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COMBINE-lab / SalmonTools

Useful tools for working with Salmon output
BSD 3-Clause "New" or "Revised" License
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Output Files Not Created In Latest Version #3

Closed Miserlou closed 5 years ago

Miserlou commented 5 years ago

The same wrapper code running with 474ba5947711074a015a268b47058ac8930cf566 and the current master HEAD creates different behavior.

With 474ba5947711074a015a268b47058ac8930cf566, there are files at the expected location with the command:

salmontools extract-unmapped -u /home/user/data_store/salmontools/double_output/aux_info/unmapped_names.txt -o /home/user/data_store/salmontools/double_salmontools/unmapped_by_salmon -1 /home/user/data_store/salmontools/double_input/reads_1.fastq -2 /home/user/data_store/salmontools/double_input/reads_2.fastq

When using master, the output files don't exist at the location. It simply says, There were 100 unmapped reads, but no new files appear.

Any ideas?

hiraksarkar commented 5 years ago

Hi @Miserlou , Thanks for reporting the error. Trying to debug it. Is this happening just for this set of reads, or for all the samples?

Miserlou commented 5 years ago

The example is for our CI test case, which tests both single and double, both fail.

hiraksarkar commented 5 years ago

Hi @Miserlou,

Can you please confirm if the /home/user/data_store/salmontools/double_salmontools/ folder existed before running or not ?

hiraksarkar commented 5 years ago

4 This pull req will create the output directory if not exists and might be the issue for above behavior. Requesting @rob-p to merge.

hiraksarkar commented 5 years ago

@Miserlou , Was wondering if the problem is solved.

Miserlou commented 5 years ago

Yep! That got it. Sorry for the delayed reply, and thank you for your swift response!