Make.contigs process stopped before generating count.table

1

Hi. Thanks for making great software. I’ve been using it very well for my study and I really appreciate all the efforts you put into it.

I have >2000 samples and ran make.contigs on my PC. It took a few days and generated a fasta file larger than 100 GB, but the system got frozen before it generated a count_table file. The last message (log) I can see on the screen was “It took xxx secs to assemble xxx reads.” for the last pair, and the system was unresponsive for more than 10 hours.

Is there a way that I create count.table out of fasta file? Thanks.

2

Could you be running out of file disk space?

To answer your question, yes, you can generate a count file from a fasta file using the make.group command. The make.group can be used in several ways. The simplest form is:

mothur > make.group(fasta=sample1.fasta-sample2.fasta-sample3.fasta, groups=A-B-C)
Assigning sequences from file sample1.fasta to group A: 2424 sequences assigned to group A
Assigning sequences from file sample2.fasta to group B: 2402 sequences assigned to group B
Assigning sequences from file sampl31.fasta to group C: 1830 sequences assigned to group C

Group count:
A 2424
B. 2402
C. 1830
Total of all groups is 6656

Output File Names: merge.count_table

Given the number of samples and file formatting, I recommend this workflow:

// create a fasta file for each fastq file in the file file.
mothur > fastq.info(file=stability.files,qfile=f, fasta=t, outputdir=~/Desktop/tempFiles)

7793
5958
3183
…

/Users/swestcott//Desktop/tempFiles/F3D8_S196_L001_R2_001.fasta
/Users/swestcott//Desktop/tempFiles/F3D9_S197_L001_R1_001.fasta
/Users/swestcott//Desktop/tempFiles/F3D9_S197_L001_R2_001.fasta
/Users/swestcott//Desktop/tempFiles/Mock_S280_L001_R1_001.fasta
/Users/swestcott//Desktop/tempFiles/Mock_S280_L001_R2_001.fasta

// create a 3 cols paired file file
mothur > make.file(inputdir=~/Desktop/tempFiles, type=fasta, numcols=3)
Setting input directories to:
/Users/swestcott//Desktop/tempFiles/

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Output File Names:
/Users/swestcott/Desktop/tempFiles/stability.files

// create a count_table from the file file
mothur > make.count(file=current)
Using /Users/swestcott//Desktop/tempFiles/stability.files as input file for the file parameter.
…

Assigning sequences from file /Users/swestcott//Desktop/tempFiles/F3D9_S197_L001_R1_001.fasta to group F3D9: 7070 sequences assigned to group F3D9
Assigning sequences from file /Users/swestcott//Desktop/tempFiles/Mock_S280_L001_R1_001.fasta to group Mock: 4779 sequences assigned to group Mock

Group count:

F3D0 7793
F3D1 5869
F3D141 5958
F3D142 3183
F3D143 3178
F3D144 4827
F3D145 7377
F3D146 5021
F3D147 17070
F3D148 12405
F3D149 13083
F3D150 5509
F3D2 19620
F3D3 6758
F3D5 4448
F3D6 7989
F3D7 5129
F3D8 5294
F3D9 7070
Mock 4779

Total of all groups is 152360

Output File Names: /Users/swestcott//Desktop/tempFiles/stability.count_table

1 Like
3

Ok. thank you! The disk space was ok, but I was using an external HDD, so that could be the reason.
I will look into the way you suggested. Have a great day!