Hi,
I have tried to use the command pre.cluster or chimera.vsearch and each time the Mothur program crash and close the program. I have two different sets of sequences, one for 16S and another for Fungi. And for both types of the sequence appears the same problems.
Here, I pasted my program
Windows version
Using Boost
mothur v.1.44.3
Last updated: 8/27/20
by
Patrick D. Schloss
Department of Microbiology & Immunology
University of Michigan
When using, please cite:
Schloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.
Distributed under the GNU General Public License
Type ‘help()’ for information on the commands that are available
For questions and analysis support, please visit our forum at https://forum.mothur.org
Type ‘quit()’ to exit program
[NOTE]: Setting random seed to 19760620.
Interactive Mode
mothur >
make.contigs(processors=24, file=FunBW.files)
Using 24 processors.
[WARNING]: group 1-ITS 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 10-ITS 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 11-ITS 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 12-ITS 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 2-ITS 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 3-ITS 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 4-ITS 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 49-ITS 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 5-ITS 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 50-ITS 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 ****
Processing file pair 1-ITS_S49_L001_R1_001.fastq - 1-ITS_S49_L001_R2_001.fastq (files 1 of 24) <<<<<
Making contigs…
Done.
It took 90 secs to assemble 194788 reads.
Processing file pair 10-ITS_S58_L001_R1_001.fastq - 10-ITS_S58_L001_R2_001.fastq (files 2 of 24) <<<<<
Making contigs…
Done.
It took 67 secs to assemble 140475 reads.
Processing file pair 11-ITS_S59_L001_R1_001.fastq - 11-ITS_S59_L001_R2_001.fastq (files 3 of 24) <<<<<
Making contigs…
Done.
It took 93 secs to assemble 200061 reads.
Processing file pair 12-ITS_S60_L001_R1_001.fastq - 12-ITS_S60_L001_R2_001.fastq (files 4 of 24) <<<<<
Making contigs…
Done.
It took 111 secs to assemble 221963 reads.
Processing file pair 2-ITS_S50_L001_R1_001.fastq - 2-ITS_S50_L001_R2_001.fastq (files 5 of 24) <<<<<
Making contigs…
Done.
It took 120 secs to assemble 232707 reads.
Processing file pair 3-ITS_S51_L001_R1_001.fastq - 3-ITS_S51_L001_R2_001.fastq (files 6 of 24) <<<<<
Making contigs…
Done.
It took 127 secs to assemble 235322 reads.
Processing file pair 4-ITS_S52_L001_R1_001.fastq - 4-ITS_S52_L001_R2_001.fastq (files 7 of 24) <<<<<
Making contigs…
Done.
It took 122 secs to assemble 236583 reads.
Processing file pair 49-ITS_S73_L001_R1_001.fastq - 49-ITS_S73_L001_R2_001.fastq (files 8 of 24) <<<<<
Making contigs…
Done.
It took 63 secs to assemble 114754 reads.
Processing file pair 5-ITS_S53_L001_R1_001.fastq - 5-ITS_S53_L001_R2_001.fastq (files 9 of 24) <<<<<
Making contigs…
Done.
It took 70 secs to assemble 155593 reads.
Processing file pair 50-ITS_S74_L001_R1_001.fastq - 50-ITS_S74_L001_R2_001.fastq (files 10 of 24) <<<<<
Making contigs…
Done.
It took 89 secs to assemble 184711 reads.
Processing file pair 51-ITS_S75_L001_R1_001.fastq - 51-ITS_S75_L001_R2_001.fastq (files 11 of 24) <<<<<
Making contigs…
Done.
It took 85 secs to assemble 181312 reads.
Processing file pair 52-ITS_S76_L001_R1_001.fastq - 52-ITS_S76_L001_R2_001.fastq (files 12 of 24) <<<<<
Making contigs…
Done.
It took 74 secs to assemble 163061 reads.
Processing file pair 53-ITS_S77_L001_R1_001.fastq - 53-ITS_S77_L001_R2_001.fastq (files 13 of 24) <<<<<
Making contigs…
Done.
It took 88 secs to assemble 191395 reads.
Processing file pair 54-ITS_S78_L001_R1_001.fastq - 54-ITS_S78_L001_R2_001.fastq (files 14 of 24) <<<<<
Making contigs…
Done.
It took 89 secs to assemble 185533 reads.
Processing file pair 55-ITS_S79_L001_R1_001.fastq - 55-ITS_S79_L001_R2_001.fastq (files 15 of 24) <<<<<
Making contigs…
Done.
It took 75 secs to assemble 132640 reads.
Processing file pair 56-ITS_S80_L001_R1_001.fastq - 56-ITS_S80_L001_R2_001.fastq (files 16 of 24) <<<<<
Making contigs…
Done.
It took 74 secs to assemble 136571 reads.
Processing file pair 57-ITS_S81_L001_R1_001.fastq - 57-ITS_S81_L001_R2_001.fastq (files 17 of 24) <<<<<
Making contigs…
Done.
It took 121 secs to assemble 232386 reads.
Processing file pair 58-ITS_S82_L001_R1_001.fastq - 58-ITS_S82_L001_R2_001.fastq (files 18 of 24) <<<<<
Making contigs…
Done.
It took 93 secs to assemble 187602 reads.
Processing file pair 59-ITS_S83_L001_R1_001.fastq - 59-ITS_S83_L001_R2_001.fastq (files 19 of 24) <<<<<
Making contigs…
Done.
It took 105 secs to assemble 206577 reads.
Processing file pair 6-ITS_S54_L001_R1_001.fastq - 6-ITS_S54_L001_R2_001.fastq (files 20 of 24) <<<<<
Making contigs…
Done.
It took 103 secs to assemble 201671 reads.
Processing file pair 60-ITS_S84_L001_R1_001.fastq - 60-ITS_S84_L001_R2_001.fastq (files 21 of 24) <<<<<
Making contigs…
Done.
It took 93 secs to assemble 182401 reads.
Processing file pair 7-ITS_S55_L001_R1_001.fastq - 7-ITS_S55_L001_R2_001.fastq (files 22 of 24) <<<<<
Making contigs…
Done.
It took 107 secs to assemble 201249 reads.
Processing file pair 8-ITS_S56_L001_R1_001.fastq - 8-ITS_S56_L001_R2_001.fastq (files 23 of 24) <<<<<
Making contigs…
Done.
It took 107 secs to assemble 210000 reads.
Processing file pair 9-ITS_S57_L001_R1_001.fastq - 9-ITS_S57_L001_R2_001.fastq (files 24 of 24) <<<<<
Making contigs…
Done.
It took 105 secs to assemble 206654 reads.
Group count:
1-ITS 194788
10-ITS 140475
11-ITS 200061
12-ITS 221963
2-ITS 232707
3-ITS 235322
4-ITS 236583
49-ITS 114754
5-ITS 155593
50-ITS 184711
51-ITS 181312
52-ITS 163061
53-ITS 191395
54-ITS 185533
55-ITS 132640
56-ITS 136571
57-ITS 232386
58-ITS 187602
59-ITS 206577
6-ITS 201671
60-ITS 182401
7-ITS 201249
8-ITS 210000
9-ITS 206654
Total of all groups is 4536009
It took 2335 secs to process 4536009 sequences.
Output File Names:
FunBW.trim.contigs.fasta
FunBW.scrap.contigs.fasta
FunBW.contigs.report
FunBW.contigs.groups
mothur >
summary.seqs(fasta=E:\Black Walnut project\Fungi BW\FunBW.trim.contigs.fasta)
Using 24 processors.
Start End NBases Ambigs Polymer NumSeqs
Minimum: 1 292 292 0 3 1
2.5%-tile: 1 305 305 0 4 113401
25%-tile: 1 322 322 0 4 1134003
Median: 1 338 338 0 5 2268005
75%-tile: 1 354 354 0 6 3402007
97.5%-tile: 1 580 580 22 11 4422609
Maximum: 1 602 602 118 301 4536009
Mean: 1 354 354 1 5
of Seqs: 4536009
It took 2574 secs to summarize 4536009 sequences.
Output File Names:
E:\Black Walnut project\Fungi BW\FunBW.trim.contigs.summary
mothur >
screen.seqs(fasta=E:\Black Walnut project\Fungi BW\FunBW.trim.contigs.fasta, group=E:\Black Walnut project\Bacteria BW\BacBW.contigs.groups, maxambig=0, maxlength=580)
Using 24 processors.
It took 69 secs to screen 4536009 sequences, removed 904217.
/******************************************/
Running command: remove.seqs(accnos=E:\Black Walnut project\Fungi BW\FunBW.trim.contigs.bad.accnos.temp, group=E:\Black Walnut project\Bacteria BW\BacBW.contigs.groups)
Removed 0 sequences from your group file.
Output File Names:
E:\Black Walnut project\Bacteria BW\BacBW.contigs.pick.groups
/******************************************/
Output File Names:
E:\Black Walnut project\Fungi BW\FunBW.trim.contigs.good.fasta
E:\Black Walnut project\Fungi BW\FunBW.trim.contigs.bad.accnos
E:\Black Walnut project\Fungi BW\BacBW.contigs.good.groups
It took 378 secs to screen 4536009 sequences.
mothur >
summary.seqs(fasta=E:\Black Walnut project\Fungi BW\FunBW.trim.contigs.good.fasta)
Using 24 processors.
Start End NBases Ambigs Polymer NumSeqs
Minimum: 1 300 300 0 3 1
2.5%-tile: 1 305 305 0 4 90795
25%-tile: 1 322 322 0 5 907949
Median: 1 337 337 0 5 1815897
75%-tile: 1 351 351 0 6 2723845
97.5%-tile: 1 520 520 0 11 3540998
Maximum: 1 580 580 0 251 3631792
Mean: 1 345 345 0 5
of Seqs: 3631792
It took 94 secs to summarize 3631792 sequences.
Output File Names:
E:\Black Walnut project\Fungi BW\FunBW.trim.contigs.good.summary
mothur >
unique.seqs(fasta=E:\Black Walnut project\Fungi BW\FunBW.trim.contigs.good.fasta)
3631792 796413
Output File Names:
E:\Black Walnut project\Fungi BW\FunBW.trim.contigs.good.names
E:\Black Walnut project\Fungi BW\FunBW.trim.contigs.good.unique.fasta
mothur >
count.seqs(name=E:\Black Walnut project\Fungi BW\FunBW.trim.contigs.good.names, group=E:\Black Walnut project\Fungi BW\FunBW.contigs.good.groups)
[WARNING]: group 23-ITS 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 8-ITS 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 60-ITS 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 65-ITS 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 53-ITS 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 5-ITS 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 5-ITS 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 68-ITS 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 23-ITS 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 23-ITS 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 ****
Removing group: 13-ITS because all sequences have been removed.
Removing group: 14-ITS because all sequences have been removed.
Removing group: 15-ITS because all sequences have been removed.
Removing group: 16-ITS because all sequences have been removed.
Removing group: 17-ITS because all sequences have been removed.
Removing group: 18-ITS because all sequences have been removed.
Removing group: 19-ITS because all sequences have been removed.
Removing group: 20-ITS because all sequences have been removed.
Removing group: 21-ITS because all sequences have been removed.
Removing group: 22-ITS because all sequences have been removed.
Removing group: 23-ITS because all sequences have been removed.
Removing group: 24-ITS because all sequences have been removed.
Removing group: 61-ITS because all sequences have been removed.
Removing group: 62-ITS because all sequences have been removed.
Removing group: 63-ITS because all sequences have been removed.
Removing group: 64-ITS because all sequences have been removed.
Removing group: 65-ITS because all sequences have been removed.
Removing group: 66-ITS because all sequences have been removed.
Removing group: 67-ITS because all sequences have been removed.
Removing group: 68-ITS because all sequences have been removed.
Removing group: 69-ITS because all sequences have been removed.
Removing group: 70-ITS because all sequences have been removed.
Removing group: 71-ITS because all sequences have been removed.
Removing group: 72-ITS because all sequences have been removed.
It took 2691 secs to create a table for 3631792 sequences.
Total number of sequences: 3631792
Output File Names:
E:\Black Walnut project\Fungi BW\FunBW.trim.contigs.good.count_table
mothur >
summary.seqs(fasta=current, count=current)
Using E:\Black Walnut project\Fungi BW\FunBW.trim.contigs.good.count_table as input file for the count parameter.
Using E:\Black Walnut project\Fungi BW\FunBW.trim.contigs.good.unique.fasta as input file for the fasta parameter.
Using 24 processors.
Start End NBases Ambigs Polymer NumSeqs
Minimum: 1 300 300 0 3 1
2.5%-tile: 1 305 305 0 4 90795
25%-tile: 1 322 322 0 5 907949
Median: 1 337 337 0 5 1815897
75%-tile: 1 351 351 0 6 2723845
97.5%-tile: 1 520 520 0 11 3540998
Maximum: 1 580 580 0 251 3631792
Mean: 1 345 345 0 5
of unique seqs: 796413
total # of seqs: 3631792
It took 56 secs to summarize 3631792 sequences.
Output File Names:
E:\Black Walnut project\Fungi BW\FunBW.trim.contigs.good.unique.summary
mothur >
chimera.vsearch(fasta=E:\Black Walnut project\Fungi BW\FunBW.trim.contigs.good.unique.fasta, count=E:\Black Walnut project\Fungi BW\FunBW.trim.contigs.good.count_table)
Using 24 processors.
Checking sequences from E:\Black Walnut project\Fungi BW\FunBW.trim.contigs.good.unique.fasta …
/******************************************/
Running command: split.groups(groups=1-ITS-10-ITS-11-ITS-12-ITS-2-ITS-3-ITS-4-ITS-49-ITS-5-ITS-50-ITS-51-ITS-52-ITS-53-ITS-54-ITS-55-ITS-56-ITS-57-ITS-58-ITS-59-ITS-6-ITS-60-ITS-7-ITS-8-ITS-9-ITS, fasta=E:\Black Walnut project\Fungi BW\FunBW.trim.contigs.good.unique.fasta, count=E:\Black Walnut project\Fungi BW\FunBW.trim.contigs.good.count_table)
Using 24 processors.
Output File Names: