Count file and fasta file mismatch

[dohan]

Hello, can somebody help me?.
at first I have no issue when running this command:
mothur > make.contigs(file=stability.files)
and this is the result:

It took 33 secs to assemble 170254 reads.


Group count: 
A0.raw	170377
A1.raw	173339
A2.raw	170834
R1.raw	173631
R2.raw	170254

Total of all groups is 858435

It took 169 secs to process 858435 sequences.

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

then the step was done and i run this command to check the summary but I got the error.

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

Using 8 processors.
[ERROR]: Your count file contains 858379 unique sequences, but your fasta file contains 858435. File mismatch detected, quitting command.

why i got this error and how to fix this
I hope I can get help in this
thank you

[pschloss]

Can you run this again and see if you still get the error message? I wonder if the process ended prematurely or if you were manually editing either of the files

Pat

[dohan]

Hi, thank you for replying my question.

I’ve successfully solved the problem by following the guide from here File mismatch detected, quitting command.
the thing I did was removing the mismatched sequence from stability.trim.contig.fasta file to match the number of sequence to count_table file because the mismatched fasta are not so much only about 56 sequences.
so I run this command:

mothur > list.seqs(fasta=stability.trim.contigs.fasta)

Output File Names: 
stability.trim.contigs.accnos

then I use stability.trim.contigs.accnos file to run this command below:

mothur > get.seqs(accnos=stability.trim.contigs.accnos, fasta=stability.trim.contigs.fasta)

Output File Names:
stability.trim.contigs.pick.fasta

finally i successfully run the summary.seqs using updated fasta file that match with the count table. here is the result:

		Start	End	NBases	Ambigs	Polymer	NumSeqs
Minimum:	1	38	38	0	3	1
2.5%-tile:	1	386	386	0	4	20747
25%-tile:	1	404	404	0	5	207461
Median: 	1	405	405	0	5	414922
75%-tile:	1	419	419	0	5	622382
97.5%-tile:	1	430	430	6	8	809096
Maximum:	1	440	440	69	220	829842
Mean:	1	409	409	0	5
# of unique seqs:	829842
total # of seqs:	829842

It took 5 secs to summarize 829842 sequences.

Output File Names:
stability.trim.contigs.pick.summary

Thank you sir!