SRST2 munges sample identifiers?

[hexylena]

I'm looking at a run of PHAC's SRST2 wrapper:

/srv/galaxy/var/shed_tools/toolshed.g2.bx.psu.edu/repos/nml/srst2/e59fdf6145db/srst2/srst2.pl /data/galaxy/jobs/020/20188/outputs/dataset_cef3ef2e-e010-4768-b36b-1de43d89b28f.dat /data/galaxy/jobs/020/20188/outputs/dataset_582ba0b2-a2eb-4918-a8b2-9f300b6f212a.dat /data/galaxy/jobs/020/20188/outputs/dataset_d6eec7c7-a2c9-4bcd-a919-63b192c9935e.dat  g /data/galaxy/jobs/020/20188/outputs/dataset_14d30ba8-5d8d-4237-a672-243227aac1d7.dat /data/galaxy/jobs/020/20188/outputs/dataset_473b25c9-757c-4a56-8170-df8add14378b.dat \
"ResFinder.fasta,ARGannot_r2.fasta"  \
"SRX6855211_SRR10127028_1.fastq uncompressed" \
--input_pe "/data/galaxy/f/e/1/dataset_fe1245a6-287d-4732-af60-37021f7eaab1.dat" \
"/data/galaxy/5/6/e/dataset_56eedb18-918a-4c26-a5db-f3504dd763c2.dat" \
 --gene_db /data/galaxy/1/6/2/dataset_162c6169-c72f-4f07-a99d-dfd15075ab8e.dat /data/galaxy/5/6/d/dataset_56da7859-6beb-47cd-b701-3b9bcae0e427.dat \
--gene_max_mismatch 250  --read_type q  --save_scores  --other "'-p ${GALAXY_SLOTS:-1}'"  --output ${PWD}/out

(line breaks manually inserted for clarity)

However the output sample table has only part of the sample identifier:

Column 1	Column 2	Column 3	Column 4	Column 5	Column 6	Column 7	Column 8	Column 9	Column 10	Column 11	Column 12	Column 13	Column 14
Sample	DB	gene	allele	coverage	depth	diffs	uncertainty	divergence	length	maxMAF	clusterid	seqid	annotation
SRX6855211	ARGannot_r2	AmpC2_Ecoli_Bla	AmpC2_346	99.735	86.838	22snp3indel		1.94	1134	0.091	99	346	no;no;AmpC2;Bla;CP002970;332756-333889;1134
SRX6855211	ARGannot_r2	MrdA_Bla	MrdA_836	100.0	66.382	25snp		1.314	1902	0.143	16	836	no;no;MrdA;Bla;CP002291;666340-664439;1902
SRX6855211	ARGannot_r2	MphA_MLS	MphA_1663	100.0	69.11			0.0	906	0.096	158	1663	no;no;MphA;MLS;KR091911;890-1795;906
SRX6855211	ARGannot_r2	CTX-M-9_Bla	CTX-M-27_109	100.0	60.304			0.0	876	0.078	190	109	no;no;CTX-M-27;Bla;AY156923;1-876;876

which means I can't match them back up with their input sample once they've gone through hamronize (which I really love.)