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psathyrella / partis

B- and T-cell receptor sequence annotation, simulation, clonal family and germline inference, and affinity prediction
GNU General Public License v3.0
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ig-sw binary d.n.e #241

Closed ecudone closed 6 years ago

ecudone commented 6 years ago

Ran this annotation query, but ran into an issue where it seems a file, "ig-sw binary" does not exis. I uninsulated and reinstalled for sanity sake and got the same issue. I looked through the files and couldn't find any /partis/packages/ig-sw/src/ig_align/ig-sw file, so it appears to be missing.

root@5884105ead26:/partis# ./bin/partis annotate --infname /host/NE2_3.fa --outfname /host/NE2_3_annotated.csv

caching parameters vsearch: 3658 v annotations in 0.3 sec keeping 60 / 239 v genes smith-waterman Traceback (most recent call last): File "./bin/partis", line 597, in args.func(args) File "./bin/partis", line 185, in run_partitiondriver parter.cache_parameters() File "/partis/python/partitiondriver.py", line 247, in cache_parameters self.run_waterer() File "/partis/python/partitiondriver.py", line 153, in run_waterer simglfo=self.simglfo, duplicates=self.duplicates, pre_failed_queries=pre_failed_queries, aligned_gl_seqs=self.aligned_gl_seqs) File "/partis/python/waterer.py", line 74, in init raise Exception('ig-sw binary d.n.e: %s' % self.args.ig_sw_binary) Exception: ig-sw binary d.n.e: /partis/packages/ig-sw/src/ig_align/ig-sw Traceback (most recent call last): File "./bin/partis", line 597, in args.func(args) File "./bin/partis", line 198, in run_partitiondriver check_call(newargv) File "/usr/local/lib/python2.7/subprocess.py", line 540, in check_call raise CalledProcessError(retcode, cmd) CalledProcessError: Command '['./bin/partis', 'cache-parameters', '--infname', '/host/NE2_3.fa', '--outfname', '/host/NE2_3_annotated.csv']' returned non-zero exit status 1

psathyrella commented 6 years ago

hm, did you compile by running ./bin/build.sh first?