Make.contigs doesn’t create stability.contigs.count_table

1

Hi,

I couldn’t find stability.contigs.count_table to run commands like summary.seqs(fasta=stability.trim.contigs.fasta, count=stability.contigs.count_table). I am using version1.48.5. need suggestions/advise please.

2

Can you tell us how you are running make.contigs? Can you post the command you’re usin gand the output that’s going to the screen?

Pat

3

Hi Pat,

Below is hte command and the output.

make.contigs(file=stability.files, oligos=Oligos31052021.txt, maxambig=0, maxlength=275, maxhomop=8)

It took 47648 secs to process 29231563 sequences.

Output File Names:
stability.trim.contigs.fasta
stability.scrap.contigs.fasta
stability.contigs_report

Really appritiate your help and advise,

Raj

4

Can you post the contents of Oligos31052021.txt?

5

primer GTGYCAGCMGCCGCGGTAA GGACTACNVGGGTWTCTAAT V4

6

Hi Pat,
Attached is the Oligos file with contents.
Also, attached the log file that I used previously(2 years ago approx.) for an experiment that I am trying to replicate for identical experiment now with different sample files.

I have since gone back to referring the MiSeq Sop and I am progressing further with the commands from the SOP.

Please advise any changes I will have to make/understand to input /info values suitable in a command for my project ? Hope I am making sense (still learning about command prompts and how they work).

Thank you and Regards,
Raj

(Attachment Oligos31052021.txt is missing)

7

mothur > summary.seqs(fasta=stability.trim.contigs.fasta, count=stability.contigs.count_table)

Using 14 processors.

            Start   End     NBases  Ambigs  Polymer NumSeqs

Minimum: 1 300 300 0 3 1
2.5%-tile: 1 308 308 0 4 366283
25%-tile: 1 308 308 0 4 3662826
Median: 1 308 308 1 5 7325651
75%-tile: 1 309 309 3 5 10988476
97.5%-tile: 1 579 579 9 204 14285019
Maximum: 1 600 600 102 300 14651301
Mean: 1 331 331 1 21

of unique seqs: 14651301

total # of seqs: 14651301

It took 634 secs to summarize 14651301 sequences.

Output File Names:
stability.trim.contigs.summary

screen.seqs(fasta=stability.trim.contigs.fasta, count=stability.contigs.count_table, maxambig=0, maxlength=275, maxhomop=8)

Should be be changing the maxlength based on my summary table?

8

Is it working for you now? You don’t have any group information in your oligos file.

If you still need help, can you post all of the commands you are running along with what version number of mothur you are using?

Pat