Snap index error

[asan-emirsaleh]

Hello! Great tool. I have heard a lot about it before tried to use. I went by conda-way, just installing all dependencies described in recipe. But every attempt to run the transrate lead me to the error in the very basic stages of alignment metrics computing. I also noted that there are no programs found by which command of the shell, in report. Here I place the transrate output:

[DEPRECATION] The trollop gem has been renamed to optimist and will no longer be supported. Please switch to optimist as soon as possible.
[ INFO] 2023-04-25 16:03:18 : Loading assembly: /project/asm/MeJa_rnaspades_def-k/PRJNA745038/transcripts.fasta
[ INFO] 2023-04-25 16:03:28 : Analysing assembly: /project/asm/MeJa_rnaspades_def-k/PRJNA745038/transcripts.fasta
[ INFO] 2023-04-25 16:03:28 : Results will be saved in /project/qc/MeJa_transrate/spades_K49-K73/transcripts
[DEBUG] 2023-04-25 16:03:28 : running command:
[DEBUG] 2023-04-25 16:03:28 : which snap-aligner
[DEBUG] 2023-04-25 16:03:28 : running command:
[DEBUG] 2023-04-25 16:03:28 : which salmon
[DEBUG] 2023-04-25 16:03:28 : running command:
[DEBUG] 2023-04-25 16:03:28 : which bam-read
[ INFO] 2023-04-25 16:03:28 : Calculating contig metrics...
[ INFO] 2023-04-25 16:03:43 : Contig metrics:
[ INFO] 2023-04-25 16:03:43 : -----------------------------------
[ INFO] 2023-04-25 16:03:43 : n seqs                       287895
[ INFO] 2023-04-25 16:03:43 : smallest                         73
[ INFO] 2023-04-25 16:03:43 : largest                       23622
[ INFO] 2023-04-25 16:03:43 : n bases                   290176352
[ INFO] 2023-04-25 16:03:43 : mean len                    1007.73
[ INFO] 2023-04-25 16:03:43 : n under 200                     369
[ INFO] 2023-04-25 16:03:43 : n over 1k                    105698
[ INFO] 2023-04-25 16:03:43 : n over 10k                       82
[ INFO] 2023-04-25 16:03:43 : n with orf                   100227
[ INFO] 2023-04-25 16:03:43 : mean orf percent               52.5
[ INFO] 2023-04-25 16:03:43 : n90                             387
[ INFO] 2023-04-25 16:03:43 : n70                            1063
[ INFO] 2023-04-25 16:03:43 : n50                            1634
[ INFO] 2023-04-25 16:03:43 : n30                            2309
[ INFO] 2023-04-25 16:03:43 : n10                            3753
[ INFO] 2023-04-25 16:03:43 : gc                             0.41
[ INFO] 2023-04-25 16:03:43 : bases n                       26148
[ INFO] 2023-04-25 16:03:43 : proportion n                    0.0
[ INFO] 2023-04-25 16:03:43 : Contig metrics done in 15 seconds
[ INFO] 2023-04-25 16:03:43 : Calculating read diagnostics...
[DEBUG] 2023-04-25 16:03:43 : running command:
[DEBUG] 2023-04-25 16:03:43 : /home/asan/miniconda3/envs/transrate-env/bin/snap-aligner index /project/asm/MeJa_rnaspades_def-k/PRJNA745038/transcripts.fasta transcripts -s 23 -t100 -bSpace -locationSize 4
[ERROR] 2023-04-25 16:03:49 : Failed to build Snap index
Welcome to SNAP version 1.0dev.96.

Saving genome...0s

[DEBUG] 2023-04-25 16:03:49 : /home/asan/miniconda3/envs/transrate-env/lib/ruby/gems/2.5.0/gems/transrate-1.0.3/bin/transrate:13:in `raise' /home/asan/miniconda3/envs/transrate-env/lib/ruby/gems/2.5.0/gems/transrate-1.0.3/lib/transrate/snap.rb:147:in `block in build_index' /home/asan/miniconda3/envs/transrate-env/lib/ruby/gems/2.5.0/gems/transrate-1.0.3/lib/transrate/snap.rb:125:in `loop' /home/asan/miniconda3/envs/transrate-env/lib/ruby/gems/2.5.0/gems/transrate-1.0.3/lib/transrate/snap.rb:125:in `build_index' /home/asan/miniconda3/envs/transrate-env/lib/ruby/gems/2.5.0/gems/transrate-1.0.3/lib/transrate/read_metrics.rb:52:in `run' /home/asan/miniconda3/envs/transrate-env/lib/ruby/gems/2.5.0/gems/transrate-1.0.3/lib/transrate/transrater.rb:98:in `read_metrics' /home/asan/miniconda3/envs/transrate-env/lib/ruby/gems/2.5.0/gems/transrate-1.0.3/lib/transrate/cmdline.rb:506:in `read_metrics' /home/asan/miniconda3/envs/transrate-env/lib/ruby/gems/2.5.0/gems/transrate-1.0.3/lib/transrate/cmdline.rb:402:in `block in analyse_assembly' /home/asan/miniconda3/envs/transrate-env/lib/ruby/gems/2.5.0/gems/transrate-1.0.3/lib/transrate/cmdline.rb:398:in `chdir' /home/asan/miniconda3/envs/transrate-env/lib/ruby/gems/2.5.0/gems/transrate-1.0.3/lib/transrate/cmdline.rb:398:in `analyse_assembly' /home/asan/miniconda3/envs/transrate-env/lib/ruby/gems/2.5.0/gems/transrate-1.0.3/lib/transrate/cmdline.rb:38:in `block (2 levels) in run' /home/asan/miniconda3/envs/transrate-env/lib/ruby/gems/2.5.0/gems/transrate-1.0.3/lib/transrate/cmdline.rb:37:in `zip' /home/asan/miniconda3/envs/transrate-env/lib/ruby/gems/2.5.0/gems/transrate-1.0.3/lib/transrate/cmdline.rb:37:in `block in run' /home/asan/miniconda3/envs/transrate-env/lib/ruby/gems/2.5.0/gems/transrate-1.0.3/lib/transrate/cmdline.rb:32:in `chdir' /home/asan/miniconda3/envs/transrate-env/lib/ruby/gems/2.5.0/gems/transrate-1.0.3/lib/transrate/cmdline.rb:32:in `run' /home/asan/miniconda3/envs/transrate-env/lib/ruby/gems/2.5.0/gems/transrate-1.0.3/bin/transrate:23:in `<top (required)>' /home/asan/miniconda3/envs/transrate-env/bin/transrate:23:in `load' /home/asan/miniconda3/envs/transrate-env/bin/transrate:23:in `<main>'

Are there any suggestion how to make it working? What does cause the problem? Do you plan to update Snap aligner version? Why the filds of running commands and which are blank?

Best regards Asan

[bpenaud]

Hello,

I also install transrate with conda and I'm encountering the same error. Have you finally found a solution?

Best Regards, Benjamin

[asan-emirsaleh]

Hello @bpenaud ! It did finally work for me. I have used a transrate binary bundled with the Oyster River Protocol pipeline. If I find additional details I will notify you.

Best regards Asan

[doctor-patient]

Hello @asan-emirsaleh. I'm having the same problem. I'm using Windows Subsystem for Linux. How did you solve it?