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tseemann / nullarbor

:floppy_disk: :page_with_curl: "Reads to report" for public health and clinical microbiology
GNU General Public License v2.0
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error2 in make preview command #270

Closed mdiricks closed 4 years ago

mdiricks commented 4 years ago

I tested the nullarbor default command on a set of 4 samples First time I tried it, the program ran succesfully. However, there was no report folder created and I could thus not see any results in a web browser. Then I tried make preview and the report folder was created and I could see the preview results. I decided to run the program again with the --prefill option to try to only recover the right results file now. But it didnt worked. I changed the config file again, removed the OUTDIR folder and started all over. However, now I already get an error in the make preview command: fq --ref ref.fa B-10-e1/R1.fq.gz B-10-e1/R2.fq.gz > B-10-e1/yield.tab [fq] running command: cat B-10-e1/R1.fq.gz B-10-e1/R2.fq.gz | seqtk fqchk -q0 - [fq] processed 535574 reads. [fq] calculating depth, using size (via --ref ref.fa) Illegal division by zero at /home/mdiricks/bin/miniconda2/bin/fq line 67, <$IN> line 254. make: [Makefile:136: B-10-e1/yield.tab] Error 2 make: Deleting file 'B-10-e1/yield.tab'

Any suggestions?

mdiricks commented 4 years ago

Easy solution: use make ref.fa preview instead of make preview Alternative solution: Change the FASTAREF at line 136 in the makefile into REF. REF is the path to the reference you file you give as input. FASTAREF is assigned ref.fa (which is probably only the correct file once you have run the complete pipeline?)