make.contigs error

mothur bugs
1

I am unable to use the make.contigs command with my files.

mothur > make.contigs(ffastq=CD34_5_1.fastq, rfastq=CD34_5_2.fastq)


Using 1 processors. Reading fastq data... [ERROR]: read HWI-ST1207:222:C166PACXX:5:1101:4344:2181 1:N:0:ACTT from CD34_5_1.fastq, but read HWI-ST1207:222:C166PACXX:5:1101:4344:2181 2:N:0:ACTT from CD34_5_2.fastq. Done.


mothur > make.contigs(ffastq=CD34_5_1.fastq, rfastq=CD34_5_2.fastq, format=illumina)

format is not a valid parameter.
The valid parameters are: ffastq, rfastq, align, match, mismatch, gapopen, gapextend, threshold, processors, inputdir, and outputdir.

Using 1 processors.
[ERROR]: did not complete make.contigs.

2

What version of mothur are you using?

3

The same error occurs with v.1.27.0 and v.1.29.1

4

Could you send your fastq files to mothur.bugs@gmail.com?

5

I have almost similar problem with make.contigs
I am running v.1.29.2 on Win7 64 bit machine. Problem appears with MiSeq SOP data set.

This is the start:
mothur > make.contigs(file=stability.files1.txt, processors=8)

Using 8 processors.
Reading fastq data…
[WARNING]: can’t find F3D0, ignoring pair.
[WARNING]: can’t find F3D141, ignoring pair.
…
Here it continues:

[WARNING]: For sequence M00967:43:000000000-A3JHG:1:1101:11786:2744 I read a sequence of length 251 from F3D141_S207_L001_R1_001.fastq, but read a sequence of length 250 from F3D141_S207_L001_R2_001.fastq, ignoring.
[WARNING]: For sequence M00967:43:000000000-A3JHG:1:1101:11786:2744 I read 251 quality scores from F3D141_S207_L001_R1_001.fastq, but read 250 quality scores from F3D141_S207_L001_R2_001.fastq, ignoring.
…

At the end of run program created no “group” output.
Program has processed only 10 out of 21 files from the SOP data set. Program uses only each first file and skips second file and so on. Please see log file record:
…
It took 113 secs to process 52299 sequences.
Output File Names:
stability.files1.trim.contigs.fasta
stability.files1.trim.contigs.qual
stability.files1.contigs.mismatch
stability.files1.scrap.contigs.fasta
stability.files1.scrap.contigs.qual
F3D141_S207_L001_R1_001.trim.contigs.fasta
F3D141_S207_L001_R1_001.scrap.contigs.fasta
F3D141_S207_L001_R1_001.trim.contigs.qual
F3D141_S207_L001_R1_001.scrap.contigs.qual
F3D141_S207_L001_R1_001.contigs.mismatch
F3D143_S209_L001_R1_001.trim.contigs.fasta
F3D143_S209_L001_R1_001.scrap.contigs.fasta
F3D143_S209_L001_R1_001.trim.contigs.qual
F3D143_S209_L001_R1_001.scrap.contigs.qual
F3D143_S209_L001_R1_001.contigs.mismatch
F3D145_S211_L001_R1_001.trim.contigs.fasta
F3D145_S211_L001_R1_001.scrap.contigs.fasta
F3D145_S211_L001_R1_001.trim.contigs.qual
F3D145_S211_L001_R1_001.scrap.contigs.qual
F3D145_S211_L001_R1_001.contigs.mismatch
F3D147_S213_L001_R1_001.trim.contigs.fasta
F3D147_S213_L001_R1_001.scrap.contigs.fasta
F3D147_S213_L001_R1_001.trim.contigs.qual
F3D147_S213_L001_R1_001.scrap.contigs.qual
F3D147_S213_L001_R1_001.contigs.mismatch
F3D149_S215_L001_R1_001.trim.contigs.fasta
F3D149_S215_L001_R1_001.scrap.contigs.fasta
F3D149_S215_L001_R1_001.trim.contigs.qual
F3D149_S215_L001_R1_001.scrap.contigs.qual
F3D149_S215_L001_R1_001.contigs.mismatch
F3D1_S189_L001_R1_001.trim.contigs.fasta
F3D1_S189_L001_R1_001.scrap.contigs.fasta
F3D1_S189_L001_R1_001.trim.contigs.qual
F3D1_S189_L001_R1_001.scrap.contigs.qual
F3D1_S189_L001_R1_001.contigs.mismatch
F3D3_S191_L001_R1_001.trim.contigs.fasta
F3D3_S191_L001_R1_001.scrap.contigs.fasta
F3D3_S191_L001_R1_001.trim.contigs.qual
F3D3_S191_L001_R1_001.scrap.contigs.qual
F3D3_S191_L001_R1_001.contigs.mismatch
F3D6_S194_L001_R1_001.trim.contigs.fasta
F3D6_S194_L001_R1_001.scrap.contigs.fasta
F3D6_S194_L001_R1_001.trim.contigs.qual
F3D6_S194_L001_R1_001.scrap.contigs.qual
F3D6_S194_L001_R1_001.contigs.mismatch
F3D8_S196_L001_R1_001.trim.contigs.fasta
F3D8_S196_L001_R1_001.scrap.contigs.fasta
F3D8_S196_L001_R1_001.trim.contigs.qual
F3D8_S196_L001_R1_001.scrap.contigs.qual
F3D8_S196_L001_R1_001.contigs.mismatch
Mock_S280_L001_R1_001.trim.contigs.fasta
Mock_S280_L001_R1_001.scrap.contigs.fasta
Mock_S280_L001_R1_001.trim.contigs.qual
Mock_S280_L001_R1_001.scrap.contigs.qual
Mock_S280_L001_R1_001.contigs.mismatch

The “real MiSeq files” were behaving in the similar way. Program ignores grouping information and uses only half of the files.
Sincerely yours,

6

Ahem… You aren’t supposed to know about the MiSeq_SOP page yet! This will only work with the version that we will release on Monday.

7

Ups… Until Monday then. I am looking forward to see the release.

8

I am having a problem with the make.contigs command in mothur. I am a newbie to using this pipeline so it is likely something simple but I just have no clue :slight_smile:

When I run the command:

mothur > make.contigs(file=/Users/Molly-Mac/Desktop/Next_gen_data_analysis/Test_Germany/amphibian_Test.files)


I get the following:
Using 2 processors. Reading fastq data... [WARNING]: can't find AltB2_S407_L001_R1_001.fastq, ignoring pair. [WARNING]: can't find AltB2_S407_L001_R2_001.fastq, ignoring pair. [WARNING]: can't find AltB3_S408_L001_R1_001.fastq, ignoring pair. [WARNING]: can't find AltB3_S408_L001_R2_001.fastq, ignoring pair. [WARNING]: can't find AltB4_S409_L001_R1_001.fastq, ignoring pair. [WARNING]: can't find AltB4_S409_L001_R2_001.fastq, ignoring pair. [WARNING]: can't find AltB5_S410_L001_R1_001.fastq, ignoring pair. [WARNING]: can't find AltB5_S410_L001_R2_001.fastq, ignoring pair. [WARNING]: can't find AltB6_S411_L001_R1_001.fastq, ignoring pair. [WARNING]: can't find AltB6_S411_L001_R2_001.fastq, ignoring pair. [WARNING]: can't find AltB7_S412_L001_R1_001.fastq, ignoring pair. [WARNING]: can't find AltB7_S412_L001_R2_001.fastq, ignoring pair. [WARNING]: can't find AltB8_S413_L001_R1_001.fastq, ignoring pair. [WARNING]: can't find AltB8_S413_L001_R2_001.fastq, ignoring pair. [WARNING]: can't find AltB9_S414_L001_R1_001.fastq, ignoring pair. [WARNING]: can't find AltB9_S414_L001_R2_001.fastq, ignoring pair. Done. It took 0 secs to process 0 sequences.



Output File Names:

The files are housed in the same folder as the inputed file. I have also tried running this with the example data set form the Wiki page, using the stability.files as the input and I get the same error.

Can anyone direct me on how to solve this and get it to “find” the files?

Thanks!

9

http://www.mothur.org/wiki/Frequently_asked_questions#Mothur_can.27t_find_my_input_files