`capmq -I cram,reference=reference.fa` fails if there is no internet connection
Opened this issue · 0 comments
ThomasHickman commented
[job capmq] /private/var/folders/5p/p6z8hhy174q_ctt3pn7mx5_c000h1t/T/tmpqi6kfkti$ docker \
run \
-i \
--volume=/private/var/folders/5p/p6z8hhy174q_ctt3pn7mx5_c000h1t/T/tmpqi6kfkti:/private/var/spool/cwl:rw \
--volume=/private/var/folders/5p/p6z8hhy174q_ctt3pn7mx5_c000h1t/T/tmp_9196g7n:/tmp:rw \
--volume=/Users/th10/checkouts/arvados-pipeline/arvados-pipelines/cwl/tests/cwl-example-data/chr22_cwl_test_1.cram:/private/var/lib/cwl/stg72d7999c-faa0-4505-9f60-4d7da1568e7c/chr22_cwl_test_1.cram:ro \
--volume=/Users/th10/checkouts/arvados-pipeline/arvados-pipelines/cwl/tests/cwl-example-data/chr22_cwl_test_1.cram.crai:/private/var/lib/cwl/stg72d7999c-faa0-4505-9f60-4d7da1568e7c/chr22_cwl_test_1.cram.crai:ro \
--volume=/private/var/folders/5p/p6z8hhy174q_ctt3pn7mx5_c000h1t/T/tmpmsioa0e0/caps_file:/private/var/lib/cwl/stgbb85097b-5acd-494e-9f93-f0523956d6d7/caps_file:ro \
--volume=/private/var/folders/5p/p6z8hhy174q_ctt3pn7mx5_c000h1t/T/tmpncytitgb/reference.fa:/private/var/lib/cwl/stg4f06bd0e-52b0-46fe-a924-375a147d01cc/reference.fa:ro \
--volume=/private/var/folders/5p/p6z8hhy174q_ctt3pn7mx5_c000h1t/T/tmpmkte7x03/reference.fa.fai:/private/var/lib/cwl/stg4f06bd0e-52b0-46fe-a924-375a147d01cc/reference.fa.fai:ro \
--volume=/private/var/folders/5p/p6z8hhy174q_ctt3pn7mx5_c000h1t/T/tmpmdmt03wl/reference.dict:/private/var/lib/cwl/stg4f06bd0e-52b0-46fe-a924-375a147d01cc/reference.dict:ro \
--workdir=/private/var/spool/cwl \
--read-only=true \
--user=16442:1312 \
--rm \
--env=TMPDIR=/tmp \
--env=HOME=/private/var/spool/cwl \
mercury/capmq:v1 \
capmq \
-G \
/private/var/lib/cwl/stgbb85097b-5acd-494e-9f93-f0523956d6d7/caps_file \
-I \
cram,reference=/private/var/lib/cwl/stg4f06bd0e-52b0-46fe-a924-375a147d01cc/reference.fa \
/private/var/lib/cwl/stg72d7999c-faa0-4505-9f60-4d7da1568e7c/chr22_cwl_test_1.cram \
chr22_cwl_test_1.cram
[E::cram_get_ref] Failed to populate reference for id 0
[E::cram_encode_container] Failed to load reference #0
Failed to write to output file
[job capmq] completed permanentFail
[step capmq] completed permanentFail
[workflow cap_crams] completed permanentFail
[step cap_crams] completed permanentFail