Try adding UROBORUS

[kopardev]

UROBORUS is a single perl script with uses

• output bam files from tophat

[kopardev]

tophat is very resource intensive ... provide large number of cpus!

[kopardev]

Observations:

• requires tophat to run the perl script
• requires bowtie1 in path module load tophat doesn't load bowtie1 properly... have to reload bowtie1 after loading tophat

  module load tophat
  module load bowtie/1.2.2

• requires bowtie1 index of the ref .... created!

[kopardev]

editing tophat like so https://groups.google.com/g/tuxedo-tools-users/c/vG5Rn0IgxoA/m/plOE89Yi55kJ to get around the bowtie1 error when run via tophat

[kopardev]

continue to get the error

[Thu Oct  6 10:58:56 2022] Preparing the reads..........finished!
[Thu Oct  6 11:00:33 2022] Now tophat..........
[2022-10-06 11:00:34] Beginning TopHat run (v2.1.2)
-----------------------------------------------
[2022-10-06 11:00:34] Checking for Bowtie
          Bowtie version:    1.2.2.0
[2022-10-06 11:00:34] Checking for Bowtie index files (genome)..
    Found both Bowtie1 and Bowtie2 indexes.
[2022-10-06 11:00:34] Checking for reference FASTA file
[2022-10-06 11:00:34] Generating SAM header for /data/Ziegelbauer_lab/circRNADetection/testing_092227/ref/ref
[2022-10-06 11:00:34] Preparing reads
     left reads: min. length=20, max. length=20, 21561293 kept reads (22809 discarded)
    right reads: min. length=20, max. length=20, 21486589 kept reads (97513 discarded)
Warning: you have only one segment per read.
    If the read length is greater than or equal to 45bp,
    we strongly recommend that you decrease --segment-length to about half the read length because TopHat will work better with multiple segments
[2022-10-06 11:03:21] Mapping left_kept_reads to genome ref with Bowtie
    [FAILED]
Error running bowtie:
Error while flushing and closing output
terminate called after throwing an instance of 'int'

finished!
[E::hts_open_format] Failed to open file "accepted_hits.bam" : No such file or directory
samtools view: failed to open "accepted_hits.bam" for reading: No such file or directory

[kopardev]

Keeps failing... DO NOT include in pipeline