ncsa/Swift-T-Variant-Calling

Spacing problem in tmp timing logs

Closed this issue · 1 comments

When looking at the tmp/timing.logs I noticed that there is an issue with spacing

Here is an example

SRR1303883	ALL	NOVOSORT start	1511291146DedupSort
SRR1303883	ALL	NOVOSORT end	1511291286DedupSort
SRR1335748	ALL	NOVOSORT start	1511291146DedupSort
SRR1335748	ALL	NOVOSORT end	1511291268DedupSort
SRR1362011	ALL	NOVOSORT start	1511291146DedupSort
SRR1362011	ALL	NOVOSORT end	1511291298DedupSort
SRR1369398	ALL	NOVOSORT start	1511291146DedupSort
SRR1369398	ALL	NOVOSORT end	1511291322DedupSort
SRR1383541	ALL	NOVOSORT start	1511291146DedupSort
SRR1383541	ALL	NOVOSORT end	1511291319DedupSort
SRR1403775	ALL	NOVOSORT start	1511291146DedupSort
SRR1403775	ALL	NOVOSORT end	1511291310DedupSort
SRR1423710	ALL	NOVOSORT start	1511291146DedupSort
SRR1423710	ALL	NOVOSORT end	1511291314DedupSort
SRR1423881	ALL	NOVOSORT start	1511291146DedupSort
SRR1423881	ALL	NOVOSORT end	1511291332DedupSort

Thank you @jacobrh91. Yes, this error must be coming from in an older version of the code, but it was fixed a few weeks earlier: 81a0d67
This data is still usable however.. I would fix the formating in shell as below"

sed -i  's/\([0-9]\+\)\([A-Za-z]\+\)/\1\t\2/' <file_with_misformatted_last_column>

Then use the logging app as usual.