[External] [Bug] Docker profile bug for submission

[kyleoconnell]

Ran on this branch: docker_testing_kao
Ran this command:
nextflow run main.nf -profile test,docker --species virus --annotation true --submission true --output_dir test --submission_config $Config_Path -resume

Got this output:

executor > local (5)
[cf/89df1e] process > TOSTADAS_WORKFLOW:TOSTADAS:VALIDATE_PARAMS [100%] 1 of 1, cached: 1 ✔
[d4/533f7f] process > TOSTADAS_WORKFLOW:TOSTADAS:METADATA_VALIDATION [100%] 1 of 1, cached: 1 ✔
[84/d0d234] process > TOSTADAS_WORKFLOW:TOSTADAS:REPEATMASKER_LIFTOFF:REPEA... [100%] 5 of 5, cached: 5 ✔
[c6/0c589a] process > TOSTADAS_WORKFLOW:TOSTADAS:REPEATMASKER_LIFTOFF:LIFTO... [100%] 5 of 5, cached: 5 ✔
[19/509f1b] process > TOSTADAS_WORKFLOW:TOSTADAS:REPEATMASKER_LIFTOFF:CONCA... [100%] 5 of 5, cached: 5 ✔
[27/595fc5] process > TOSTADAS_WORKFLOW:TOSTADAS:GET_WAIT_TIME [100%] 1 of 1, cached: 1 ✔
executor > local (5)
[cf/89df1e] process > TOSTADAS_WORKFLOW:TOSTADAS:VALIDATE_PARAMS [100%] 1 of 1, cached: 1 ✔
[d4/533f7f] process > TOSTADAS_WORKFLOW:TOSTADAS:METADATA_VALIDATION [100%] 1 of 1, cached: 1 ✔
[84/d0d234] process > TOSTADAS_WORKFLOW:TOSTADAS:REPEATMASKER_LIFTOFF:REPEA... [100%] 5 of 5, cached: 5 ✔
[c6/0c589a] process > TOSTADAS_WORKFLOW:TOSTADAS:REPEATMASKER_LIFTOFF:LIFTO... [100%] 5 of 5, cached: 5 ✔
[19/509f1b] process > TOSTADAS_WORKFLOW:TOSTADAS:REPEATMASKER_LIFTOFF:CONCA... [100%] 5 of 5, cached: 5 ✔
[27/595fc5] process > TOSTADAS_WORKFLOW:TOSTADAS:GET_WAIT_TIME [100%] 1 of 1, cached: 1 ✔[52/55a1d2] process > TOSTADAS_WORKFLOW:TOSTADAS:INITIAL_SUBMISSION:SUBMISS... [100%] 1 of 1, failed: 1
[- ] process > TOSTADAS_WORKFLOW:TOSTADAS:INITIAL_SUBMISSION:WAIT -
[- ] process > TOSTADAS_WORKFLOW:TOSTADAS:INITIAL_SUBMISSION:UPDATE_... -
ERROR ~ Error executing process > 'TOSTADAS_WORKFLOW:TOSTADAS:INITIAL_SUBMISSION:SUBMISSION (5)'
Caused by: Process TOSTADAS_WORKFLOW:TOSTADAS:INITIAL_SUBMISSION:SUBMISSION (5) terminated with an error exit status (1)

Command executed:

submission_new.py --submit --submission_name TX0001 --config_file submission_config.yaml --metadata_file TX0001.tsv --species virus --output_dir . --fasta_file TX0001.fasta --annotation_file TX0001_reformatted.gff --fastq1 2022-034-7690_S9_L001_R1_001.fastq.gz --fastq2 2022-034-7690_S9_L001_R2_001.fastq.gz --submission_mode ftp --test --genbank --sra --biosample

Command exit status:
1

Command output:
(empty)

Command error:
Traceback (most recent call last):
File "bin/submission_new.py", line 20, in from nameparser import HumanName
ModuleNotFoundError: No module named 'nameparser'

Work dir:
tostadas/work/dd/f1f5a126e732ccbd18501dc5f451c3

Tip: view the complete command output by changing to the process work dir and entering the command cat .command.out

-- Check '.nextflow.log' file for details

[kyleoconnell]

issue with container, resolved when updated local container