# Need help with the dataset error report on MITOS (version 1.1.7) de-novo annotation tool of metazoan mitochondrial genomes **URL:** \ **Category:** Resources\ **Tags:** tool-help, mitos\ **Created:** [September 18, 2024, 4:13am UTC](https://help.galaxyproject.org/t/need-help-with-the-dataset-error-report-on-mitos-version-1-1-7-de-novo-annotation-tool-of-metazoan-mitochondrial-genomes/13474 "2024-09-18T04:13:24Z")\ **Posts on this page:** 6\ **Page:** 1
**Author:** ![gerry\_ramos\_jr](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/gerry_ramos_jr/32/6086_2.png) [@gerry\_ramos\_jr](https://help.galaxyproject.org/u/gerry_ramos_jr)\ **Post date:** [September 18, 2024, 4:13am UTC](https://help.galaxyproject.org/t/need-help-with-the-dataset-error-report-on-mitos-version-1-1-7-de-novo-annotation-tool-of-metazoan-mitochondrial-genomes/13474/1 "2024-09-18T04:13:24Z")
An error occurred while running the tool **toolshed.g2.bx.psu.edu/repos/iuc/mitos/mitos/1.1.7+galaxy0**. Execution resulted in “Fatal error: Exit code 1 ()” message. Tool generated the following standard error: Traceback (most recent call last): File “/usr/local/tools/\_conda/envs/\_\_mitos@1.1.7/bin/runmitos.py”, line 458, in featurelist = mitos(fname, args.code, args.outdir, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File “/usr/local/tools/\_conda/envs/\_\_mitos@1.1.7/bin/runmitos.py”, line 238, in mitos checklokalfeature(localcheck, featurelist, sequence, refdir) File “/usr/local/tools/\_conda/envs/\_\_mitos@1.1.7/lib/python3.12/site-packages/mitos/mergefeature/ **init**.py”, line 563, in checklokalfeature struct = cmrealign(sseq, lname, refdir) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File “/usr/local/tools/\_conda/envs/\_\_mitos@1.1.7/lib/python3.12/site-packages/mitos/mitfi/ **init**.py”, line 147, in cmrealign with open(tdir + “/cmrealign.str”) as f: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ FileNotFoundError: [Errno 2] No such file or directory: ‘/data/jwd02f/main/073/463/73463100/tmp/tmp\_3k9sbm0/cmrealign.str’ Need some help to troubleshoot the error on the execution of the MITOS tool version 1.1.7 on my one input file in fasta format. The rest input files have good, well-generated output files using the tool. Here is the link of my history: [https://usegalaxy.eu/u/gerry\_ramos\_jr/h/unnamed-history](https://usegalaxy.eu/u/gerry_ramos_jr/h/unnamed-history) ---
**Author:** ![igor](https://avatars.discourse-cdn.com/v4/letter/i/dec6dc/32.png) [@igor](https://help.galaxyproject.org/u/igor)\ **Post date:** [September 18, 2024, 7:23am UTC](https://help.galaxyproject.org/t/need-help-with-the-dataset-error-report-on-mitos-version-1-1-7-de-novo-annotation-tool-of-metazoan-mitochondrial-genomes/13474/2 "2024-09-18T07:23:54Z")
Hi @gerry_ramos_jr I cannot decipher the error message, but have you considered MITOS2? I have impression it is significantly faster that the original software. I tested MITOS2 in Europe using another file and don’t see any issue with it. I have some reservation about the input file used for the failed job: 45% of bases are unknown (N), the remaning nucleotides are recorded in low case characters often reserved for masked sequences and the sequence name is rather long. The test file I used contains only one unknown nucleotides and no low case characters. Kind regards, Igor ---
**Author:** ![gerry\_ramos\_jr](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/gerry_ramos_jr/32/6086_2.png) [@gerry\_ramos\_jr](https://help.galaxyproject.org/u/gerry_ramos_jr)\ **Post date:** [September 20, 2024, 2:33am UTC](https://help.galaxyproject.org/t/need-help-with-the-dataset-error-report-on-mitos-version-1-1-7-de-novo-annotation-tool-of-metazoan-mitochondrial-genomes/13474/3 "2024-09-20T02:33:08Z")
I have acknowledged these recommendations, @igor. If I remove the multiple N characters within the sequence in the FASTA file, does it affect the data output/result? Thank you in advance. Regards, Gerry ---
**Author:** ![igor](https://avatars.discourse-cdn.com/v4/letter/i/dec6dc/32.png) [@igor](https://help.galaxyproject.org/u/igor)\ **Post date:** [September 22, 2024, 11:10pm UTC](https://help.galaxyproject.org/t/need-help-with-the-dataset-error-report-on-mitos-version-1-1-7-de-novo-annotation-tool-of-metazoan-mitochondrial-genomes/13474/4 "2024-09-22T23:10:57Z")
Hi @gerry_ramos_jr I don’t know why the original MITOS has failed on your data. I tested it in Europe, and it works on a test file. You can remove excessive unknown nucleotide and test if it resolves the issue. However, MITOS2 is faster and less sensitive to data. Unless you have to use the original software, MITOS2 might be a good option. Kind regards, Igor ---
**Author:** ![gerry\_ramos\_jr](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/gerry_ramos_jr/32/6086_2.png) [@gerry\_ramos\_jr](https://help.galaxyproject.org/u/gerry_ramos_jr)\ **Post date:** [September 24, 2024, 6:31am UTC](https://help.galaxyproject.org/t/need-help-with-the-dataset-error-report-on-mitos-version-1-1-7-de-novo-annotation-tool-of-metazoan-mitochondrial-genomes/13474/5 "2024-09-24T06:31:53Z")
I tried removing the unknown nucleotide bases within the sequence and finally it worked regardless of the used letter case and the sequence name length. I think, too much N characters or unknown bases can actually affect the processing of an input data in the server. Thanks for this suggestion, @igor! 🙂 Sincerely, Gerry ---
**Author:** ![igor](https://avatars.discourse-cdn.com/v4/letter/i/dec6dc/32.png) [@igor](https://help.galaxyproject.org/u/igor)\ **Post date:** [September 24, 2024, 11:03pm UTC](https://help.galaxyproject.org/t/need-help-with-the-dataset-error-report-on-mitos-version-1-1-7-de-novo-annotation-tool-of-metazoan-mitochondrial-genomes/13474/6 "2024-09-24T23:03:58Z")
Hi Gerry, Thank you for the update! I am not familiar with MITOS, so, it is good to know the software limits. Kind regards, Igor