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DaehwanKimLab / hisat-genotype

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It seems that fastq file path cannot be parsed #62

Closed gudeqing closed 2 years ago

gudeqing commented 2 years ago

hisatgenotype --base hla -1 /disk/biodatabase/testdata/dnaseq_somatic/GS82-171024C1_combined_R1.fastq.gz -2 /disk/biodatabase/testdata/dnaseq_somatic/GS82-171024C1_combined_R2.fastq.gz -p 3 --out-dir GS82 --pp 3 .//disk/biodatabase/testdata/dnaseq_somatic/GS82-171024C1_combined_R2.fastq.gz does not exist. Traceback (most recent call last): File "/home/danny.gu/softwares/hisat-genotype-master/hisatgenotype", line 771, in typing_process(args) File "/home/danny.gu/softwares/hisat-genotype-master/hisatgenotype", line 539, in typing_process assert fq_fname_base AssertionError

parkchanhee commented 2 years ago

@gudeqing Could you try with the --in-dir option?

ex> hisatgenotype --base hla -1 /disk/biodatabase/testdata/dnaseq_somatic/GS82-171024C1_combined_R1.fastq.gz -2 /disk/biodatabase/testdata/dnaseq_somatic/GS82-171024C1_combined_R2.fastq.gz -p 3 --in-dir "" --out-dir GS82 --pp 3

gudeqing commented 2 years ago

@parkchanhee Thank you, that solved my problem. Sorry that I did not notice this argument before.