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