mothur

Pre.cluster crash v1.46.1

Mothur crashes when running pre.clsuter with 16S seqs. I have 72 samples, about 100,000 unique contigs and 500,000 seqs. I tried to limit the processor to 4, 2, or even 1, but it still crashed. I use window machines, 64-bit, 16 GB RAM. I can send you the log files.

I encountered this problem before while using v1.43.0. I got around by downloading an older version, v.1.39.5, which is already 5 years old by now and I do not want to go backward that far unless there is no other way around. Thank you for helping.

Can you send your logfile to mothur.bugs@gmail.com?

I cannot help thinking maybe there are too many samples and unique contigs in my dataset. However, this dataset is a subset of the one I ran with v.1.39.5 last year. The full dataset has 80 samples and 110,016 unique contigs. It went through that time.

On the other hand, these 72 samples represent 18 treatments with 4 replicates for each treatment. Should I pool the contigs of the replicates and continue with Mothur as 18 samples?

I can’t find the logfile. Did you send it to mothur.bugs@gmail.com?

I sent 4 log files to the email address on Oct 26. Just resent them a moment ago. Please check and let me know if they failed to be delivered again. Thank you!

Sorry I missed the log files initially. The issue is caused by the sample names including the ‘-’ character. The pre.cluster command splits the data by samples, and ‘-’ characters in the sample names are causing the split to fail. You can see warnings about it in the count.seqs command below:

mothur >
count.seqs(name=soy72.trim.contigs.good.names, group=soy72.contigs.good.groups)

[WARNING]: group DM100-D0-d contains illegal characters in the name. Group names should not include :, -, or / characters. The ‘:’ character is a special character used in trees. Using ‘:’ will result in your tree being unreadable by tree reading software. The ‘-’ character is a special character used by mothur to parse group names. Using the ‘-’ character will prevent you from selecting groups. The ‘/’ character will created unreadable filenames when mothur includes the group in an output filename.

[WARNING]: group DM100-D25S-a contains illegal characters in the name. Group names should not include :, -, or / characters. The ‘:’ character is a special character used in trees. Using ‘:’ will result in your tree being unreadable by tree reading software. The ‘-’ character is a special character used by mothur to parse group names. Using the ‘-’ character will prevent you from selecting groups. The ‘/’ character will created unreadable filenames when mothur includes the group in an output filename.

[WARNING]: group DM10-D123S-a contains illegal characters in the name. Group names should not include :, -, or / characters. The ‘:’ character is a special character used in trees. Using ‘:’ will result in your tree being unreadable by tree reading software. The ‘-’ character is a special character used by mothur to parse group names. Using the ‘-’ character will prevent you from selecting groups. The ‘/’ character will created unreadable filenames when mothur includes the group in an output filename.

[WARNING]: group DM100-D123S-a contains illegal characters in the name. Group names should not include :, -, or / characters. The ‘:’ character is a special character used in trees. Using ‘:’ will result in your tree being unreadable by tree reading software. The ‘-’ character is a special character used by mothur to parse group names. Using the ‘-’ character will prevent you from selecting groups. The ‘/’ character will created unreadable filenames when mothur includes the group in an output filename.

[WARNING]: group DM100-D0-b contains illegal characters in the name. Group names should not include :, -, or / characters. The ‘:’ character is a special character used in trees. Using ‘:’ will result in your tree being unreadable by tree reading software. The ‘-’ character is a special character used by mothur to parse group names. Using the ‘-’ character will prevent you from selecting groups. The ‘/’ character will created unreadable filenames when mothur includes the group in an output filename.

[WARNING]: group DM20-D25S-d contains illegal characters in the name. Group names should not include :, -, or / characters. The ‘:’ character is a special character used in trees. Using ‘:’ will result in your tree being unreadable by tree reading software. The ‘-’ character is a special character used by mothur to parse group names. Using the ‘-’ character will prevent you from selecting groups. The ‘/’ character will created unreadable filenames when mothur includes the group in an output filename.

[WARNING]: group DM100-D0-b contains illegal characters in the name. Group names should not include :, -, or / characters. The ‘:’ character is a special character used in trees. Using ‘:’ will result in your tree being unreadable by tree reading software. The ‘-’ character is a special character used by mothur to parse group names. Using the ‘-’ character will prevent you from selecting groups. The ‘/’ character will created unreadable filenames when mothur includes the group in an output filename.

[WARNING]: group DM10-D123-d contains illegal characters in the name. Group names should not include :, -, or / characters. The ‘:’ character is a special character used in trees. Using ‘:’ will result in your tree being unreadable by tree reading software. The ‘-’ character is a special character used by mothur to parse group names. Using the ‘-’ character will prevent you from selecting groups. The ‘/’ character will created unreadable filenames when mothur includes the group in an output filename.

[WARNING]: group DM100-D123S-d contains illegal characters in the name. Group names should not include :, -, or / characters. The ‘:’ character is a special character used in trees. Using ‘:’ will result in your tree being unreadable by tree reading software. The ‘-’ character is a special character used by mothur to parse group names. Using the ‘-’ character will prevent you from selecting groups. The ‘/’ character will created unreadable filenames when mothur includes the group in an output filename.

[WARNING]: group DM0-D25S-a contains illegal characters in the name. Group names should not include :, -, or / characters. The ‘:’ character is a special character used in trees. Using ‘:’ will result in your tree being unreadable by tree reading software. The ‘-’ character is a special character used by mothur to parse group names. Using the ‘-’ character will prevent you from selecting groups. The ‘/’ character will created unreadable filenames when mothur includes the group in an output filename.

**** Exceeded maximum allowed command warnings, silencing warnings ****

It took 58 secs to create a table for 472709 sequences.

Total number of sequences: 472709

Output File Names:
C:\Users\zxulocal\OneDrive - Bowling Green State University\soybean_paper\soy72\results\soy72.trim.contigs.good.count_table

You can correct the issue by changing the ‘-’'s to ‘_’'s. We are adding an autocorrect for sample names that include '-'s in our next release.

Problem solved. Thank you, Sarah!

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