pipeline should try to keep going after problem with walkin keyfile

[afmcc]

see example below , should be a warning not a fatal error

checking if run is in the database...

240109_A01439_0232_AHNGHFDRX3 is not in the database - will generate keyfiles and set up run in the database first. About to execute

gupdate --explain -t create_gbs_keyfiles -p "fastq_folder_root=/dataset/2023_illumina_sequencing_c/scratch/postprocessing/illumina/novaseq;run_folder_root=/dataset/2023_illumina_sequencing_c/active;out_folder=/dataset/hiseq/active/key-files;sample_sheet=/dataset/2023_illumina_sequencing_c/active/240109_A01439_0232_AHNGHFDRX3/SampleSheet.csv;import" all

OK ? (y/n, default = y)

Default response: y
backing up GBS tables using psql -U agrbrdf -d agrbrdf -h postgres -f dump_gbs_tables.psql
running gupdate --explain -t create_gbs_keyfiles -p "fastq_folder_root=/dataset/2023_illumina_sequencing_c/scratch/postprocessing/illumina/novaseq;run_folder_root=/dataset/2023_illumina_sequencing_c/active;out_folder=/dataset/hiseq/active/key-files;sample_sheet=/dataset/2023_illumina_sequencing_c/active/240109_A01439_0232_AHNGHFDRX3/SampleSheet.csv;import" all

#!!!!!!
# oops something went wrong :(
# The original exeption encountered is below. To help debug the
# problem, a log of this session is here :
# /dataset/genophyle_data/scratch/gupdate/all-job.7.log
#!!!****!!!

Traceback (most recent call last):
File "/dataset/gseq_processing/active/bin/gquery/gupdate.py", line 378, in
sys.exit(main())
File "/dataset/gseq_processing/active/bin/gquery/gupdate.py", line 324, in main
illumina.illumina(s).create_gbs_keyfiles()
File "/bifo/active/gseq_processing/bin/gquery/sequencing/illumina.py", line 127, in create_gbs_keyfiles
platform.create_gbs_keyfiles()
File "/bifo/active/gseq_processing/bin/gquery/sequencing/illumina.py", line 1685, in create_gbs_keyfiles
columns=self.create_gbs_keyfile(parameters_dict, key_path, append = False)
File "/bifo/active/gseq_processing/bin/gquery/sequencing/illumina.py", line 1726, in create_gbs_keyfile
walkin_columns = self.create_or_append_external_gbs_keyfile(predicates, key_path, append_existing)
File "/bifo/active/gseq_processing/bin/gquery/sequencing/illumina.py", line 1771, in create_or_append_external_gbs_keyfile
( get_predicate("walkins_file"), len(walkin_columns),len(fields)))
sequencing.illumina.illumina_sequencing_exception: number of fields in in header of walkins file /dataset/hiseq/active/key-files/SQ3047.txt (15) is not always the same as in the rest of the file (27)

sorry - quitting after received bad return code from database import -try looking at the log file shown above