{"action":"created","issue":{"url":"https://api.github.com/repos/jdidion/atropos/issues/62","repository_url":"https://api.github.com/repos/jdidion/atropos","labels_url":"https://api.github.com/repos/jdidion/atropos/issues/62/labels{/name}","comments_url":"https://api.github.com/repos/jdidion/atropos/issues/62/comments","events_url":"https://api.github.com/repos/jdidion/atropos/issues/62/events","html_url":"https://github.com/jdidion/atropos/issues/62","id":305411130,"number":62,"title":"gzip process returned non-zero exit code -15","user":{"login":"gmagoon","id":94181,"avatar_url":"https://avatars2.githubusercontent.com/u/94181?v=4","gravatar_id":"","url":"https://api.github.com/users/gmagoon","html_url":"https://github.com/gmagoon","followers_url":"https://api.github.com/users/gmagoon/followers","following_url":"https://api.github.com/users/gmagoon/following{/other_user}","gists_url":"https://api.github.com/users/gmagoon/gists{/gist_id}","starred_url":"https://api.github.com/users/gmagoon/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/gmagoon/subscriptions","organizations_url":"https://api.github.com/users/gmagoon/orgs","repos_url":"https://api.github.com/users/gmagoon/repos","events_url":"https://api.github.com/users/gmagoon/events{/privacy}","received_events_url":"https://api.github.com/users/gmagoon/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":2,"created_at":"2018-03-15T04:22:57Z","updated_at":"2018-03-16T16:54:16Z","closed_at":null,"author_association":"NONE","body":"Hi John,\r\nI've just set up Atropos v. 1.1.17 on Ubuntu 16.04 via `pip3 install atropos`. I'm encountering issues like shown below when running basic commands with the `error` and `detect` modules. I've checked the input files with`gzip -t` and `gzip -l` and no problems show up (other than the known issue for the latter with files above 4GB). I've tried several fastq pairs and encountered the same error. Am I correct in suspecting that the -15 exit code corresponds to termination via SIGTERM? And if so, does this necessarily indicate a problem, if, for example, the termination signal came from atropos? I'm probably overlooking something that should be obvious, since it doesn't look like anyone else has reported seeing this error. Thanks in advance for any tips you can provide,\r\nGreg\r\n\r\n> ~$ atropos error -pe1 R1_001.fastq.gz -pe2 R2_001.fastq.gz \r\n> 2018-03-14 23:26:24,086 INFO: This is Atropos 1.1.17 with Python 3.5.2\r\n> 2018-03-14 23:26:28,428 ERROR: Atropos error\r\n> Traceback (most recent call last):\r\n>   File \"/home/gmagoon/.local/lib/python3.5/site-packages/atropos/util/__init__.py\", line 727, in run_interruptible\r\n>     func(*args, **kwargs)\r\n>   File \"/home/gmagoon/.local/lib/python3.5/site-packages/atropos/commands/base.py\", line 22, in __call__\r\n>     for batch in command_runner.iterator():\r\n>   File \"/home/gmagoon/.local/lib/python3.5/site-packages/atropos/commands/base.py\", line 290, in __next__\r\n>     self.finish()\r\n>   File \"/home/gmagoon/.local/lib/python3.5/site-packages/atropos/commands/base.py\", line 358, in finish\r\n>     self.reader.close()\r\n>   File \"/home/gmagoon/.local/lib/python3.5/site-packages/atropos/io/seqio.py\", line 463, in close\r\n>     self.reader1.close()\r\n>   File \"/home/gmagoon/.local/lib/python3.5/site-packages/atropos/io/seqio.py\", line 92, in close\r\n>     self._file.close()\r\n>   File \"/home/gmagoon/.local/lib/python3.5/site-packages/atropos/io/compression.py\", line 105, in close\r\n>     self._raise_if_error()\r\n>   File \"/home/gmagoon/.local/lib/python3.5/site-packages/atropos/io/compression.py\", line 121, in _raise_if_error\r\n>     \"input file truncated or corrupt?\".format(retcode))\r\n> EOFError: gzip process returned non-zero exit code -15. Is the input file truncated or corrupt?\r\n"},"comment":{"url":"https://api.github.com/repos/jdidion/atropos/issues/comments/373776874","html_url":"https://github.com/jdidion/atropos/issues/62#issuecomment-373776874","issue_url":"https://api.github.com/repos/jdidion/atropos/issues/62","id":373776874,"user":{"login":"jdidion","id":125854,"avatar_url":"https://avatars3.githubusercontent.com/u/125854?v=4","gravatar_id":"","url":"https://api.github.com/users/jdidion","html_url":"https://github.com/jdidion","followers_url":"https://api.github.com/users/jdidion/followers","following_url":"https://api.github.com/users/jdidion/following{/other_user}","gists_url":"https://api.github.com/users/jdidion/gists{/gist_id}","starred_url":"https://api.github.com/users/jdidion/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jdidion/subscriptions","organizations_url":"https://api.github.com/users/jdidion/orgs","repos_url":"https://api.github.com/users/jdidion/repos","events_url":"https://api.github.com/users/jdidion/events{/privacy}","received_events_url":"https://api.github.com/users/jdidion/received_events","type":"User","site_admin":false},"created_at":"2018-03-16T16:54:16Z","updated_at":"2018-03-16T16:54:16Z","author_association":"OWNER","body":"Thanks for reporting this. As you've probably figured out, Atropos tries to use system gzip for compression when available, because it's much faster than using the python gzip module. However, there should probably be a way to turn off this behavior when it causes problems like what you observe. I am going to update this issue to be a request for this enhancement."}}
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