| /net/eichler/vol21/projects/bac_assembly/nobackups/FCGR/CHM13/FCGR/group.1/WH.reads.fasta | |
| Parameters | preset = N/A |
| defaultQV = 20 | |
| isNonRandom = false | |
| removeDuplicateReads = true | |
| finalTrim = true | |
| removeSpurReads = true | |
| removeChimericReads = true | |
| checkForSubReads = true | |
| FASTA | 340 reads (4625514 bp) |
| 0 reads (0 bp) were short and not loaded | |
| FASTQ | 0 reads (0 bp) |
| 0 reads (0 bp) were short and not loaded | |
| 340 reads (4625514 bp) loaded, 0 reads (0 bp) skipped, 0 warnings | |
| correction/asm.gkpStore | |
| readsLoaded | 340 reads (4625514 bp) |
| readsSkipped | 0 reads (0 bp) (read was too short) |
| warnings | 0 warnings (invalid base or quality value) |
Image 'correction/asm.gkpStore/readlengths' not found.
Image 'correction/0-mercounts/asm.ms16.histogram' not found.
No statistics available for store 'correction/asm.ovlStore'.
| PARAMETERS | ||
|---|---|---|
| 300 | expected coverage | |
| 0 | don't use overlaps shorter than this | |
| 0.000 | don't use overlaps with erate less than this | |
| 1.000 | don't use overlaps with erate more than this | |
| OVERLAPS | ||
| Ignored | 0 | < 0.0000 fraction error |
| 0 | > 0.4095 fraction error | |
| 0 | < 0 bases long | |
| 0 | > 2097151 bases long | |
| Filtered | 0 | too many overlaps, discard these shortest ones |
| Evidence | 23864 | longest overlaps |
| Total | 23864 | all overlaps |
| READS | ||
| 0 | no overlaps | |
| 340 | no overlaps filtered | |
| 0 | < 50% overlaps filtered | |
| 0 | < 80% overlaps filtered | |
| 0 | < 95% overlaps filtered | |
| 0 | < 100% overlaps filtered | |
Filter method: corFilter=expensive. Expect to correct 340 reads with bp to bp.
| INPUTS | ||
|---|---|---|
| 340 | input reads | |
| 4625514 | input bases | |
| OUTPUTS | ||
| 2 | reads that failed to generate any corrected bases | |
| 341 | corrected read pieces | |
| 4268346 | corrected bases | |
| PIECES PER READ | ||
| 0 | 2 | |
| 1 | 335 | |
| 2 | 3 | |
A single input read can be split into multiple output reads, or possibly not even output at all.
Image 'correction/2-correction/asm.estimate.original-x-corrected' not found.
Image 'correction/2-correction/asm.originalLength-vs-expectedLength' not found.
Image 'correction/2-correction/asm.originalLength-vs-correctedLength' not found.
Image 'correction/2-correction/asm.expectedLength-vs-correctedLength' not found.
Image 'correction/2-correction/asm.length-difference-histograms' not found.
Image 'correction/2-correction/asm.length-histograms' not found.