# Make.contigs doesn’t create stability.contigs.count\_table **URL:** \ **Category:** Uncategorized\ **Created:** [March 17, 2026, 10:58am UTC](https://forum.mothur.org/t/make-contigs-doesn-t-create-stability-contigs-count-table/22409 "2026-03-17T10:58:11Z")\ **Posts on this page:** 8\ **Page:** 1
**Author:** ![Raj](https://avatars.discourse-cdn.com/v4/letter/r/c0e974/32.png) [@Raj](https://forum.mothur.org/u/Raj)\ **Post date:** [March 17, 2026, 10:58am UTC](https://forum.mothur.org/t/make-contigs-doesn-t-create-stability-contigs-count-table/22409/1 "2026-03-17T10:58:11Z")
Hi, I couldn’t find stability.contigs.count\_table to run commands like summary.seqs(fasta=stability.trim.contigs.fasta, count=stability.contigs.count\_table). I am using version1.48.5. need suggestions/advise please. ---
**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:** [March 17, 2026, 12:41pm UTC](https://forum.mothur.org/t/make-contigs-doesn-t-create-stability-contigs-count-table/22409/2 "2026-03-17T12:41:13Z")
Can you tell us how you are running `make.contigs`? Can you post the command you’re usin gand the output that’s going to the screen? Pat ---
**Author:** ![Raj](https://avatars.discourse-cdn.com/v4/letter/r/c0e974/32.png) [@Raj](https://forum.mothur.org/u/Raj)\ **Post date:** [March 18, 2026, 12:03am UTC](https://forum.mothur.org/t/make-contigs-doesn-t-create-stability-contigs-count-table/22409/3 "2026-03-18T00:03:48Z")
Hi Pat, Below is hte command and the output. make.contigs(file=stability.files, oligos=Oligos31052021.txt, maxambig=0, maxlength=275, maxhomop=8) It took 47648 secs to process 29231563 sequences. Output File Names: stability.trim.contigs.fasta stability.scrap.contigs.fasta stability.contigs\_report Really appritiate your help and advise, Raj ---
**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:** [March 18, 2026, 12:14pm UTC](https://forum.mothur.org/t/make-contigs-doesn-t-create-stability-contigs-count-table/22409/4 "2026-03-18T12:14:10Z")
Can you post the contents of Oligos31052021.txt? ---
**Author:** ![Raj](https://avatars.discourse-cdn.com/v4/letter/r/c0e974/32.png) [@Raj](https://forum.mothur.org/u/Raj)\ **Post date:** [March 19, 2026, 12:34am UTC](https://forum.mothur.org/t/make-contigs-doesn-t-create-stability-contigs-count-table/22409/5 "2026-03-19T00:34:52Z")
primer GTGYCAGCMGCCGCGGTAA GGACTACNVGGGTWTCTAAT V4 ---
**Author:** ![Raj](https://avatars.discourse-cdn.com/v4/letter/r/c0e974/32.png) [@Raj](https://forum.mothur.org/u/Raj)\ **Post date:** [March 19, 2026, 12:48am UTC](https://forum.mothur.org/t/make-contigs-doesn-t-create-stability-contigs-count-table/22409/6 "2026-03-19T00:48:12Z")
Hi Pat, Attached is the Oligos file with contents. Also, attached the log file that I used previously(2 years ago approx.) for an experiment that I am trying to replicate for identical experiment now with different sample files. I have since gone back to referring the MiSeq Sop and I am progressing further with the commands from the SOP. Please advise any changes I will have to make/understand to input /info values suitable in a command for my project ? Hope I am making sense (still learning about command prompts and how they work). Thank you and Regards, Raj (Attachment Oligos31052021.txt is missing) ---
**Author:** ![Raj](https://avatars.discourse-cdn.com/v4/letter/r/c0e974/32.png) [@Raj](https://forum.mothur.org/u/Raj)\ **Post date:** [March 19, 2026, 3:00am UTC](https://forum.mothur.org/t/make-contigs-doesn-t-create-stability-contigs-count-table/22409/7 "2026-03-19T03:00:44Z")
mothur \> summary.seqs(fasta=stability.trim.contigs.fasta, count=stability.contigs.count\_table) Using 14 processors. ```auto Start End NBases Ambigs Polymer NumSeqs ``` Minimum: 1 300 300 0 3 1 2.5%-tile: 1 308 308 0 4 366283 25%-tile: 1 308 308 0 4 3662826 Median: 1 308 308 1 5 7325651 75%-tile: 1 309 309 3 5 10988476 97.5%-tile: 1 579 579 9 204 14285019 Maximum: 1 600 600 102 300 14651301 Mean: 1 331 331 1 21 # of unique seqs: 14651301 total # of seqs: 14651301 It took 634 secs to summarize 14651301 sequences. Output File Names: stability.trim.contigs.summary screen.seqs(fasta=stability.trim.contigs.fasta, count=stability.contigs.count\_table, maxambig=0, maxlength=275, maxhomop=8) Should be be changing the maxlength based on my summary table? ---
**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:** [March 19, 2026, 1:00pm UTC](https://forum.mothur.org/t/make-contigs-doesn-t-create-stability-contigs-count-table/22409/8 "2026-03-19T13:00:47Z")
Is it working for you now? You don’t have any group information in your oligos file. If you still need help, can you post all of the commands you are running along with what version number of mothur you are using? Pat