# make.contigs sample run twice

**URL:** <https://forum.mothur.org/t/make-contigs-sample-run-twice/3018>\
**Category:** Commands in mothur\
**Created:** [October 17, 2016, 3:23pm UTC](https://forum.mothur.org/t/make-contigs-sample-run-twice/3018 "2016-10-17T15:23:01Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![Kendra](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/kendra/32/112_2.png) [@Kendra](https://forum.mothur.org/u/Kendra)\
**Post date:** [October 17, 2016, 3:23pm UTC](https://forum.mothur.org/t/make-contigs-sample-run-twice/3018/1 "2016-10-17T15:23:01Z")

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What does make.contigs do if a sample is in the stability file twice? Same sample name but different R1 and R2 fastq. Does it concatenate all the seqs together, only take the first/second line?

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**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:** [November 1, 2016, 5:49pm UTC](https://forum.mothur.org/t/make-contigs-sample-run-twice/3018/2 "2016-11-01T17:49:31Z")

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It will pool the data for the two sets of files.

Pat