mothur

Missing pcr.seqs output


#1

Hi All-

So I ran:
pcr.seqs(fasta=silva.bacteria.fasta, start=11894, stop=25319, keepdots=F, processors=4)
And got:
Using 4 processors.
1000
1000
1000
1000
2000
2000
2000
2000
3000
3000
3000
3000
3739
3739
3739
3739
[NOTE]: no sequences were bad, removing Seqs\silva.bacteria.bad.accnos

It took 12 secs to screen 14956 sequences.

Output File Names:
Seqs\silva.bacteria.pcr.fasta

But my output file is no where to be found… I’ve looked every where.

Thoughts?

Thanks!
-Anne


#2

are you running this in windows, mac, or linux? If you’re in mac or linux, then from the mothur prompt you can type…

mothur > system(ls)
mothur > system(ls Seqs)
mothur > system(pwd)

The first will tell you what is in your current directory. There you should see files and a directory called Seqs. The second will tell you what is in the Seqs directory. The third command will tell you the path to the directory you are currently in. The following commands will work if you are using windows…

mothur > system(dir)
mothur > system(dir Seqs)
mothur > system(cd)

If you can report back what you see when running these commands we can go from there


#3

So the weird thing is, the first time I ran pcr.seqs I got the above output and tried running the rename.file like in the SOP, and got an error it couldn’t find the pcr.seqs output file. So I re-downloaded the silva file, re-ran pcr.seqs, got the same output and couldn’t find the output file anywhere but didn’t check and just ran the rename.file command per the SOP. It ran, but I still can’t find that pcr.seqs file anywhere. The output from the rename command put the silva.v4.fasta not in my Seqs file, so I moved it there and could run summary.seqs and align.seqs with no issues–well the commands ran with no errors, but I think I’ve messed some things up in previous steps thus the reason I’ll be at the workshop next month!

Anyways, I’m running Windows and this is the outputs I got from the commands you suggested to run:

mothur > system(dir)

Volume in drive C is Windows

Volume Serial Number is 7A47-01CD

Directory of C:\mothur\mothur

11/09/2018 09:23 AM <DIR> .

11/09/2018 09:23 AM <DIR> …

10/30/2018 12:38 PM 6,148 .DS_Store

10/30/2018 12:38 PM <DIR> blast

10/30/2018 12:38 PM 804,864 CatchAllCmdW.exe

11/09/2018 09:23 AM 0 commandScreen.output

11/07/2018 08:29 PM 385 current_files.summary

10/30/2018 02:12 PM 1,162,535,599 fasta.tar.gz

10/30/2018 01:06 PM 4,277,514,240 fastq.tar

11/01/2018 07:18 PM <DIR> GZ Seqs

10/30/2018 12:38 PM 31,944 LICENSE

11/06/2018 08:11 PM 1,485,113,010 mothur.1541120528.logfile

11/06/2018 08:58 PM 62,940,821 mothur.1541556718.logfile

11/06/2018 08:59 PM 26,689 mothur.1541559548.logfile

10/30/2018 12:38 PM 16,444,928 mothur.exe

11/08/2018 07:39 AM <DIR> Seqs

10/30/2018 12:38 PM 404,618 uchime.exe

10/30/2018 12:38 PM 6,591,456 vsearch.exe

11/07/2018 01:27 PM <DIR> __MACOSX

          13 File(s)  7,012,414,702 bytes

           6 Dir(s)  78,828,699,648 bytes free

mothur > system(dir Seqs)

Volume in drive C is Windows

Volume Serial Number is 7A47-01CD

Directory of C:\mothur\mothur\Seqs

11/08/2018 07:39 AM <DIR> .

11/08/2018 07:39 AM <DIR> …

09/13/2018 10:28 AM 143,877,011 BXR17001_10_R1.fastq

09/13/2018 10:28 AM 143,877,011 BXR17001_10_R2.fastq

09/13/2018 10:28 AM 123,145,273 BXR17001_11_R1.fastq

09/13/2018 10:28 AM 123,145,273 BXR17001_11_R2.fastq

09/13/2018 10:28 AM 120,321,791 BXR17001_12_R1.fastq

09/13/2018 10:28 AM 120,321,791 BXR17001_12_R2.fastq

09/13/2018 10:28 AM 139,328,479 BXR17001_13_R1.fastq

09/13/2018 10:28 AM 139,328,479 BXR17001_13_R2.fastq

09/13/2018 10:28 AM 120,533,807 BXR17001_14_R1.fastq

09/13/2018 10:28 AM 120,533,807 BXR17001_14_R2.fastq

09/13/2018 10:28 AM 116,445,073 BXR17001_15_R1.fastq

09/13/2018 10:28 AM 116,445,073 BXR17001_15_R2.fastq

09/13/2018 10:28 AM 137,760,234 BXR17001_16_R1.fastq

09/13/2018 10:28 AM 137,760,234 BXR17001_16_R2.fastq

09/13/2018 10:28 AM 122,960,776 BXR17001_17_R1.fastq

09/13/2018 10:28 AM 122,960,776 BXR17001_17_R2.fastq

09/13/2018 10:28 AM 165,291,799 BXR17001_18_R1.fastq

09/13/2018 10:28 AM 165,291,799 BXR17001_18_R2.fastq

09/13/2018 10:28 AM 122,587,936 BXR17001_19_R1.fastq

09/13/2018 10:28 AM 122,587,936 BXR17001_19_R2.fastq

09/13/2018 10:28 AM 379,101 BXR17001_1_R1.fastq

09/13/2018 10:28 AM 379,101 BXR17001_1_R2.fastq

09/13/2018 10:28 AM 116,903,737 BXR17001_20_R1.fastq

09/13/2018 10:28 AM 116,903,737 BXR17001_20_R2.fastq

09/13/2018 10:28 AM 145,541,326 BXR17001_21_R1.fastq

09/13/2018 10:28 AM 145,541,326 BXR17001_21_R2.fastq

09/13/2018 10:28 AM 94,326,496 BXR17001_22_R1.fastq

09/13/2018 10:28 AM 94,326,496 BXR17001_22_R2.fastq

09/13/2018 10:28 AM 131,163,344 BXR17001_23_R1.fastq

09/13/2018 10:28 AM 131,163,344 BXR17001_23_R2.fastq

09/13/2018 10:28 AM 113,134,603 BXR17001_24_R1.fastq

09/13/2018 10:28 AM 113,134,603 BXR17001_24_R2.fastq

09/13/2018 10:28 AM 93,215,142 BXR17001_25_R1.fastq

09/13/2018 10:28 AM 93,215,142 BXR17001_25_R2.fastq

09/13/2018 10:28 AM 120,450,717 BXR17001_26_R1.fastq

09/13/2018 10:28 AM 120,450,717 BXR17001_26_R2.fastq

09/13/2018 10:28 AM 104,927,531 BXR17001_27_R1.fastq

09/13/2018 10:28 AM 104,927,531 BXR17001_27_R2.fastq

09/13/2018 10:28 AM 112,091,446 BXR17001_28_R1.fastq

09/13/2018 10:28 AM 112,091,446 BXR17001_28_R2.fastq

09/13/2018 10:28 AM 141,866,200 BXR17001_29_R1.fastq

09/13/2018 10:28 AM 141,866,200 BXR17001_29_R2.fastq

09/13/2018 10:28 AM 144,813,540 BXR17001_2_R1.fastq

09/13/2018 10:28 AM 144,813,540 BXR17001_2_R2.fastq

09/13/2018 10:28 AM 117,233,049 BXR17001_30_R1.fastq

09/13/2018 10:28 AM 117,233,049 BXR17001_30_R2.fastq

09/13/2018 10:28 AM 115,408,589 BXR17001_31_R1.fastq

09/13/2018 10:28 AM 115,408,589 BXR17001_31_R2.fastq

09/13/2018 10:28 AM 109,266,038 BXR17001_32_R1.fastq

09/13/2018 10:28 AM 109,266,038 BXR17001_32_R2.fastq

09/13/2018 10:28 AM 92,995,783 BXR17001_33_R1.fastq

09/13/2018 10:28 AM 92,995,783 BXR17001_33_R2.fastq

09/13/2018 10:28 AM 99,419,765 BXR17001_34_R1.fastq

09/13/2018 10:28 AM 99,419,765 BXR17001_34_R2.fastq

09/13/2018 10:28 AM 95,786,276 BXR17001_35_R1.fastq

09/13/2018 10:28 AM 95,786,276 BXR17001_35_R2.fastq

09/13/2018 10:28 AM 95,555,328 BXR17001_36_R1.fastq

09/13/2018 10:29 AM 95,555,328 BXR17001_36_R2.fastq

09/13/2018 10:29 AM 109,594,958 BXR17001_37_R1.fastq

09/13/2018 10:29 AM 109,594,958 BXR17001_37_R2.fastq

09/13/2018 10:29 AM 148,088,584 BXR17001_38_R1.fastq

09/13/2018 10:29 AM 148,088,584 BXR17001_38_R2.fastq

09/13/2018 10:29 AM 96,751,943 BXR17001_39_R1.fastq

09/13/2018 10:29 AM 96,751,943 BXR17001_39_R2.fastq

09/13/2018 10:29 AM 116,871,525 BXR17001_3_R1.fastq

09/13/2018 10:29 AM 116,871,525 BXR17001_3_R2.fastq

09/13/2018 10:29 AM 93,981,181 BXR17001_40_R1.fastq

09/13/2018 10:29 AM 93,981,181 BXR17001_40_R2.fastq

09/13/2018 10:29 AM 100,637,480 BXR17001_41_R1.fastq

09/13/2018 10:29 AM 100,637,480 BXR17001_41_R2.fastq

09/13/2018 10:29 AM 107,979,585 BXR17001_42_R1.fastq

09/13/2018 10:29 AM 107,979,585 BXR17001_42_R2.fastq

09/13/2018 10:29 AM 94,873,869 BXR17001_43_R1.fastq

09/13/2018 10:29 AM 94,873,869 BXR17001_43_R2.fastq

09/13/2018 10:29 AM 107,490,080 BXR17001_44_R1.fastq

09/13/2018 10:29 AM 107,490,080 BXR17001_44_R2.fastq

09/13/2018 10:29 AM 124,130,475 BXR17001_45_R1.fastq

09/13/2018 10:29 AM 124,130,475 BXR17001_45_R2.fastq

09/13/2018 10:29 AM 99,890,831 BXR17001_46_R1.fastq

09/13/2018 10:29 AM 99,890,831 BXR17001_46_R2.fastq

09/13/2018 10:29 AM 117,369,879 BXR17001_47_R1.fastq

09/13/2018 10:29 AM 117,369,879 BXR17001_47_R2.fastq

09/13/2018 10:29 AM 113,339,126 BXR17001_48_R1.fastq

09/13/2018 10:29 AM 113,339,126 BXR17001_48_R2.fastq

09/13/2018 10:29 AM 89,694,727 BXR17001_49_R1.fastq

09/13/2018 10:29 AM 89,694,727 BXR17001_49_R2.fastq

09/13/2018 10:29 AM 116,686,564 BXR17001_4_R1.fastq

09/13/2018 10:29 AM 116,686,564 BXR17001_4_R2.fastq

09/13/2018 10:29 AM 99,488,080 BXR17001_50_R1.fastq

09/13/2018 10:29 AM 99,488,080 BXR17001_50_R2.fastq

09/13/2018 10:29 AM 91,798,300 BXR17001_51_R1.fastq

09/13/2018 10:29 AM 91,798,300 BXR17001_51_R2.fastq

09/13/2018 10:29 AM 80,197,562 BXR17001_52_R1.fastq

09/13/2018 10:29 AM 80,197,562 BXR17001_52_R2.fastq

09/13/2018 10:29 AM 112,439,322 BXR17001_53_R1.fastq

09/13/2018 10:29 AM 112,439,322 BXR17001_53_R2.fastq

09/13/2018 10:29 AM 82,624,928 BXR17001_54_R1.fastq

09/13/2018 10:29 AM 82,624,928 BXR17001_54_R2.fastq

09/13/2018 10:29 AM 86,156,062 BXR17001_55_R1.fastq

09/13/2018 10:29 AM 86,156,062 BXR17001_55_R2.fastq

09/13/2018 10:29 AM 116,582,965 BXR17001_56_R1.fastq

09/13/2018 10:29 AM 116,582,965 BXR17001_56_R2.fastq

09/13/2018 10:29 AM 114,052,217 BXR17001_57_R1.fastq

09/13/2018 10:29 AM 114,052,217 BXR17001_57_R2.fastq

09/13/2018 10:29 AM 64,806,302 BXR17001_58_R1.fastq

09/13/2018 10:29 AM 64,806,302 BXR17001_58_R2.fastq

09/13/2018 10:29 AM 79,457,504 BXR17001_59_R1.fastq

09/13/2018 10:29 AM 79,457,504 BXR17001_59_R2.fastq

09/13/2018 10:29 AM 141,044,885 BXR17001_5_R1.fastq

09/13/2018 10:29 AM 141,044,885 BXR17001_5_R2.fastq

09/13/2018 10:29 AM 98,411,163 BXR17001_60_R1.fastq

09/13/2018 10:29 AM 98,411,163 BXR17001_60_R2.fastq

09/13/2018 10:29 AM 69,639,889 BXR17001_61_R1.fastq

09/13/2018 10:29 AM 69,639,889 BXR17001_61_R2.fastq

09/13/2018 10:29 AM 101,670,097 BXR17001_62_R1.fastq

09/13/2018 10:29 AM 101,670,097 BXR17001_62_R2.fastq

09/13/2018 10:29 AM 103,454,030 BXR17001_63_R1.fastq

09/13/2018 10:29 AM 103,454,030 BXR17001_63_R2.fastq

09/13/2018 10:29 AM 79,847,814 BXR17001_64_R1.fastq

09/13/2018 10:29 AM 79,847,814 BXR17001_64_R2.fastq

09/13/2018 10:29 AM 115,024,284 BXR17001_65_R1.fastq

09/13/2018 10:29 AM 115,024,284 BXR17001_65_R2.fastq

09/13/2018 10:29 AM 116,588,602 BXR17001_66_R1.fastq

09/13/2018 10:29 AM 116,588,602 BXR17001_66_R2.fastq

09/13/2018 10:29 AM 96,397,216 BXR17001_67_R1.fastq

09/13/2018 10:29 AM 96,397,216 BXR17001_67_R2.fastq

09/13/2018 10:29 AM 95,791,243 BXR17001_68_R1.fastq

09/13/2018 10:29 AM 95,791,243 BXR17001_68_R2.fastq

09/13/2018 10:29 AM 113,373,624 BXR17001_69_R1.fastq

09/13/2018 10:29 AM 113,373,624 BXR17001_69_R2.fastq

09/13/2018 10:29 AM 76,727,406 BXR17001_6_R1.fastq

09/13/2018 10:29 AM 76,727,406 BXR17001_6_R2.fastq

09/13/2018 10:29 AM 94,627,651 BXR17001_70_R1.fastq

09/13/2018 10:29 AM 94,627,651 BXR17001_70_R2.fastq

09/13/2018 10:29 AM 114,956,314 BXR17001_71_R1.fastq

09/13/2018 10:29 AM 114,956,314 BXR17001_71_R2.fastq

09/13/2018 10:29 AM 114,488,825 BXR17001_72_R1.fastq

09/13/2018 10:29 AM 114,488,825 BXR17001_72_R2.fastq

09/13/2018 10:29 AM 112,173,894 BXR17001_73_R1.fastq

09/13/2018 10:29 AM 112,173,894 BXR17001_73_R2.fastq

09/13/2018 10:29 AM 195,770,089 BXR17001_74_R1.fastq

09/13/2018 10:29 AM 195,770,089 BXR17001_74_R2.fastq

09/13/2018 10:29 AM 108,455,444 BXR17001_75_R1.fastq

09/13/2018 10:29 AM 108,455,444 BXR17001_75_R2.fastq

09/13/2018 10:29 AM 161,948,044 BXR17001_76_R1.fastq

09/13/2018 10:29 AM 161,948,044 BXR17001_76_R2.fastq

09/13/2018 10:29 AM 158,093,551 BXR17001_77_R1.fastq

09/13/2018 10:29 AM 158,093,551 BXR17001_77_R2.fastq

09/13/2018 10:29 AM 132,140,323 BXR17001_78_R1.fastq

09/13/2018 10:29 AM 132,140,323 BXR17001_78_R2.fastq

09/13/2018 10:29 AM 121,720,546 BXR17001_79_R1.fastq

09/13/2018 10:29 AM 121,720,546 BXR17001_79_R2.fastq

09/13/2018 10:29 AM 116,063,439 BXR17001_7_R1.fastq

09/13/2018 10:29 AM 116,063,439 BXR17001_7_R2.fastq

09/13/2018 10:29 AM 120,942,144 BXR17001_80_R1.fastq

09/13/2018 10:29 AM 120,942,144 BXR17001_80_R2.fastq

09/13/2018 10:29 AM 125,257,133 BXR17001_81_R1.fastq

09/13/2018 10:29 AM 125,257,133 BXR17001_81_R2.fastq

09/13/2018 10:29 AM 125,233,683 BXR17001_82_R1.fastq

09/13/2018 10:29 AM 125,233,683 BXR17001_82_R2.fastq

09/13/2018 10:29 AM 101,394,174 BXR17001_83_R1.fastq

09/13/2018 10:29 AM 101,394,174 BXR17001_83_R2.fastq

09/13/2018 10:29 AM 111,001,594 BXR17001_84_R1.fastq

09/13/2018 10:29 AM 111,001,594 BXR17001_84_R2.fastq

09/13/2018 10:29 AM 11,288,688 BXR17001_8_R1.fastq

09/13/2018 10:29 AM 11,288,688 BXR17001_8_R2.fastq

09/13/2018 10:29 AM 147,781,357 BXR17001_9_R1.fastq

09/13/2018 10:29 AM 147,781,357 BXR17001_9_R2.fastq

09/13/2018 10:29 AM 131,184,490 BXR17028_85_R1.fastq

09/13/2018 10:29 AM 131,184,490 BXR17028_85_R2.fastq

09/13/2018 10:29 AM 110,073,671 BXR17028_86_R1.fastq

09/13/2018 10:29 AM 110,073,671 BXR17028_86_R2.fastq

09/13/2018 10:29 AM 107,510,802 BXR17028_87_R1.fastq

09/13/2018 10:29 AM 107,510,802 BXR17028_87_R2.fastq

11/07/2018 06:10 PM 50,014 ecoli_primers.align

11/07/2018 06:10 PM 316 ecoli_primers.align.report

11/07/2018 06:08 PM 315 ecoli_primers.fas

11/07/2018 06:11 PM 82 ecoli_primers.summary

11/07/2018 06:04 PM 304 ecoli_primers.txt

11/07/2018 08:09 PM <DIR> Silva.nr_v132

11/07/2018 06:10 PM 83,681,579 silva.seed_v132.8mer

01/09/2018 02:53 PM 560,365,850 silva.seed_v132.align

01/09/2018 03:03 PM 561,551,360 Silva.seed_v132.tar

11/07/2018 09:13 PM 22,820,618 silva.v4.8mer

11/07/2018 06:23 PM 200,990,528 silva.v4.fasta

11/07/2018 06:29 AM 537,928,040 stability.contigs.good.groups

11/06/2018 11:16 PM 772,679,098 stability.contigs.groups

11/06/2018 11:16 PM 1,030,135,410 stability.contigs.report

11/06/2018 09:33 PM 4,593 stability.files

11/06/2018 09:34 PM 0 stability.scrap.contigs.fasta

11/06/2018 09:34 PM 0 stability.scrap.contigs.qual

11/07/2018 06:28 AM 229,549,829 stability.trim.contigs.bad.accnos

11/06/2018 11:16 PM 5,344,737,967 stability.trim.contigs.fasta

11/07/2018 06:39 AM 141,574,453 stability.trim.contigs.good.count_table

11/07/2018 06:28 AM 3,683,007,108 stability.trim.contigs.good.fasta

11/07/2018 06:35 AM 563,934,867 stability.trim.contigs.good.names

11/07/2018 09:56 PM 37,070,755,975 stability.trim.contigs.good.unique.align

11/07/2018 09:56 PM 314,547,430 stability.trim.contigs.good.unique.align.report

11/07/2018 06:35 AM 1,023,640,657 stability.trim.contigs.good.unique.fasta

11/07/2018 09:56 PM 292,206 stability.trim.contigs.good.unique.flip.accnos

11/08/2018 07:39 AM 174,520,685 stability.trim.contigs.good.unique.summary

11/06/2018 11:16 PM 14,219,480,510 stability.trim.contigs.qual

11/07/2018 06:18 AM 873,049,919 stability.trim.contigs.summary

         202 File(s) 86,712,880,409 bytes

           3 Dir(s)  78,902,579,200 bytes free

mothur > system(cd)

C:\mothur\mothur

Thoughts?

Thanks!
-Anne


#4

Where is the silva.bacteria.fasta file located? The silva.bacteria.pcr.fasta file should be created in the same place. You can redirect the output to the Seqs directory using the outputdir parameter as follows:

mothur > pcr.seqs(fasta=silva.bacteria.fasta, start=11894, end=25319, keepdots=F, processors=4, outputdir=C:\mothur\mothur\Seqs)


#5

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