# make.contigs with oligo creating new names **URL:** \ **Category:** Commands in mothur\ **Created:** [October 3, 2018, 5:50pm UTC](https://forum.mothur.org/t/make-contigs-with-oligo-creating-new-names/3542 "2018-10-03T17:50:22Z")\ **Posts on this page:** 10\ **Page:** 1
**Author:** ![tallcuppajoe](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/tallcuppajoe/32/6_2.png) [@tallcuppajoe](https://forum.mothur.org/u/tallcuppajoe)\ **Post date:** [October 3, 2018, 5:50pm UTC](https://forum.mothur.org/t/make-contigs-with-oligo-creating-new-names/3542/1 "2018-10-03T17:50:22Z")
I’ve just upgraded to 1.40 finally, but I’ve found that the output of make.contigs results in names that are different from what they were in 1.39.5. I ran them back to back the other day to make sure. Here it is in 1.39.5, with output that I expect. mothur \> make.contigs(ffastq=Run4\_18S\_R1.fastq, rfastq=Run4\_18S\_R2.fastq, rindex=Run4\_18S\_I1.fastq, oligos=Run4\_18S\_oligos.txt, processors=2) Using 2 processors. Making contigs… Done. It took 5909 secs to process 16561081 sequences. Group count: DNA\_JL1001 88891 DNA\_JL1002 30488 DNA\_JL1003 64703 DNA\_JL1004 46793 DNA\_JL1005 63429 DNA\_JL1006 49208 DNA\_JL1007 51655 DNA\_JL1008 44797 DNA\_JL1009 63942 DNA\_JL1010 42425 … And here it is in 1.40, where all the names have .DNA\_JL1001 added to the end. mothur \> make.contigs(ffastq=Run4\_18S\_R1.fastq, rfastq=Run4\_18S\_R2.fastq, rindex=Run4\_18S\_I1.fastq, oligos=Run4\_18S\_oligos.txt, processors=2) Using 2 processors. Making contigs… Done. Group count: DNA\_JL1001.DNA\_JL1001 88891 DNA\_JL1002.DNA\_JL1001 30488 DNA\_JL1003.DNA\_JL1001 64703 DNA\_JL1004.DNA\_JL1001 46793 DNA\_JL1005.DNA\_JL1001 63429 DNA\_JL1006.DNA\_JL1001 49208 DNA\_JL1007.DNA\_JL1001 51655 DNA\_JL1008.DNA\_JL1001 44797 DNA\_JL1009.DNA\_JL1001 63942 DNA\_JL1010.DNA\_JL1001 42425 … It’s playing havoc with my downstream analysis when the names start changing from what they are in all the other databases. ---
**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:** [October 4, 2018, 8:19pm UTC](https://forum.mothur.org/t/make-contigs-with-oligo-creating-new-names/3542/2 "2018-10-04T20:19:35Z")
Is the “.DNA\_JL1001” appended to the group names in your oligos file? ---
**Author:** ![tallcuppajoe](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/tallcuppajoe/32/6_2.png) [@tallcuppajoe](https://forum.mothur.org/u/tallcuppajoe)\ **Post date:** [October 19, 2018, 8:11pm UTC](https://forum.mothur.org/t/make-contigs-with-oligo-creating-new-names/3542/3 "2018-10-19T20:11:28Z")
Sorry for the delay, due to hurricane evacuation and vacation. The oligos file looks like this: barcode NONE GGTGAAGATACA DNA\_JL1001 barcode NONE GACGAGTCAGTC DNA\_JL1002 barcode NONE AGCTATCCACGA DNA\_JL1003 barcode NONE ATGATGACCCGT DNA\_JL1004 barcode NONE ACGTAAATCGCC DNA\_JL1005 etc. There are not column headers. ---
**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:** [October 23, 2018, 1:48pm UTC](https://forum.mothur.org/t/make-contigs-with-oligo-creating-new-names/3542/4 "2018-10-23T13:48:06Z")
Are you seeing this issue with our pre-release 1.41.0, [https://github.com/mothur/mothur/releases/tag/v1.41.0.pre-release](https://github.com/mothur/mothur/releases/tag/v1.41.0.pre-release)? ---
**Author:** ![tallcuppajoe](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/tallcuppajoe/32/6_2.png) [@tallcuppajoe](https://forum.mothur.org/u/tallcuppajoe)\ **Post date:** [October 25, 2018, 6:58pm UTC](https://forum.mothur.org/t/make-contigs-with-oligo-creating-new-names/3542/5 "2018-10-25T18:58:21Z")
I’ve tried it with 1.41 and got the same result. (As an unrelated comment, I really like the “Current files saved by mothur:” output at the bottom of my script. Very helpful.) ---
**Author:** ![tallcuppajoe](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/tallcuppajoe/32/6_2.png) [@tallcuppajoe](https://forum.mothur.org/u/tallcuppajoe)\ **Post date:** [October 25, 2018, 10:56pm UTC](https://forum.mothur.org/t/make-contigs-with-oligo-creating-new-names/3542/6 "2018-10-25T22:56:16Z")
I also received this email from a colleague, working on a different set of sequences, with his own commands file. He’s having the same experience. "Hi Joe, I have a couple of questions. I am finally able to work a little on my GoM sequences. It has been so long that I was able to do that, that I thought it best to start from the beginning. I like to make the contigs using the oligo file so I don’t have to type out a long command to get or remove groups. When I run that, the list of sequences / group comes out like this: GoM\_8045.GoM\_8045 29241 GoM\_8046.GoM\_8045 29849 GoM\_8047.GoM\_8045 11863 GoM\_8048.GoM\_8045 22640 GoM\_8049.GoM\_8045 22306 GoM\_8050.GoM\_8045 20589 GoM\_8051.GoM\_8045 27726 GoM\_8052.GoM\_8045 23874 GoM\_8053.GoM\_8045 26772 GoM\_8045 is the first sample listed in the oligos file, and the .GoM\_8045 gets appended onto the name of the other samples. This happens in v139 and v140. The oligo file looks ok. I went ahead and used get.groups." ---
**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:** [November 1, 2018, 1:19pm UTC](https://forum.mothur.org/t/make-contigs-with-oligo-creating-new-names/3542/7 "2018-11-01T13:19:44Z")
Thanks for bringing this to our attention. I resolved the issue and the change will be part of the 1.41.0 release coming within the week. ---
**Author:** ![tallcuppajoe](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/tallcuppajoe/32/6_2.png) [@tallcuppajoe](https://forum.mothur.org/u/tallcuppajoe)\ **Post date:** [November 7, 2018, 8:16pm UTC](https://forum.mothur.org/t/make-contigs-with-oligo-creating-new-names/3542/8 "2018-11-07T20:16:15Z")
I downloaded the 1.41.0 version from github on 11/5 (Linux version) and ran my script again, but still got the same result. Batch Mode mothur \> make.contigs(ffastq=Run4\_18S\_R1.fastq, rfastq=Run4\_18S\_R2.fastq, rindex=Run4\_18S\_I1.fastq, oligos=Run4\_18S\_oligos.txt, processors=2) Using 2 processors. Making contigs… Done. Group count: DNA\_JL1001.DNA\_JL1001 88891 DNA\_JL1002.DNA\_JL1001 30488 DNA\_JL1003.DNA\_JL1001 64703 DNA\_JL1004.DNA\_JL1001 46793 DNA\_JL1005.DNA\_JL1001 63429 DNA\_JL1006.DNA\_JL1001 49208 DNA\_JL1007.DNA\_JL1001 51655 DNA\_JL1008.DNA\_JL1001 44797 DNA\_JL1009.DNA\_JL1001 63942 DNA\_JL1010.DNA\_JL1001 42425 And so on. ---
**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:** [November 8, 2018, 2:49pm UTC](https://forum.mothur.org/t/make-contigs-with-oligo-creating-new-names/3542/9 "2018-11-08T14:49:16Z")
We have not officially released 1.41.0; it’s coming soon. The bug is present in the 1.41.0 pre release available on github. ---
**Author:** ![tallcuppajoe](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/tallcuppajoe/32/6_2.png) [@tallcuppajoe](https://forum.mothur.org/u/tallcuppajoe)\ **Post date:** [November 8, 2018, 3:09pm UTC](https://forum.mothur.org/t/make-contigs-with-oligo-creating-new-names/3542/10 "2018-11-08T15:09:30Z")
Okay, thanks. I’ll look for the official release.😀