find_circ.py show error

[aman21392]

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 + ($(<78<?F<BB>BFK=$'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]

@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.