# align.seqs errors to 1 processor

**URL:** <https://forum.mothur.org/t/align-seqs-errors-to-1-processor/3095>\
**Category:** mothur bugs\
**Created:** [January 25, 2017, 3:55pm UTC](https://forum.mothur.org/t/align-seqs-errors-to-1-processor/3095 "2017-01-25T15:55:36Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![jjknack](https://avatars.discourse-cdn.com/v4/letter/j/f19dbf/32.png) [@jjknack](https://forum.mothur.org/u/jjknack)\
**Post date:** [January 25, 2017, 3:55pm UTC](https://forum.mothur.org/t/align-seqs-errors-to-1-processor/3095/1 "2017-01-25T15:55:36Z")

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I’m running a modified version of the batch file found in the MiSeq SOP. I’m using a linux server node with 24 processors, and I’m successfully able to run all the commands in the batch file until I reach align.seqs. The following is from the standard output:

```nohighlight
mothur v.1.38.1
Last updated: 8/9/2016

...

mothur > set.current(fasta=HP012.trim.contigs.good.unique.fasta, group=HP012.contigs.good.groups, accnos=HP012.trim.contigs.bad.accnos, name=HP012.trim.contigs.good.names, count=HP012.trim.contigs.good.count_table, processors=24)

Using 24 processors.

Current files saved by mothur:
accnos=HP012.trim.contigs.bad.accnos
fasta=HP012.trim.contigs.good.unique.fasta
group=HP012.contigs.good.groups
name=HP012.trim.contigs.good.names
count=HP012.trim.contigs.good.count_table
processors=24

Output File Names: 
current_files.summary

mothur > align.seqs(fasta=current, reference=SILVA_128_SSURef_Nr99_tax_silva_full_align_trunc.fasta)
Using HP012.trim.contigs.good.unique.fasta as input file for the fasta parameter.

Using 24 processors.

Reading in the SILVA_128_SSURef_Nr99_tax_silva_full_align_trunc.fasta template sequences... DONE.
It took 875 to read 645151 sequences.
Aligning sequences from HP012.trim.contigs.good.unique.fasta ...
[ERROR]: unable to spawn the number of processes you requested, reducing number to 1
100
200

...

```

As you can see, there’s an error as soon as align.seqs tries to align my sequences to the reference, and it defaults to 1 processor. This only happens in align.seqs; all the previous commands successfully use 24 processors.

Am I doing something wrong? :?

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<div class="post-metadata">

**Author:** ![pschloss](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/pschloss/32/4_2.png) [@pschloss](https://forum.mothur.org/u/pschloss)\
**Post date:** [January 30, 2017, 1:57pm UTC](https://forum.mothur.org/t/align-seqs-errors-to-1-processor/3095/2 "2017-01-30T13:57:12Z")

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The problem is that it’s making 24 copies of the reference file. For this command, you might use processors=2 or 4 and see if that helps.

Pat

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<div class="post-metadata">

**Author:** ![jjknack](https://avatars.discourse-cdn.com/v4/letter/j/f19dbf/32.png) [@jjknack](https://forum.mothur.org/u/jjknack)\
**Post date:** [January 31, 2017, 10:50pm UTC](https://forum.mothur.org/t/align-seqs-errors-to-1-processor/3095/3 "2017-01-31T22:50:04Z")

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lol Cody and I just figured that out. Thanks tho!!!  
Jen