# Screen.seqs generating weird result **URL:** \ **Category:** Commands in mothur\ **Created:** [February 8, 2026, 3:51pm UTC](https://forum.mothur.org/t/screen-seqs-generating-weird-result/22405 "2026-02-08T15:51:08Z")\ **Posts on this page:** 9\ **Page:** 1
**Author:** ![John\_Kelly](https://avatars.discourse-cdn.com/v4/letter/j/a698b9/32.png) [@John\_Kelly](https://forum.mothur.org/u/John_Kelly)\ **Post date:** [February 8, 2026, 3:51pm UTC](https://forum.mothur.org/t/screen-seqs-generating-weird-result/22405/1 "2026-02-08T15:51:09Z")
After aligning my sequences to silva.seed\_v138 I ran summary.seqs: ```auto mothur > summary.seqs(fasta=csp_bact.trim.contigs.good.unique.align, count=csp_bact.trim.contigs.good.count_table) ``` And the results looked fine : ```auto Start End NBases Ambigs Polymer NumSeqs Minimum: 0 0 0 0 1 1 2.5%-tile: 13862 23444 252 0 3 170812 25%-tile: 13862 23444 253 0 4 1708117 Median: 13862 23444 253 0 4 3416233 75%-tile: 13862 23444 253 0 5 5124349 97.5%-tile: 13862 23444 254 0 6 6661653 Maximum: 23484 23491 295 0 8 6832464 Mean: 13865 23407 252 0 4 # of unique seqs: 3423400 total # of seqs: 6832464 ``` I then ran screen seqs: ```auto mothur > screen.seqs(fasta=csp_bact.trim.contigs.good.unique.align, count=csp_bact.trim.contigs.good.count_table, summary=csp_bact.trim.contigs.good.unique.summary, start=13862, end=23444) ``` And the results did not make sense: ```auto It took 169 secs to screen 3423400 sequences, removed 18745. ****************************************************************************** Running command: remove.seqs(accnos=csp_bact.trim.contigs.good.unique.bad.accnos.temp, count=csp_bact.trim.contigs.good.count_table) Removed 0 sequences from csp_bact.trim.contigs.good.count_table. Output File Names: csp_bact.trim.contigs.good.pick.count_table ****************************************************************************** Output File Names: csp_bact.trim.contigs.good.unique.good.summary csp_bact.trim.contigs.good.unique.good.align csp_bact.trim.contigs.good.unique.bad.accnos csp_bact.trim.contigs.good.good.count_table ``` Specifically, the output file csp\_bact.trim.contigs.good.good.count\_table is empty, and the summary.seqs of the output files shows much lower total number of sequences and it looks like they have not been trimmed based on my start and end values. ```auto summary.seqs(fasta=csp_bact.trim.contigs.good.unique.good.align, count=csp_bact.trim.contigs.good.good.count_table) [ERROR]: csp_bact.trim.contigs.good.good.count_table is blank, aborting. Start End NBases Ambigs Polymer NumSeqs Minimum: 13835 23444 227 0 3 1 2.5%-tile: 13862 23444 252 0 3 11723 25%-tile: 13862 23444 253 0 4 117224 Median: 13862 23444 253 0 4 234448 75%-tile: 13862 23444 253 0 5 351671 97.5%-tile: 13862 23444 254 0 6 457172 Maximum: 13862 23486 292 0 8 468894 Mean: 13861 23444 253 0 4 # of Seqs: 468894 It took 9 secs to summarize 468894 sequences. ``` I’ve run this multiple times and keep getting the same result. I’ve even gone back to the beginning and started the mothur analysis from scratch and the result is the same. Any suggestions would be appreciated. ---
**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 9, 2026, 4:49pm UTC](https://forum.mothur.org/t/screen-seqs-generating-weird-result/22405/2 "2026-02-09T16:49:19Z")
I am happy to help. Can you tell me what version of mothur you are using? Also, the results of the first summary.seqs command look off. It appears to indicate you have sequences with a length of 0. Could you post the commands you ran before this issue? ---
**Author:** ![John\_Kelly](https://avatars.discourse-cdn.com/v4/letter/j/a698b9/32.png) [@John\_Kelly](https://forum.mothur.org/u/John_Kelly)\ **Post date:** [February 19, 2026, 3:59pm UTC](https://forum.mothur.org/t/screen-seqs-generating-weird-result/22405/3 "2026-02-19T15:59:46Z")
We are using mothur v.1.48.0 mothur \> make.file(inputdir=., type=fastq, prefix=csp\_bact) Output File Names: csp\_bact.files mothur \> make.contigs(file=csp\_bact.files) Group count: 3429 138741 3429\_054 72943 3429\_055 133730 3429\_056 137291 3429\_057 126135 3429\_058 94121 3429\_059 115847 3429\_060 54472 3429\_061 129139 3429\_062 117871 3429\_063 124400 3429\_064 117099 3429\_065 136891 3429\_066 134079 3429\_067 135028 3429\_068 128333 3429\_069 131371 3429\_070 182815 3429\_071 193017 3429\_072 178557 3429\_073 138175 3429\_074 157246 3429\_075 143929 3429\_076 121179 3429\_081 142772 3429\_082 161533 3429\_083 128257 3429\_084 150879 3429\_089 114588 3429\_090 121028 3429\_091 129672 3429\_092 153985 3429\_093 145101 3429\_094 173435 3429\_095 136221 3429\_096 168714 3429\_097 198212 3429\_098 203622 3429\_099 237756 3429\_100 220755 3429\_101 180031 3429\_102 214197 3429\_103 205486 3429\_104 218382 3429b 80371 3429b\_02 74021 3429b\_03 77665 3429b\_04 74341 3429b\_05 80934 3429b\_06 83707 3429b\_07 68833 3429b\_08 66747 Total of all groups is 7153654 It took 349 secs to process 7153654 sequences. Output File Names: csp\_bact.trim.contigs.fasta csp\_bact.scrap.contigs.fasta csp\_bact.contigs\_report csp\_bact.contigs.count\_table mothur \> summary.seqs(fasta=csp\_bact.trim.contigs.fasta) Start End NBases Ambigs Polymer NumSeqs Minimum: 1 309 309 0 3 1 2.5%-tile: 1 325 325 0 3 178842 25%-tile: 1 326 326 0 4 1788414 Median: 1 326 326 0 4 3576828 75%-tile: 1 326 326 0 5 5365241 97.5%-tile: 1 327 327 1 7 6974813 Maximum: 1 618 618 123 309 7153654 Mean: 1 327 327 0 5 # of Seqs: 7153654 It took 39 secs to summarize 7153654 sequences. Output File Names: csp\_bact.trim.contigs.summary mothur \> screen.seqs(fasta=csp\_bact.trim.contigs.fasta, count=csp\_bact.contigs.count\_table, maxambig=0, maxlength=330, maxhomop=8) Using 80 processors. It took 48 secs to screen 7153654 sequences, removed 321190. /\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*/ Running command: remove.seqs(accnos=csp\_bact.trim.contigs.bad.accnos.temp, count=csp\_bact.contigs.count\_table) Removed 321190 sequences from csp\_bact.contigs.count\_table. Output File Names: csp\_bact.contigs.pick.count\_table /\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*/ Output File Names: csp\_bact.trim.contigs.good.fasta csp\_bact.trim.contigs.bad.accnos csp\_bact.contigs.good.count\_table It took 117 secs to screen 7153654 sequences. mothur \> summary.seqs(fasta=csp\_bact.trim.contigs.good.fasta) Using 80 processors. Start End NBases Ambigs Polymer NumSeqs Minimum: 1 309 309 0 3 1 2.5%-tile: 1 325 325 0 3 170812 25%-tile: 1 326 326 0 4 1708117 Median: 1 326 326 0 4 3416233 75%-tile: 1 326 326 0 5 5124349 97.5%-tile: 1 327 327 0 6 6661653 Maximum: 1 330 330 0 8 6832464 Mean: 1 325 325 0 4 # of Seqs: 6832464 It took 63 secs to summarize 6832464 sequences. Output File Names: csp\_bact.trim.contigs.good.summary mothur \> unique.seqs(fasta=csp\_bact.trim.contigs.good.fasta, count= csp\_bact.contigs.good.count\_table) 6832464 3423400 Output File Names: csp\_bact.trim.contigs.good.unique.fasta csp\_bact.trim.contigs.good.count\_table mothur \> summary.seqs(fasta=csp\_bact.trim.contigs.good.unique.fasta, count=csp\_bact.trim.contigs.good.count\_table)summary.seqs(fasta=csp\_bact.trim.contigs.good.unique.fasta, count=csp\_bact.trim.contigs.good.count\_table) Start End NBases Ambigs Polymer NumSeqs Minimum: 1 309 309 0 3 1 2.5%-tile: 1 325 325 0 3 170812 25%-tile: 1 326 326 0 4 1708117 Median: 1 326 326 0 4 3416233 75%-tile: 1 326 326 0 5 5124349 97.5%-tile: 1 327 327 0 6 6661653 Maximum: 1 330 330 0 8 6832464 Mean: 1 325 325 0 4 # of unique seqs: 3423400 total # of seqs: 6832464 It took 179 secs to summarize 6832464 sequences. Output File Names: csp\_bact.trim.contigs.good.unique.summary mothur \> pcr.seqs(fasta=silva.seed\_v138\_2.align, oligos=oligos.txt) Using 80 processors. It took 0 secs to screen 8696 sequences. Output File Names: silva.seed\_v138\_2.pcr.align silva.seed\_v138\_2.bad.accnos silva.seed\_v138\_2.scrap.pcr.align mothur \> rename.file(input=silva.seed\_v138\_2.pcr.align, new=silva.v138.fasta) mothur \> summary.seqs(fasta=silva.v138.fasta) Start End NBases Ambigs Polymer NumSeqs Minimum: 13836 23444 230 0 3 1 2.5%-tile: 13862 23444 252 0 3 151 25%-tile: 13862 23444 253 0 4 1504 Median: 13862 23444 253 0 4 3007 75%-tile: 13862 23444 253 0 5 4510 97.5%-tile: 13862 23444 254 1 6 5862 Maximum: 13862 23491 311 4 10 6012 Mean: 13861 23444 252 0 4 # of Seqs: 6012 It took 0 secs to summarize 6012 sequences. Output File Names: silva.v138.summary mothur \> align.seqs(fasta=csp\_bact.trim.contigs.good.unique.fasta, reference=silva.v138.fasta) Using 80 processors. Reading in the silva.v138.fasta template sequences… DONE. It took 4 to read 6012 sequences. Aligning sequences from csp\_bact.trim.contigs.good.unique.fasta … It took 509 secs to align 3423400 sequences. [WARNING]: 15996 of your sequences generated alignments that eliminated too many bases, a list is provided in csp\_bact.trim.contigs.good.unique.flip.accnos. [NOTE]: 8927 of your sequences were reversed to produce a better alignment. It took 509 seconds to align 3423400 sequences. Output File Names: csp\_bact.trim.contigs.good.unique.align csp\_bact.trim.contigs.good.unique.align\_report csp\_bact.trim.contigs.good.unique.flip.accnos mothur \> summary.seqs(fasta=csp\_bact.trim.contigs.good.unique.align, count=csp\_bact.trim.contigs.good.count\_table) Using 80 processors. Start End NBases Ambigs Polymer NumSeqs Minimum: 0 0 0 0 1 1 2.5%-tile: 13862 23444 252 0 3 170812 25%-tile: 13862 23444 253 0 4 1708117 Median: 13862 23444 253 0 4 3416233 75%-tile: 13862 23444 253 0 5 5124349 97.5%-tile: 13862 23444 254 0 6 6661653 Maximum: 23484 23491 295 0 8 6832464 Mean: 13865 23407 252 0 4 # of unique seqs: 3423400 total # of seqs: 6832464 It took 220 secs to summarize 6832464 sequences. Output File Names: csp\_bact.trim.contigs.good.unique.summary mothur \> screen.seqs(fasta=csp\_bact.trim.contigs.good.unique.align, count=csp\_bact.trim.contigs.good.count\_table, summary=csp\_bact.trim.contigs.good.unique.summary, start=13862, end=23444) It took 169 secs to screen 3423400 sequences, removed 18745. * * * Running command: remove.seqs(accnos=csp\_bact.trim.contigs.good.unique.bad.accnos.temp, count=csp\_bact.trim.contigs.good.count\_table) Removed 0 sequences from csp\_bact.trim.contigs.good.count\_table. Output File Names: csp\_bact.trim.contigs.good.pick.count\_table * * * Output File Names: csp\_bact.trim.contigs.good.unique.good.summary csp\_bact.trim.contigs.good.unique.good.align csp\_bact.trim.contigs.good.unique.bad.accnos csp\_bact.trim.contigs.good.good.count\_table mothur \> summary.seqs(fasta=csp\_bact.trim.contigs.good.unique.good.align, count=csp\_bact.trim.contigs.good.good.count\_table) [ERROR]: csp\_bact.trim.contigs.good.good.count\_table is blank, aborting. Start End NBases Ambigs Polymer NumSeqs Minimum: 13835 23444 227 0 3 1 2.5%-tile: 13862 23444 252 0 3 11723 25%-tile: 13862 23444 253 0 4 117224 Median: 13862 23444 253 0 4 234448 75%-tile: 13862 23444 253 0 5 351671 97.5%-tile: 13862 23444 254 0 6 457172 Maximum: 13862 23486 292 0 8 468894 Mean: 13861 23444 253 0 4 _# of Seqs: 468894_ It took 9 secs to summarize 468894 sequences ---
**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 20, 2026, 2:45pm UTC](https://forum.mothur.org/t/screen-seqs-generating-weird-result/22405/4 "2026-02-20T14:45:45Z")
Thanks for posting the log file. I am unable to reproduce the screen.seqs error with our test files. I tried including blank sequences as well and still not a problem. It appears the remove.seqs command run by the screen.seqs command is failing to generate a correct count file. Can you try running the commands separately like this? mothur \> screen.seqs(fasta=csp\_bact.trim.contigs.good.unique.align, summary=csp\_bact.trim.contigs.good.unique.summary, start=13862, end=23444) mothur \> remove.seqs(accnos=csp\_bact.trim.contigs.good.unique.bad.accnos, count=csp\_bact.trim.contigs.good.count\_table) mothur \> summary.seqs(fasta=csp\_bact.trim.contigs.good.unique.good.align, count=current) ---
**Author:** ![John\_Kelly](https://avatars.discourse-cdn.com/v4/letter/j/a698b9/32.png) [@John\_Kelly](https://forum.mothur.org/u/John_Kelly)\ **Post date:** [February 20, 2026, 10:17pm UTC](https://forum.mothur.org/t/screen-seqs-generating-weird-result/22405/5 "2026-02-20T22:17:12Z")
I re-ran the summary seqs and then tried your suggestion: mothur \> summary.seqs(fasta=csp\_bact.trim.contigs.good.unique.align, count=csp\_bact.trim.contigs.good.count\_table) Using 80 processors. ``` Start End NBases Ambigs Polymer NumSeqs ``` Minimum: 0 0 0 0 1 1 2.5%-tile: 13862 23444 252 0 3 170812 25%-tile: 13862 23444 253 0 4 1708117 Median: 13862 23444 253 0 4 3416233 75%-tile: 13862 23444 253 0 5 5124349 97.5%-tile: 13862 23444 254 0 6 6661653 Maximum: 23484 23491 295 0 8 6832464 Mean: 13865 23407 252 0 4 # of unique seqs: 3423400 total # of seqs: 6832464 It took 353 secs to summarize 6832464 sequences. Output File Names: csp\_bact.trim.contigs.good.unique.summary mothur \> screen.seqs(fasta=csp\_bact.trim.contigs.good.unique.align, summary=csp\_bact.trim.contigs.good.unique.summary, start=13862, end=23444) Using 80 processors. It took 168 secs to screen 3423400 sequences, removed 227. [ERROR]: found 3423400 sequences in your fasta file, and 42813 sequences in your summary file, quitting. mothur \> remove.seqs(accnos=csp\_bact.trim.contigs.good.unique.bad.accnos, count=csp\_bact.trim.contigs.good.count\_table) Removed 0 sequences from csp\_bact.trim.contigs.good.count\_table. Output File Names: csp\_bact.trim.contigs.good.pick.count\_table ---
**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 23, 2026, 2:25pm UTC](https://forum.mothur.org/t/screen-seqs-generating-weird-result/22405/6 "2026-02-23T14:25:36Z")
Could you be running out of disk space for the output files? ERROR]: found 3423400 sequences in your fasta file, and 42813 sequences in your summary file, quitting. The above error indicates the summary file was not completely written to file. ---
**Author:** ![John\_Kelly](https://avatars.discourse-cdn.com/v4/letter/j/a698b9/32.png) [@John\_Kelly](https://forum.mothur.org/u/John_Kelly)\ **Post date:** [February 24, 2026, 3:46pm UTC](https://forum.mothur.org/t/screen-seqs-generating-weird-result/22405/7 "2026-02-24T15:46:59Z")
That’s possible. I’ll check. Thanks so much for all of the quick responses. I really appreciate it. ---
**Author:** ![John\_Kelly](https://avatars.discourse-cdn.com/v4/letter/j/a698b9/32.png) [@John\_Kelly](https://forum.mothur.org/u/John_Kelly)\ **Post date:** [February 26, 2026, 2:42pm UTC](https://forum.mothur.org/t/screen-seqs-generating-weird-result/22405/8 "2026-02-26T14:42:22Z")
I moved the files to a larger cluster and re-ran the screen-seqs command and it worked! I guess that was the issue! Thank you so much for the help! ---
**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:** [March 8, 2026, 2:42pm UTC](https://forum.mothur.org/t/screen-seqs-generating-weird-result/22405/9 "2026-03-08T14:42:33Z")
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