"No such file or directory" error when searching Test_data

[eselimnl]

Hi Stephen, I am not experienced Docker user and couldn't solve the issue by myself. I am running Docker on WSL (Cygwin and Ubuntu). After running exogene in Docker, I use this command as you described:
./Exogene-SR.sh -f1 test_data/SRR3104446_1.fq.gz -f2 test_data/SRR3104446_2.fq.gz -r refs/HumanViral_Reference_12-12-2018.fa -o output

Even though the path is true, gzip can't open or read the files:

gzip: test_data/SRR3104446_1.fq.gz: No such file or directory
gzip: test_data/SRR3104446_2.fq.gz: No such file or directory
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[main] Version: 0.7.17-r1188
[main] CMD: /usr/bin/bwa mem -k 30 -t 4 /home/refs/HumanViral_Reference_12-12-2018.fa -
[main] Real time: 0.018 sec; CPU: 0.020 sec
Traceback (most recent call last):
File "/home/exogene/dev/readlist_2_fq.py", line 38, in
fi_1 = get_file_handle(IN_R1, 'r')
File "/home/exogene/dev/readlist_2_fq.py", line 17, in get_file_handle
return open(fn, rw)
IOError: [Errno 2] No such file or directory: 'test_data/SRR3104446_1.fq'
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] EOF marker is absent. The input is probably truncated.
We were unable to grab template length stats from bwa.log, making a complete guess...
estimated template length: 350 50
=== BREAKPOINT DEVIATIONS:

CHR INTEGRATION_POS #READS VIRUS ANNOTATION SOFTCLIP_POS #SOFTCLIP D
ISCORDANT_POS #DISCORDANT LONGREAD_POS #LONGREAD NEAREST_GENE

mv: cannot stat '*_hits.ids': No such file or directory

Thank you for your time.

[skoczylass]

Hi, It seems that this is how it should be done.
docker run -it -v ${HOME}:${HOME} zstephens/exogene:v15
cd home
(base) root@a07eef7e2214:/home# ./Exogene-SR.sh -f1 /home/test_data/SRR3104446_1.fq.gz -f2 /home/test_data/SRR3104446_2.fq.gz -r /home/your/path/hg38_plus_viral.fa.sa -o /home/your/path/OUT/