTCTGCCGGTAACGTCGGTGACGAAGGTGGTGTTGCTCCAAACATTCAAACCGCTGAAGAAGCTTGGACTTGATTGTTGACGCCATCAAGGCTGCTGGTCACGACGGTAAGGTCAAGATCGGTTTGGACTGTGCTCTGAATTCTTCAAGGACGGTAAGTACGACTTGGACTTAGAACCCAGAATCTGACAAATCCAAGTGGTTGACTGGTGTCGAATTGGCTAGACATGTACCGCCTTGATGAAGAGATACCCAATTGTCTCCATCGAAGATCCATTTGCTGAAAGATGACTGGGAAGCTTGGGTCTCACTTCAAGACCGCTGGTATCCAAATTGTTGCTGATGACTTGACTGTCACCAACCCAGCTAGAATTATACCGCCATCGAAAGAAGGCTGCTGACGCTTTGGTTAGCGTTGAAGGTTAACCAAATCGGTACCTTGTCTGAATCCATCAAGGCTGCTCAAGACTTCGCAGCCAACTGGGTGTCATGGTTTCCCACAGATCTGGCTGAAACTGAAGACACTTTCTCATTGCTGACTTGGTTGTCGGTTTGAAGAACTGGTCAAATCAAGACTGGTGCTCCAGCTAGATCCGAAAGATTGGCTAAGTTGAACCAATTGTTGAGAATCGAAGAAGAATTGGGTGACAAGGCTGTCTATGCCGGTAG
TTTGACCAAGAAGAGATACG
+
($(<78<?FBFK=$'0
@bf0c7879-f557-4fd4-bbfa-2e789855dc27_B
AAGGCTGTCTATGCCGGTAG
+
??86*+6,(*((0217:'$.
837dd288-73fd-40ab-9acb-4e3a455c0562_A__AATTCATGATTGCCTTAACTGGTGCTAAGACCTCTGAAGCCAAAGAATTGGTTCCGGTTTACCACAACTTGAAGTCTTTGACCAAGAAGAGATTCGGTGCTTCTGCCGGTAACGTCGGTGACGAAGGTGGTGTTGCTCCAAACATTCAAACCGCTGAAGAAGCTTTGGACTTGATTGTTGACGCTATCAAGGCTGCTGGTCACACGGTAAGGTCAAGATCGGTTTGGACTGTGCCACCTTGAATTCAAGGACGGTAAGTACGACTTGGACTCAAGAACCCAGAAATCTGACAAATCCAAGTGGTTGACTGGTGTCGAATTGGCTGACATGTACCATTTCCTTGATGAAGAGATACTCAATTGTCTCCATCGAAGATCCATTTGCTGAAGATGACTGGGAAGCTTGGTCTCATTTTCAAGACCGTTGGTATCCAAATATCGTTGATGACTTGACTGTCACCATTCCCGGCTAGAATTCGCCAAAGAAGGCTGCTGACGCTTTGTTGTTGAAGTTAACCAATTCAAGTACCTTGTCTGAAACCCATCAAGGCTGCTCAAGACTCATTGCCAACTTGGGGTGTCATGGTTTCCCACAGATCTGGTGAAAACTGAAGACTTCATTGCTGACTTGGTTGTCGGTTTGAGAACGGTCAAATCAAGACTGGTGCTCCAGCTAGATCCGAAAAGATTGGCTAAGTTGAACCAATTGTGAGAATCGAAGAAGAATTGGGTGACAAGGCTGTCTACGCCGGTG
AATTCATGATTGCCTTAACT

So plz can you tell me is it possible to run find_circ on this fastq file. If yes then please suggest me.
Thanks in advance

@mschilli87
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@aman21392: I'd suggest you have a look at https://github.com/rajewsky-lab/find_circ2 and if you have issues with this version, open a new issue there. Also, make sure to include what operating system you are on and how you installed the software if you want people to be able to help you.

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