ecopcr fails unexpectedly
I have been following the tutorial here and downloaded about 20M reads from the EMBL database. (all files matching _std_ and any of the following _fun_|_inv_|_mam_|_phg_|_pln_|_pro_|_rod_|_vrl_|_vrt_)
After importing all files with
obi import --embl /Volumes/Elements/EMBL /Volumes/Elements/EMBL_dms/EMBL_ref
and importing the taxdump with
obi import --taxdump /Volumes/Elements/taxdump.tar.gz /Volumes/Elements/EMBL_dms/taxonomy/my_tax
I now want to run ecopcr using the following command:
obi ecopcr -e 5 -l 400 -L 500 -F CCHGAYATRGCHTTYCCHCG -R TCDGGRTGNCCRAARAAYCA --taxonomy /Volumes/Elements/EMBL_dms/taxonomy/my_tax /Volumes/Elements/EMBL_dms/EMBL_ref /Volumes/Elements/EMBL_dms/COI_BF3_BR2_refs
It starts out fine but always fails at exactly 10.680869 %. I tried running only the first 5% of sequences with --only 1000000 but it still fails at the same point.
Output:
2020-04-08 22:03:54,811 [ecopcr : INFO ] obi ecopcr Reading 2238873 taxa... No local taxa Done : 10.680869 % DEBUG /Applications/OBITools/obitools3/src/obi_ecopcr.c:438:print_seq, obi_errno = 0, errno = 2 : Error reading the taxonomic information of a sequence DEBUG /Applications/OBITools/obitools3/src/obi_ecopcr.c:1095:obi_ecopcr, obi_errno = 0, errno = 2 : Error writing the ecopcr result Traceback (most recent call last): File "/Applications/OBITools/obitools3/obi3-env/bin/obi", line 62, in <module> config[root_config_name]['module'].run(config) File "python/obitools3/commands/ecopcr.pyx", line 195, in obitools3.commands.ecopcr.run Exception: Error running ecopcr
I am running OBITools3 on a MacBook pro with 16 GB Memory under macOS Catalina V 10.15. The Volumes/Elements path directs to an external HDD hard-drive with >500 GB of free space.
Any help on debugging this error is greatly appreciated!