Error with gaps in fasta file

[AleSR13]

Hello! I am trying to run CanSNPer2 in three F. tularensis samples. With one sample it works as expected. However, with the other two I get this error:

Run 1 alignments to references using progressiveMauve
2021-07-30 10:55:06,036 CanSNPer2 [WARNI]  Input sequence is not free of gaps, replace gaps with N and retry!!
2021-07-30 10:55:06,047 CanSNPer2 [WARNI]  Input sequence is not free of gaps, replace gaps with N and retry!!
2021-07-30 10:55:06,056 CanSNPer2 [WARNI]  Input sequence is not free of gaps, replace gaps with N and retry!!
2021-07-30 10:55:06,060 CanSNPer2 [WARNI]  Input sequence is not free of gaps, replace gaps with N and retry!!
2021-07-30 10:55:06,525 CanSNPer2 [WARNI]  Input sequence is not free of gaps, replace gaps with N and retry!!
Traceback (most recent call last):
  File ".../conda/envs/cansnper/lib/python3.9/site-packages/CanSNPer2/modules/CanSNPer2.py", line 350, in run
    logger.warning("Mauve error skip {sample}".format(q))
KeyError: 'sample'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File ".../conda/envs/cansnper/bin/CanSNPer2", line 10, in <module>
    sys.exit(main())
  File "/mnt/scratch_dir/hernanda/conda/envs/cansnper/lib/python3.9/site-packages/CanSNPer2/CanSNPerTree.py", line 164, in main
    CanSNPer2_obj.run(database=args.database)
  File ".../conda/envs/cansnper/lib/python3.9/site-packages/CanSNPer2/modules/CanSNPer2.py", line 407, in run
    raise CanSNPer2Error("A file did not run correctly exit CanSNPer2 (use --keep_going to continue with next file!)")
CanSNPer2.modules.CanSNPer2.CanSNPer2Error: 'A file did not run correctly exit CanSNPer2 (use --keep_going to continue with next file!)'

I saw in #15 that a function had been implemented to correct for these gaps but either it is not working or I don't know how to activate it. I tried also to simly look for them and replace them but if I do:

grep "-" samples/my_sample1.fasta

I cannot find any dashes. Am I missing something?

Btw, I installed CanSNPer through conda using this yaml file:

name: cansnper
channels:
  - bioconda
  - conda-forge
  - defaults
dependencies:
  - cansnper2=2.0.6
  - ete3

[CarolineOhrman]

Hi AleSR13,
Sorry for not replying untli now. Have totally missed it.

I dont know if you still have this problem but I will try to answer from my perspective.

We are trying to find a replacement for progressiveMauve for doing the alignments in canSNPer2 but have not implemented this yet. My experience is that it is not always easy to know why progressiveMauve crashes and the dashes is only one reason, but "-" isnt always the problem. Try to reformat the headers in your fasta to something simple like ">1" ">2" etc. Sometimes if the headers are too long or have any special characters this can cause the same problem. Is it working with other genomes? Try downloading a public one and try and tell me if that one has the same problem., or could you send me the fasta so I can try?

Kind regards
Caroline

[habix87]

Hi! I am trying to run CanSNPer2 for one F. tularensis sample. no luck

Run 1 alignments to references using progressiveMauve
Traceback (most recent call last):
File "/home/habix87/miniforge3/envs/myenvname/lib/python3.6/site-packages/CanSNPer2/modules/CanSNPer2.py", line 350, in run
logger.warning("Mauve error skip {sample}".format(q))
KeyError: 'sample'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/home/habix87/miniforge3/envs/myenvname/bin/CanSNPer2", line 10, in
sys.exit(main())
File "/home/habix87/miniforge3/envs/myenvname/lib/python3.6/site-packages/CanSNPer2/CanSNPerTree.py", line 164, in main
CanSNPer2_obj.run(database=args.database)
File "/home/habix87/miniforge3/envs/myenvname/lib/python3.6/site-packages/CanSNPer2/modules/CanSNPer2.py", line 407, in run
raise CanSNPer2Error("A file did not run correctly exit CanSNPer2 (use --keep_going to continue with next file!)")
CanSNPer2.modules.CanSNPer2.CanSNPer2Error: 'A file did not run correctly exit CanSNPer2 (use --keep_going to continue with next file!)'

[CarolineOhrman]

Hi! Could you please specify which database (own or dowloaded from CanSNPer2-data), the references and also the command you are using when you get this error, or if you are able to share the sequence I can make a try.

progressiveMauve are prone to get errors when the sequence id contains characters like "-". One thing to test is to rename the sequence ids to something like ">mygenome1" ">mygenome2" and so on.

Kind regards
Caroline

[habix87]

Hi, i realised that i had installled cansnper instead of cansnper2. So I installed cansnper2 back and try again. However I still getting error message. I'm using francisella_tularensis.db downloaded from CaSNPer2 and I already renamed sequence ID to >mygenome1.

(cansnper2) habix87@DESKTOP-1L3NIPV:~$ CanSNPer2 --database downloaded_database.db fastadir/*.fasta --summary
Run 1 alignments to references using progressiveMauve
2024-01-23 13:51:29,664 CanSNPer2 [WARNI] WARNING progressiveMauve finished with a exitcode: 11
2024-01-23 13:51:29,676 CanSNPer2 [WARNI] WARNING progressiveMauve finished with a exitcode: 11
2024-01-23 13:51:29,679 CanSNPer2 [WARNI] WARNING progressiveMauve finished with a exitcode: 11
2024-01-23 13:51:29,682 CanSNPer2 [WARNI] WARNING progressiveMauve finished with a exitcode: 11
2024-01-23 13:51:29,685 CanSNPer2 [WARNI] WARNING progressiveMauve finished with a exitcode: 11
2024-01-23 13:51:29,685 CanSNPer2 [WARNI] Mauve ran into an error with sequence fastadir/RZ272.fasta may contain a dash, replace with N characters and retry mauve
2024-01-23 13:51:29,707 CanSNPer2 [WARNI] WARNING progressiveMauve finished with a exitcode: 11
2024-01-23 13:51:29,709 CanSNPer2 [WARNI] WARNING progressiveMauve finished with a exitcode: 11
2024-01-23 13:51:29,715 CanSNPer2 [WARNI] WARNING progressiveMauve finished with a exitcode: 11
2024-01-23 13:51:29,719 CanSNPer2 [WARNI] WARNING progressiveMauve finished with a exitcode: 11
2024-01-23 13:51:29,722 CanSNPer2 [WARNI] WARNING progressiveMauve finished with a exitcode: 11
Traceback (most recent call last):
File "/home/habix87/miniforge3/envs/cansnper2/lib/python3.6/site-packages/CanSNPer2/modules/CanSNPer2.py", line 350, in run
logger.warning("Mauve error skip {sample}".format(q))
KeyError: 'sample'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/home/habix87/miniforge3/envs/cansnper2/bin/CanSNPer2", line 10, in
sys.exit(main())
File "/home/habix87/miniforge3/envs/cansnper2/lib/python3.6/site-packages/CanSNPer2/CanSNPerTree.py", line 164, in main
CanSNPer2_obj.run(database=args.database)
File "/home/habix87/miniforge3/envs/cansnper2/lib/python3.6/site-packages/CanSNPer2/modules/CanSNPer2.py", line 407, in run
raise CanSNPer2Error("A file did not run correctly exit CanSNPer2 (use --keep_going to continue with next file!)")
CanSNPer2.modules.CanSNPer2.CanSNPer2Error: 'A file did not run correctly exit CanSNPer2 (use --keep_going to continue with next file!)'
(cansnper2) habix87@DESKTOP-1L3NIPV:~$

[habix87]

Hi! Could you please specify which database (own or dowloaded from CanSNPer2-data), the references and also the command you are using when you get this error, or if you are able to share the sequence I can make a try.

progressiveMauve are prone to get errors when the sequence id contains characters like "-". One thing to test is to rename the sequence ids to something like ">mygenome1" ">mygenome2" and so on.

Kind regards Caroline

How can I share the sequence with you?

[CarolineOhrman]

Zip the file and upload it here or send it to my email caroline.ohrman[at]foi.se

[habix87]

Hi, I already share the sequence. Have you tried yet?