Request

[a-espuela]

Hi,

I have recently started to use Evolinc1 and I find it very useful but I have a couple of questions.

When I run the sample_data command, I get this on screen along with other information but I am not sure where this information is coming from:

Generating Number of transcripts
       448 transcripts.o.fa
       422 transcripts.o.filter.fa
       233 transcripts.u.fa
        37 transcripts.x.fa
        36 transcripts.x.filter.fa

Generating Number of coding and noncoding
putative_intergenic_coding_transcripts 21
putative_intergenic_noncoding_transcripts 212
overlapping_coding_transcripts 320
overlapping_coding_transcripts 139

[INFO] read file 'transcripts.all.overlapping.filter.fa'

Also, I got the following:

***** WARNING: File lncRNA.prefilter.bed has inconsistent naming convention for record:1       76856   77892   .       .       +       Cufflinks       exon    .       gene_id "XLOC_000008"; transcript_id "TCONS_00000014"; exon_number "1"; gene_name "MIR165A"; oId "CUFF.10.2"; nearest_ref "AT1G01183.1"; class_code "x"; tss_id "TSS11";

After outputting the messages printed to screen during execution, I have found also this:
/evolinc_docker/evolinc-part-I.sh: line 654: ../Evolinc-I/sample_data/test_out_mandatory_files_log/elapsed_time-evolinc-i.txt: No such file or directory

In my output folder I have a file called Sample_cuffcompare_out.gtf.elapsed_time-evolinc-i
Is it the same file? Should I be worried about this warning?

It would be nice to have this information stored in a log file along with the command run and other output information so we can check it after the command has been run.

Thanks for creating Evolinc!
Antonio

[a-espuela]

Hi again,

I have been trying to run evolinc with my own data but I can't seem to make it work.
My data is separated in two different folders but Docker supposedly is able to access them.
Nevertheless, when I run evolinc with the following command, it outputs this error grep: transcripts.*.fa: No such file or directory
Command:
docker run --rm \
-v /Users/Documents/:/working-dir \
-w /working-dir evolinc/evolinc-i:1.7.5 \
-c /working-dir/Folder1/annotated.gtf \
-g /working-dir/Folder2/genomic.fna \
-u /working-dir/Folder2/genomic.gtf \
-o /working-dir/lncRNA_identification \
-n 20 > lncRNA_identification/Logfile.log 2>&1

Can I run the evolinc using docker if my files are in different locations in my PC?

Thanks in advance

[andrew-d-l-nelson]

Hi Antonio,
What happens if you navigate to /Users/Documents/ and then use -v $(pwd):/working-dir ? This would take the present working directory (like in R) and pass it through to Docker to use as the working-dir.

My worry is that /Users/Documents is likely not the absolute path, and as such may cause issues. Feel free to reach out to me at andrewdlnelson at gmail to get quicker response times!