# Segfault with screen.seqs

**URL:** <https://forum.mothur.org/t/segfault-with-screen-seqs/20856>\
**Category:** mothur bugs\
**Created:** [January 31, 2021, 11:40am UTC](https://forum.mothur.org/t/segfault-with-screen-seqs/20856 "2021-01-31T11:40:08Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![genex](https://avatars.discourse-cdn.com/v4/letter/g/898d66/32.png) [@genex](https://forum.mothur.org/u/genex)\
**Post date:** [January 31, 2021, 11:40am UTC](https://forum.mothur.org/t/segfault-with-screen-seqs/20856/1 "2021-01-31T11:40:08Z")

</div>

Hi, I am using latest version of mothur (1.44.3) in Ubuntu 18. I have followed MiSeq SOP guide and everything went fine until the step of re-screening for making sure that all sequences overlap the same regions:

![Captura de pantalla 2021-01-31 a las 12.39.30](https://canada1.discourse-cdn.com/flex036/uploads/mothur/original/1X/07a671fa4012c1c31973b115bdcc25bcf30a5423.png)

```
screen.seqs(fasta=example.trim.contigs.good.unique.align, 
count=example.trim.contigs.good.count_table, 
summary=example.trim.contigs.good.unique.summary, start=1, end=18928)

```

The process seems to run properly but at the last step I always get a segfault when remove.seqs is triggered to update the count table giving the following error:

```
/ ****************************************** /
Running command: 
remove.seqs(accnos=example.trim.contigs.good.unique.bad.accnos.temp, 
count=example.trim.contigs.good.count_table)
[ERROR]: example.trim.contigs.good.unique.bad.accnos.temp is blank, aborting.
[ERROR]: You have no valid accnos file and accnos is required.
/ ****************************************** /
Segmentation fault

```

Any idea about what could be going on?

Thank you.

---

<div class="post-metadata">

**Author:** ![genex](https://avatars.discourse-cdn.com/v4/letter/g/898d66/32.png) [@genex](https://forum.mothur.org/u/genex)\
**Post date:** [January 31, 2021, 1:43pm UTC](https://forum.mothur.org/t/segfault-with-screen-seqs/20856/2 "2021-01-31T13:43:11Z")

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Update: I have tried the same but forcing to execute in a single CPU (processors=1) and still getting the same error but no segfault was triggered (altough example.trim.contigs.good.good.count\_table is a blank file).

```
/ ****************************************** /
Running command: 
remove.seqs(accnos=example.trim.contigs.good.unique.bad.accnos.temp, 
count=example.trim.contigs.good.count_table)
[ERROR]: example.trim.contigs.good.unique.bad.accnos.temp is blank, aborting.
Using example.trim.contigs.good.unique.flip.accnos as input file for the accnos 
parameter.
Removed 6362 sequences from your count file.
Output File Names:
example.trim.contigs.good.pick.count_table
/ ****************************************** /
Output File Names:
example.trim.contigs.good.unique.good.summary
example.trim.contigs.good.unique.good.align
example.trim.contigs.good.unique.bad.accnos
example.trim.contigs.good.good.count_table
```

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<div class="post-metadata">

**Author:** ![westcott](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/westcott/32/18_2.png) [@westcott](https://forum.mothur.org/u/westcott)\
**Post date:** [February 4, 2021, 5:18pm UTC](https://forum.mothur.org/t/segfault-with-screen-seqs/20856/3 "2021-02-04T17:18:29Z")

</div>

Could you send your input files and log file to [mothur.bugs@gmail.com](mailto:mothur.bugs@gmail.com)?

---

<div class="post-metadata">

**Author:** ![genex](https://avatars.discourse-cdn.com/v4/letter/g/898d66/32.png) [@genex](https://forum.mothur.org/u/genex)\
**Post date:** [February 12, 2021, 4:51pm UTC](https://forum.mothur.org/t/segfault-with-screen-seqs/20856/4 "2021-02-12T16:51:54Z")

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Hi. The error was produced by lack of disk space as the files generated during the process were really huge. Thank you for your answer.

---

<div class="post-metadata">

**Author:** ![system](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/system/32/2_2.png) [@system](https://forum.mothur.org/u/system)\
**Post date:** [February 22, 2021, 4:52pm UTC](https://forum.mothur.org/t/segfault-with-screen-seqs/20856/5 "2021-02-22T16:52:27Z")

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