Segmentation Fault After Closing SequenceReader · Issue #88 · jdidion/atropos (original) (raw)

I cannot reliably reproduce this error, but I have been getting segmentation faults every now and then on single-end adapter-match and paired-end insert-match trimming. Upon adding faulthandler.enable() to atropos/commands/__init__.py I was able to get this output after a couple reruns of the following command (using a self-built docker image w/ a ubuntu 16.04 base on an ec2 instance with 32 cpus). I hope this information is still useful to have on hand despite the absence of the docker image and input files used (I've left off the -o, -p, -pe1, and -pe2 args).

/usr/local/bin/atropos trim \
       -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA \
       -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT \
       --no-cache-adapters \
       --no-default-adapters \
       -T 32 \
       --aligner insert \
       --preserve-order

The trace indicates the error is occurring here: https://github.com/jdidion/atropos/blob/1.1/atropos/io/seqio.py#L93

        stderr:
            Fatal Python error: Segmentation fault

            Thread 0x00007fd7bb834700 (most recent call first):
              File "/usr/lib/python3.5/threading.py", line 293 in wait
              File "/usr/lib/python3.5/multiprocessing/queues.py", line 229 in _feed
              File "/usr/lib/python3.5/threading.py", line 862 in run
              File "/usr/lib/python3.5/threading.py", line 914 in _bootstrap_inner
              File "/usr/lib/python3.5/threading.py", line 882 in _bootstrap

            Current thread 0x00007fd7bf81b700 (most recent call first):
              File "/usr/local/lib/python3.5/dist-packages/atropos-1.1.21-py3.5-linux-x86_64.egg/atropos/io/seqio.py", line 93 in close
              File "/usr/local/lib/python3.5/dist-packages/atropos-1.1.21-py3.5-linux-x86_64.egg/atropos/io/seqio.py", line 463 in close
              File "/usr/local/lib/python3.5/dist-packages/atropos-1.1.21-py3.5-linux-x86_64.egg/atropos/commands/base.py", line 358 in finish
              File "/usr/local/lib/python3.5/dist-packages/atropos-1.1.21-py3.5-linux-x86_64.egg/atropos/commands/base.py", line 283 in __next__
              File "/usr/local/lib/python3.5/dist-packages/atropos-1.1.21-py3.5-linux-x86_64.egg/atropos/commands/multicore.py", line 507 in enqueue_all
              File "/usr/local/lib/python3.5/dist-packages/atropos-1.1.21-py3.5-linux-x86_64.egg/atropos/commands/multicore.py", line 291 in __call__
              File "/usr/local/lib/python3.5/dist-packages/atropos-1.1.21-py3.5-linux-x86_64.egg/atropos/util/__init__.py", line 727 in run_interruptible
              File "/usr/local/lib/python3.5/dist-packages/atropos-1.1.21-py3.5-linux-x86_64.egg/atropos/commands/multicore.py", line 267 in run
              File "/usr/local/lib/python3.5/dist-packages/atropos-1.1.21-py3.5-linux-x86_64.egg/atropos/commands/trim/__init__.py", line 719 in run_parallel
              File "/usr/local/lib/python3.5/dist-packages/atropos-1.1.21-py3.5-linux-x86_64.egg/atropos/commands/trim/__init__.py", line 598 in __call__
              File "/usr/local/lib/python3.5/dist-packages/atropos-1.1.21-py3.5-linux-x86_64.egg/atropos/commands/base.py", line 332 in run
              File "/usr/local/lib/python3.5/dist-packages/atropos-1.1.21-py3.5-linux-x86_64.egg/atropos/commands/__init__.py", line 136 in run_command
              File "/usr/local/lib/python3.5/dist-packages/atropos-1.1.21-py3.5-linux-x86_64.egg/atropos/commands/__init__.py", line 71 in execute
              File "/usr/local/lib/python3.5/dist-packages/atropos-1.1.21-py3.5-linux-x86_64.egg/atropos/commands/__init__.py", line 219 in execute_cli
              File "/usr/local/lib/python3.5/dist-packages/atropos-1.1.21-py3.5-linux-x86_64.egg/EGG-INFO/scripts/atropos", line 23 in main
              File "/usr/local/lib/python3.5/dist-packages/atropos-1.1.21-py3.5-linux-x86_64.egg/EGG-INFO/scripts/atropos", line 26 in <module>
              File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line 1504 in run_script
              File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line 719 in run_script
              File "/usr/local/bin/atropos", line 4 in <module>