find_circ - test data error

Question

[anba]

Hi,

I'm trying to identify circRNA from RNA-seq data using find_circ tool. I have cloned repository and started the test data analysis. Error is below:

[E::hts_open_format] Failed to open file cdr1as_test.bam
samtools view: failed to open "cdr1as_test.bam" for reading: No such file or directory
Traceback (most recent call last):
  File "../unmapped2anchors.py", line 232, in <module>
    for read in pysam.Samfile(args[0],'rb'):
  File "pysam/libcalignmentfile.pyx", line 729, in pysam.libcalignmentfile.AlignmentFile.__cinit__
  File "pysam/libcalignmentfile.pyx", line 969, in pysam.libcalignmentfile.AlignmentFile._open
**ValueError: file has no sequences defined (mode='rb') - is it SAM/BAM format? Consider opening with check_sq=False
make: *** [anchors_cdr1as_test.fastq] Error 1
make: *** Deleting file 'anchors_cdr1as_test.fastq'**

All dependencies are installed correctly. What means the lowest bolded lines (the same error is when I was trying to analyse my own data).

best, anna

[Pierre Lindenbaum]

what is the output of

file cdr1as_test.bam

and

find . -type f -name "cdr1as_test.bam"

[anba]

first file command gives

cdr1as_test.bam: gzip compressed data, extra field

the output of find command is

./cdr1as_test.bam

[sh.ranjbar00]

Hi Anna I have exactly the same problem as you. Have you found any answer?