voila tsv error - more than one voila file found

[Marek Schwarz]

Hello,
newbie majiq user here.

I have experiment with 4 groups and I've used the command_builder tool to generate commands for the analysis.

After some trial and error, I've successfully finished the majiq build and 6 majiq deltapsi commands.

However, when I run the generated voila command, that I have more than one voila file in the directory.
(ERROR - In the files or directories supplied, there was more than one Voila file found.)

This is very cryptic to me, as the location of the multiple voila files is result of the generated command. Should I move them to separate directories or use different parameters?

I'm attaching the commands and outputs below.

commands:
majiq build /data/shared/work_dzamila_schwarzm/mm38_98/Mus_musculus.GRCm38.98.gff3 -o /data/shared/work_dzamila_schwarzm/majiq/default_forzen/build -c /data/shared/work_dzamila_schwarzm/majiq/majiq_default_frozen.conf -j 1

majiq deltapsi -o /data/shared/work_dzamila_schwarzm/majiq/default_forzen/deltapsi -j 1 -grp1 /data/shared/work_dzamila_schwarzm/majiq/default_forzen/build/W1_L.majiq /data/shared/work_dzamila_schwarzm/majiq/default_forzen/build/W2_L.majiq /data/shared/work_dzamila_schwarzm/majiq/default_forzen/build/W3_L.majiq -grp2 /data/shared/work_dzamila_schwarzm/majiq/default_forzen/build/W8_D.majiq /data/shared/work_dzamila_schwarzm/majiq/default_forzen/build/W9_D.majiq  -n WT_light WT_dark
majiq deltapsi -o /data/shared/work_dzamila_schwarzm/majiq/default_forzen/deltapsi -j 1 -grp1 /data/shared/work_dzamila_schwarzm/majiq/default_forzen/build/W1_L.majiq /data/shared/work_dzamila_schwarzm/majiq/default_forzen/build/W2_L.majiq /data/shared/work_dzamila_schwarzm/majiq/default_forzen/build/W3_L.majiq -grp2 /data/shared/work_dzamila_schwarzm/majiq/default_forzen/build/K1_L.majiq /data/shared/work_dzamila_schwarzm/majiq/default_forzen/build/K3_L.majiq  -n WT_light KO_light
majiq deltapsi -o /data/shared/work_dzamila_schwarzm/majiq/default_forzen/deltapsi -j 1 -grp1 /data/shared/work_dzamila_schwarzm/majiq/default_forzen/build/W1_L.majiq /data/shared/work_dzamila_schwarzm/majiq/default_forzen/build/W2_L.majiq /data/shared/work_dzamila_schwarzm/majiq/default_forzen/build/W3_L.majiq -grp2 /data/shared/work_dzamila_schwarzm/majiq/default_forzen/build/K7_D.majiq /data/shared/work_dzamila_schwarzm/majiq/default_forzen/build/K9_D.majiq  -n WT_light KO_dark
majiq deltapsi -o /data/shared/work_dzamila_schwarzm/majiq/default_forzen/deltapsi -j 1 -grp1 /data/shared/work_dzamila_schwarzm/majiq/default_forzen/build/W8_D.majiq /data/shared/work_dzamila_schwarzm/majiq/default_forzen/build/W9_D.majiq -grp2 /data/shared/work_dzamila_schwarzm/majiq/default_forzen/build/K1_L.majiq /data/shared/work_dzamila_schwarzm/majiq/default_forzen/build/K3_L.majiq  -n WT_dark KO_light
majiq deltapsi -o /data/shared/work_dzamila_schwarzm/majiq/default_forzen/deltapsi -j 1 -grp1 /data/shared/work_dzamila_schwarzm/majiq/default_forzen/build/W8_D.majiq /data/shared/work_dzamila_schwarzm/majiq/default_forzen/build/W9_D.majiq -grp2 /data/shared/work_dzamila_schwarzm/majiq/default_forzen/build/K7_D.majiq /data/shared/work_dzamila_schwarzm/majiq/default_forzen/build/K9_D.majiq  -n WT_dark KO_dark
majiq deltapsi -o /data/shared/work_dzamila_schwarzm/majiq/default_forzen/deltapsi -j 1 -grp1 /data/shared/work_dzamila_schwarzm/majiq/default_forzen/build/K1_L.majiq /data/shared/work_dzamila_schwarzm/majiq/default_forzen/build/K3_L.majiq -grp2 /data/shared/work_dzamila_schwarzm/majiq/default_forzen/build/K7_D.majiq /data/shared/work_dzamila_schwarzm/majiq/default_forzen/build/K9_D.majiq  -n KO_light KO_dark

voila tsv -j 1 -f /data/shared/work_dzamila_schwarzm/majiq/default_forzen/voila_output.tsv /data/shared/work_dzamila_schwarzm/majiq/default_forzen

voila tsv -j 1 -f /data/shared/work_dzamila_schwarzm/majiq/default_forzen/voila_output.tsv /data/shared/work_dzamila_schwarzm/majiq/default_forzen                                                      

====================================================================

                                                                   Voila output:                                                                     2021-12-01 20:07:47,160 (PID:3208) - INFO - Command: /opt/bio-class/miniconda/envs/majiq/bin/voila tsv -j 1 -f /data/shared/work_dzamila_schwarzm/majiq/default_forzen/voila_output.tsv /data/shared/work_dzamila_schwarzm/majiq/default_forzen                                                                                                                                                                     2021-12-01 20:07:47,160 (PID:3208) - INFO - Voila v2.3                                                                                                                                                    2021-12-01 20:07:47,160 (PID:3208) - INFO - config file: /tmp/tmpihcrmj56                                                                                                                                 2021-12-01 20:07:47,975 (PID:3208) - ERROR - In the files or directories supplied, there was more than one Voila file found.

================================================================

ls /data/shared/work_dzamila_schwarzm/majiq/default_forzen/deltapsi/                                                                      deltapsi_majiq.log               WT_dark-KO_dark.deltapsi.tsv    WT_dark-KO_light.deltapsi.voila  WT_light-KO_light.deltapsi.tsv    WT_light-WT_dark.deltapsi.voila                                       KO_light-KO_dark.deltapsi.tsv    WT_dark-KO_dark.deltapsi.voila  WT_light-KO_dark.deltapsi.tsv    WT_light-KO_light.deltapsi.voila                                                                        KO_light-KO_dark.deltapsi.voila  WT_dark-KO_light.deltapsi.tsv   WT_light-KO_dark.deltapsi.voila  WT_light-WT_dark.deltapsi.tsv

Thank you for any input on this

Best regards

Marek Schwarz

[Paul Jewell]

Hello Marek,

Deltapsi mode works with one voila file at a time. When you specify just "/data/shared/work_dzamila_schwarzm/majiq/default_forzen" ; voila will look iteratively to find all inputs there, as it is a folder. Instead, the command can be something like:

$ voila tsv -j 1 -f /data/shared/work_dzamila_schwarzm/majiq/default_forzen/voila_output.tsv /data/shared/work_dzamila_schwarzm/majiq/default_forzen/spliegraph.sql /data/shared/work_dzamila_schwarzm/majiq/default_forzen/deltapsi/WT_dark.deltapsi.voila

(basically just add the path to splicegraph.sql and one deltapsi.voila file)

[Laura Sloofman, M.S.]

Hello all, 
I thought I hit enter on a longer message, but the crux of it was I got a similar error when I ran: 

voila tsv -j 10 -f /path/to/majiq/build_groups//voila_output.tsv /path/to/majiq/build_groups/

This command was generated from the command builder. 

Error: 

2023-02-23 16:49:34,714 (PID:37998) - INFO - Voila v2.4.dev4+gdd43612
2023-02-23 16:49:34,714 (PID:37998) - INFO - config file: /tmp/tmpf8wd6c34
2023-02-23 16:49:34,817 (PID:37998) - ERROR - In the files or directories supplied, there was more than one Voila file found.

Thank you!

Laura

[Laura Sloofman, M.S.]

edit: it worked when I created a loop calling the command 5x with 5 voila files, for example, and hard-coding the splicegraph that was generated earlier. 

This comment was very helpful, thank you! Would it be possible to change the logic in the command builder so this doesn't happen again during my next round of analysis? 

Thank you, 

Laura  

[San Jewell]

Hi Laura,

I'm a bit confused. For one voila file you will generate one tsv output. If you just ran the same command five times with only changing the voila file name, but not changing the output file name, then it will end up overwriting the output file multiple times so you will just get the last results.

It is possible to run multiple voila tsvs in parallel for different input/output files.

Can you elaborate slightly on the behavior you would like to see for builder / voila tsv that would make it more useful for you?

Thanks.