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jpuritz / dDocent

a bash pipeline for RAD sequencing
ddocent.com
MIT License
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ReferenceOpt.sh - kopt.data output #67

Closed j-a-thia closed 4 years ago

j-a-thia commented 4 years ago

Not sure if this is a common issue, but when running ReferenceOpt.sh I got standard output in my kopt.data file.

See excerpt:

4 1 0.88 ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: DH10.F.fq.gz Reverse reads file.................: DH10.R.fq.gz PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 100 p-value............................: 0.010000 Quality score threshold (trimming).: 0 Minimum read size after trimming...: 1 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 6 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.213765 C: 0.305644 G: 0.278709 T: 0.201882 19671 uncalled bases Assemblying reads: 0%
Assemblying reads: 26%
Assemblying reads: 51%
Assemblying reads: 79%
Assemblying reads: 100% Assembled reads ...................: 248,318 / 262,242 (94.690%) Discarded reads ...................: 405 / 262,242 (0.154%) Not assembled reads ...............: 13,519 / 262,242 (5.155%) Assembled reads file...............: DH10.assembled.fastq Discarded reads file...............: DH10.discarded.fastq Unassembled forward reads file.....: DH10.unassembled.forward.fastq Unassembled reverse reads file.....: DH10.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: DH15.F.fq.gz Reverse reads file.................: DH15.R.fq.gz PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 100 p-value............................: 0.010000 Quality score threshold (trimming).: 0 Minimum read size after trimming...: 1 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 6 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.213404 C: 0.306030 G: 0.278267 T: 0.202299 9590 uncalled bases Assemblying reads: 0%
Assemblying reads: 26%
Assemblying reads: 51%
Assemblying reads: 79%
Assemblying reads: 100% Assembled reads ...................: 249,053 / 262,194 (94.988%) Discarded reads ...................: 204 / 262,194 (0.078%) Not assembled reads ...............: 12,937 / 262,194 (4.934%) Assembled reads file...............: DH15.assembled.fastq Discarded reads file...............: DH15.discarded.fastq Unassembled forward reads file.....: DH15.unassembled.forward.fastq Unassembled reverse reads file.....: DH15.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: DH16.F.fq.gz Reverse reads file.................: DH16.R.fq.gz PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 100 p-value............................: 0.010000 Quality score threshold (trimming).: 0 Minimum read size after trimming...: 1 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 6 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.213534 C: 0.306293 G: 0.278708 T: 0.201464 8191 uncalled bases Assemblying reads: 0%
Assemblying reads: 26%
Assemblying reads: 50%
Assemblying reads: 77%
Assemblying reads: 100% Assembled reads ...................: 254,211 / 267,994 (94.857%) Discarded reads ...................: 167 / 267,994 (0.062%) Not assembled reads ...............: 13,616 / 267,994 (5.081%) Assembled reads file...............: DH16.assembled.fastq Discarded reads file...............: DH16.discarded.fastq Unassembled forward reads file.....: DH16.unassembled.forward.fastq Unassembled reverse reads file.....: DH16.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: DH20.F.fq.gz Reverse reads file.................: DH20.R.fq.gz PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 100 p-value............................: 0.010000 Quality score threshold (trimming).: 0 Minimum read size after trimming...: 1 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 6 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.214051 C: 0.304835 G: 0.279797 T: 0.201317 3080 uncalled bases Assemblying reads: 0%
Assemblying reads: 22%
Assemblying reads: 43%
Assemblying reads: 67%
Assemblying reads: 90%
Assemblying reads: 100% Assembled reads ...................: 295,485 / 307,638 (96.050%) Discarded reads ...................: 70 / 307,638 (0.023%) Not assembled reads ...............: 12,083 / 307,638 (3.928%) Assembled reads file...............: DH20.assembled.fastq Discarded reads file...............: DH20.discarded.fastq Unassembled forward reads file.....: DH20.unassembled.forward.fastq Unassembled reverse reads file.....: DH20.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: DH22.F.fq.gz Reverse reads file.................: DH22.R.fq.gz PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 100 p-value............................: 0.010000 Quality score threshold (trimming).: 0 Minimum read size after trimming...: 1 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 6 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.213903 C: 0.304844 G: 0.279855 T: 0.201398 6650 uncalled bases Assemblying reads: 0%
Assemblying reads: 19%
Assemblying reads: 38%
Assemblying reads: 57%
Assemblying reads: 77%
Assemblying reads: 96%
Assemblying reads: 100% Assembled reads ...................: 344,335 / 358,909 (95.939%) Discarded reads ...................: 140 / 358,909 (0.039%) Not assembled reads ...............: 14,434 / 358,909 (4.022%) Assembled reads file...............: DH22.assembled.fastq Discarded reads file...............: DH22.discarded.fastq Unassembled forward reads file.....: DH22.unassembled.forward.fastq Unassembled reverse reads file.....: DH22.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: DH33.F.fq.gz Reverse reads file.................: DH33.R.fq.gz PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 100 p-value............................: 0.010000 Quality score threshold (trimming).: 0 Minimum read size after trimming...: 1 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 6 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.214020 C: 0.304925 G: 0.280528 T: 0.200526 12950 uncalled bases Assemblying reads: 0%
Assemblying reads: 26%
Assemblying reads: 50%
Assemblying reads: 77%
Assemblying reads: 100% Assembled reads ...................: 259,069 / 267,732 (96.764%) Discarded reads ...................: 282 / 267,732 (0.105%) Not assembled reads ...............: 8,381 / 267,732 (3.130%) Assembled reads file...............: DH33.assembled.fastq Discarded reads file...............: DH33.discarded.fastq Unassembled forward reads file.....: DH33.unassembled.forward.fastq Unassembled reverse reads file.....: DH33.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: DH34.F.fq.gz Reverse reads file.................: DH34.R.fq.gz PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 100 p-value............................: 0.010000 Quality score threshold (trimming).: 0 Minimum read size after trimming...: 1 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 6 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.214097 C: 0.304848 G: 0.279696 T: 0.201359 16310 uncalled bases Assemblying reads: 0%
Assemblying reads: 19%
Assemblying reads: 38%
Assemblying reads: 57%
Assemblying reads: 78%
Assemblying reads: 96%
Assemblying reads: 100% Assembled reads ...................: 344,165 / 355,884 (96.707%) Discarded reads ...................: 331 / 355,884 (0.093%) Not assembled reads ...............: 11,388 / 355,884 (3.200%) Assembled reads file...............: DH34.assembled.fastq Discarded reads file...............: DH34.discarded.fastq Unassembled forward reads file.....: DH34.unassembled.forward.fastq Unassembled reverse reads file.....: DH34.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: DH35.F.fq.gz Reverse reads file.................: DH35.R.fq.gz PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 100 p-value............................: 0.010000 Quality score threshold (trimming).: 0 Minimum read size after trimming...: 1 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 6 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.214095 C: 0.304591 G: 0.280127 T: 0.201186 3290 uncalled bases Assemblying reads: 0%
Assemblying reads: 23%
Assemblying reads: 44%
Assemblying reads: 69%
Assemblying reads: 92%
Assemblying reads: 100% Assembled reads ...................: 288,858 / 299,368 (96.489%) Discarded reads ...................: 64 / 299,368 (0.021%) Not assembled reads ...............: 10,446 / 299,368 (3.489%) Assembled reads file...............: DH35.assembled.fastq Discarded reads file...............: DH35.discarded.fastq Unassembled forward reads file.....: DH35.unassembled.forward.fastq Unassembled reverse reads file.....: DH35.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: DH38.F.fq.gz Reverse reads file.................: DH38.R.fq.gz PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 100 p-value............................: 0.010000 Quality score threshold (trimming).: 0 Minimum read size after trimming...: 1 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 6 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.213124 C: 0.305703 G: 0.279985 T: 0.201188 6160 uncalled bases Assemblying reads: 0%
Assemblying reads: 22%
Assemblying reads: 43%
Assemblying reads: 66%
Assemblying reads: 88%
Assemblying reads: 100% Assembled reads ...................: 300,670 / 312,379 (96.252%) Discarded reads ...................: 118 / 312,379 (0.038%) Not assembled reads ...............: 11,591 / 312,379 (3.711%) Assembled reads file...............: DH38.assembled.fastq Discarded reads file...............: DH38.discarded.fastq Unassembled forward reads file.....: DH38.unassembled.forward.fastq Unassembled reverse reads file.....: DH38.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: DH39.F.fq.gz Reverse reads file.................: DH39.R.fq.gz PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 100 p-value............................: 0.010000 Quality score threshold (trimming).: 0 Minimum read size after trimming...: 1 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 6 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.213268 C: 0.305838 G: 0.279499 T: 0.201395 9065 uncalled bases Assemblying reads: 0%
Assemblying reads: 18%
Assemblying reads: 35%
Assemblying reads: 52%
Assemblying reads: 71%
Assemblying reads: 88%
Assemblying reads: 100% Assembled reads ...................: 377,077 / 389,570 (96.793%) Discarded reads ...................: 199 / 389,570 (0.051%) Not assembled reads ...............: 12,294 / 389,570 (3.156%) Assembled reads file...............: DH39.assembled.fastq Discarded reads file...............: DH39.discarded.fastq Unassembled forward reads file.....: DH39.unassembled.forward.fastq Unassembled reverse reads file.....: DH39.unassembled.reverse.fastq 7
4 1 0.90 8
4 1 0.92 8
4 1 0.94 8
4 1 0.96 13
jpuritz commented 4 years ago

Should be fixed now.