can't detect input files

[leli-li]

Hi Anna,

Thank you very much for this nice tool.

But I really came across some problems when using it.
The system is MacOS

Here's the structure of my working directory data/
.
├── input
│   ├── Mus_musculus.GRCm39.104.gtf
│   ├── Mus_musculus.GRCm39.dna.primary_assembly.fa
│   ├── backsplice_gene_name.txt
│   ├── mm39.00.idx
│   ├── mm39.01.idx
│   ├── mm39.fa
│   ├── mm39.ndb
│   ├── mm39.nhr
│   ├── mm39.nin
│   ├── mm39.njs
│   ├── mm39.not
│   ├── mm39.nsq
│   ├── mm39.ntf
│   ├── mm39.nto
│   └── mm39.shd
├── list_backsplice.txt
├── params.txt
└── path_files.txt

my command is:
docker run -it -v $(pwd):/data annadalmolin/craft:v1.0

the path_files.txt:
/Users/lily/tool/craft/data/input/Mus_musculus.GRCm39.104.gtf
/Users/lily/tool/craft/data/input/Mus_musculus.GRCm39.dna.primary_assembly.fa

the params.txt:
MRO
mmu
.
.
mm39
.
orgdb="org.Mm.eg.db", meshdb="MeSH.Mmu.eg.db", symbol2eg="org.Mm.egSYMBOL2EG", eg2uniprot="org.Mm.egUNIPROT", org="mmusculus"
orgdb="org.Mm.eg.db", symbol2eg="org.Mm.egSYMBOL2EG", eg2uniprot="org.Mm.egUNIPROT"

reported error:
grep: /Users/lily/tool/craft/data/input/Mus_musculus.GRCm39.104.gtf: No such file or directory
grep: /Users/lily/tool/craft/data/input/Mus_musculus.GRCm39.104.gtf: No such file or directory
cat: /Users/lily/tool/craft/data/input/Mus_musculus.GRCm39.dna.primary_assembly.fa: No such file or directory
Error: The genome file annotation_chr.genome has no valid entries. Exiting.
Error: The genome file annotation_chr.genome has no valid entries. Exiting.
rm: cannot remove 'backsplice_sequence_bed*': No such file or directory
rm: cannot remove 'circ_id.txt': No such file or directory
rm: cannot remove 'circ_length.txt': No such file or directory
rm: cannot remove 'out_region*': No such file or directory
rm: cannot remove 'region_to_extract_for_?.bed': No such file or directory
rm: cannot remove 'region_to_extract_rev_?.bed': No such file or directory
mv: cannot stat '/data/sequence_extraction/backsplice_sequence_1.fa': No such file or directory
mv: cannot stat '/data/sequence_extraction/backsplice_sequence_1.txt': No such file or directory
mv: cannot stat '/data/sequence_extraction/backsplice_circRNA_length_1.txt': No such file or directory
cat: backsplice_circRNA_length_1.txt: No such file or directory
is not a valid option. Try with one of the followings: M, R, O, MR, MO, RO, MRO.

Looking forward to your response. Thank you!