ss1 < ss2 #596
Description
Hi developers,
I encountered problems when I was running flair transcriptome with commands:
flair transcriptome
-o temp1
-g $ref_fa
-t $ppn
-f $annot_gtf
-b alignment_minimap2_chopper_sorted.bam
I got error report as below:
done running chunk 1251 of 1520
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "/public/home/hesang/miniconda3/envs/flair/lib/python3.12/multiprocessing/pool.py", line 125, in worker
result = (True, func(*args, **kwds))
^^^^^^^^^^^^^^^^^^^
File "/public/home/hesang/flair-master/src/flair/flair_transcriptome.py", line 1055, in runcollapsebychrom
sjtoends = filtercorrectgroupreads(args, tempprefix, rchrom, rstart, rend, samfile, goodaligntoannot, intervalTree,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/public/home/hesang/flair-master/src/flair/flair_transcriptome.py", line 636, in filtercorrectgroupreads
correctedread = correctsingleread(bedread, intervalTree, junctionBoundaryDict)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/public/home/hesang/flair-master/src/flair/flair_transcriptome.py", line 240, in correctsingleread
blocks, sizes, starts = juncsToBed12(bedread.name, bedread.start, bedread.end, newJuncs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/public/home/hesang/flair-master/src/flair/ssPrep.py", line 168, in juncsToBed12
assert ss1 < ss2
^^^^^^^^^
AssertionError
"""
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/public/home/hesang/flair-master/src/flair/flair_cli.py", line 85, in main
flair_module_run(opts, args.module, args.module_args)
File "/public/home/hesang/flair-master/src/flair/flair_cli.py", line 55, in flair_module_run
collapsefrombam()
File "/public/home/hesang/flair-master/src/flair/flair_transcriptome.py", line 1139, in collapsefrombam
for i in p.imap(runcollapsebychrom, chunkcmds):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/public/home/hesang/miniconda3/envs/flair/lib/python3.12/multiprocessing/pool.py", line 873, in next
raise value
AssertionError
when I was adding some optional parameters:
flair transcriptome
-o temp1
-g $ref_fa
-t $ppn
-f $annot_gtf
--stringent
--check_splice
--predictCDS
-b alignment_minimap2_chopper_sorted.bam
I got one more error:
Exception ignored in: <function Pool.del at 0x2b25fa70e0c0>
Traceback (most recent call last):
File "/public/home/hesang/miniconda3/envs/flair/lib/python3.12/multiprocessing/pool.py", line 271, in del
self._change_notifier.put(None)
File "/public/home/hesang/miniconda3/envs/flair/lib/python3.12/multiprocessing/queues.py", line 399, in put
self._writer.send_bytes(obj)
File "/public/home/hesang/miniconda3/envs/flair/lib/python3.12/multiprocessing/connection.py", line 200, in send_bytes
self._send_bytes(m[offset:offset + size])
File "/public/home/hesang/miniconda3/envs/flair/lib/python3.12/multiprocessing/connection.py", line 427, in _send_bytes
self._send(header + buf)
File "/public/home/hesang/miniconda3/envs/flair/lib/python3.12/multiprocessing/connection.py", line 384, in _send
n = write(self._handle, buf)
^^^^^^^^^^^^^^^^^^^^^^^^
OSError: [Errno 9] Bad file descriptor
Here is the last chunk bed file:
9 3378206 3379847 ENSSSCT00000015984_ENSSSCG00000014633 13 + 3378206 3379847 0 2 454,628 0,1013
9 4157289 4170233 TCONS_01911742_ENSSSCG00000014670 63 - 4157289 4170233 0 8 1453,27,101,23,231,96,476,179 0,1669,1971,3306,6260,7125,8079,12765
9 4800292 4802364 ENSSSCT00000081549_ENSSSCG00000014725 1197351 - 4800292 4802364 0 3 519,223,567 0,1165,1505
9 4808578 4809853 ENSSSCT00000016078_ENSSSCG00000014727 7 - 4808578 4809853 0 4 9,117,223,144 0,12,780,1131
9 4817747 4820243 ENSSSCT00000016077_ENSSSCG00000014726 43 - 4817747 4820243 0 3 587,223,145 0,2025,2351
Do you have any clues? Thanks.
p.s. I git cloned the current repository from Github and use pip to install. Version is 2.2. All modules were available.