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Fast and frugal disk based k-mer counter
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cannot open file: 30(base) #171

Closed dcopetti closed 2 years ago

dcopetti commented 2 years ago

Hello, I am getting this error when trying to run KMC3:

(base) [dcopetti@EagI /data2/dario/sikem_2002/ONT_raw_data]$ ls Sikem*fq.gz >input_files
(base) [dcopetti@EagI /data2/dario/sikem_2002/ONT_raw_data]$ less input_files
Sikem-2002_1_SDS_2kbq7a.fq.gz
Sikem-2002_2_SDS_2kbq7a.fq.gz
Sikem-2002_3_SDS_2kbq7a.fq.gz
Sikem-2002_4_CTAB_2kbq7a.fq.gz
Sikem-2002_5_CTAB_2kbq7a.fq.gz
(base) [dcopetti@EagI /data2/dario/sikem_2002/ONT_raw_data]$ kmc -k15 -m300 -t 30 @input_files Sikem_kmc tmp
Error: cannot open file: 30(base) [dcopetti@EagI /data2/dario/sikem_2002/ONT_raw_data]$

(base) [dcopetti@EagI /data2/dario/sikem_2002/ONT_raw_data]$ kmc -k15 -m300 -t 30 Sikem-2002_3_SDS_2kbq7a.fq.gz Sikem_kmc tmp
Error: cannot open file: 30(base) [dcopetti@EagI /data2/dario/sikem_2002/ONT_raw_data]$

I can't figure out where in the command there is a problem. thanks, Dario

marekkokot commented 2 years ago

Hello, sorry for the late response. Oh, I think the reason is trivial, you should use -t30 instead of -t 30. Let me know if it helps.