Error with Trinity iterations
filonico opened this issue · 5 comments
Hi everyone! I keep getting the following error when running dnaPipeTE, even with the test dataset:
awk: fatal: cannot open file `/full/path/to/output/dir/Trinity_run0/chrysalis/readsToComponents.out.sort' for reading (No such file or directory)
The command I'm running is:
python3 ./dnaPipeTE.py -input ./test/test_dataset.fastq -output /full/path/to/output/dir -genome_size 2000000 -genome_coverage 0.5 -sample_number 2 -cpu 2
The test.config.sh is running properly.
How can I solve the issue? Thanks a lot!
Hello @filonico !
A few questions for you:
- are you using the normal (1.3) or container (1.3c) version?
- Is the run still going through or you don't have input? This error is normally a simple bug, because there is no "run0" but the iterative process still look for it. Normally, it shouldn't affect the program run.
Cheers,
Clément
Hello! Thank you very much for your quick response!
- I'm using dnaPipeTE normal version.
- If I let the run go, it actually seems to complete successfully! So I think this is just the simple bug you mentioned. I used to stop the run since my analysis is a little bit time and memory consuming, so I wanted to be sure that everything was good before letting it go.
By screening the stdout of the run, I see some other warning messagges:
- at the end of
Blast 3section I see
cannot remove ‘full/path/to/output/dir//blast_out/int.reads_vs_annoted.blast.out’: No such file or directory - in the final "graph section" I see
Drawing graphs...
null device
1
null device
1
null device
1
null device
1
Error in (function (file = ifelse(onefile, "Rplots.pdf", "Rplot%03d.pdf"), :
cannot open file 'Rplots.pdf'
Calls: <Anonymous> -> print.ggplot -> grid.newpage -> <Anonymous>
Execution halted
Done
The run finishes anyway and the results seem to be present (haven't checked them yet). Are those errors still bugs?
Hello!
It seems fine indeed. The last error is related to R, and if you happen to have missing graphs, I encourage you to try these companions scripts to re-generate them (in even better!). https://github.com/clemgoub/dnaPT_utils
Let me know though if you identify issues!
Cheers,
Clément
Hello Clément! The script seems indeed to be working and to succeed in creating the outputs. Unfortunately I bumped into another issue regarding the dnaPT_utils scripts. As a matter of fact, when running either dnaPT_chart.sh or dnaPT_landscape.sh on my output directory I get:
input dataset: /path/to/my/dir/
output folder: /path/to/my/dir/
output prefix: prefix
custom ylim: FALSE
── Attaching packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────── tidyverse 1.3.1 ──
✔ tibble 3.1.6 ✔ dplyr 1.0.9
✔ tidyr 1.2.0 ✔ stringr 1.4.0
✔ readr 2.1.2 ✔ forcats 0.5.1
✔ purrr 0.3.4
── Conflicts ──────────────────────────────────────────────────────────────────────────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag() masks stats::lag()
Error in col.bars[i] <- cols$V2[grep(pattern = paste("^", levels(as.factor(rca_t$t_subc))[i], :
replacement has length zero
Execution halted
All done, results in /path/to/my/dir/
I obviously checked whether there were problems with R or some other packages, but I couldn't find anything, also considering that the dnaPT_utils scripts runs perfectly well on the test_dataset.fastq provided with dnaPipeTE.
Do you have any guess of what might the problem be? I can provide the dnaPipeTE output files that are necessary for the script, if needed.
Thank you a lot for your time! Best regards
Hello @filonico !
It seems your issue is related to the one posted here. Would you mind reposting or commenting there according to the respond I gave to @Liuxuanzeng ?
If this is not due to the data, then I will have to see if there is not something wrong in the code!
Thanks a lot and sorry for the issue!
Clément