search

epigen-UCSD / epigen_ucsd_django

1 stars 1 forks source link

[seqManager] demux error #471

Closed biomystery closed 4 years ago

biomystery commented 4 years ago

http://epigenomics.sdsc.edu:8000/nextseq/276/

std::exception::what: Barcode collision for barcodes: GGTACGGG, TGTGCGGG
By default, bcl2fastq allows 1 mismatch in each barcode. Barcodes with too few mismatches are ambiguous ( less than 2 times the number of mismatches plus 1). To reduce the number of allowed mismatches, use the command line option: '--barcode-mismatches'. Note that particularly for barcodes with only 1 mismatch, there is the danger that some reads will be written to the wrong sample due to errors in the barcode sequence.

(bds_atac) [zhc268@tscc-login1 HCHLFAFX2]$ grep GGTACGGG /projects/ps-epigen/nextSeq/200809_NB501692_0027_AHCHLFAFX2/HCHLFAFX2/MAKE_FASTQS_CS/MAKE_FASTQS/BCL2FASTQ_WITH_SAMPLESHEET/fork0/chnk0-u4cc631f273/_stderr|less
2020-08-10 18:20:51 [189d880] INFO:     Barcode: 'GGTACGGG'
std::exception::what: Barcode collision for barcodes: GGTACGGG, TGTGCGGG
(bds_atac) [zhc268@tscc-login1 HCHLFAFX2]$ grep -B 2 GGTACGGG /projects/ps-epigen/nextSeq/200809_NB501692_0027_AHCHLFAFX2/HCHLFAFX2/MAKE_FASTQS_CS/MAKE_FASTQS/BCL2FASTQ_WITH_SAMPLESHEET/fork0/chnk0-u4cc631f273/_stderr|less
2020-08-10 18:20:51 [189d880] INFO:     Barcode: 'CACTGACT'
2020-08-10 18:20:51 [189d880] INFO:   Sample: #23 'MM_396_3' 'MM_396' [HCHLFAFX2]
2020-08-10 18:20:51 [189d880] INFO:     Barcode: 'GGTACGGG'

(bds_atac) [zhc268@tscc-login1 HCHLFAFX2]$ grep -B 2 TGTGCGGG /projects/ps-epigen/nextSeq/200809_NB501692_0027_AHCHLFAFX2/HCHLFAFX2/MAKE_FASTQS_CS/MAKE_FASTQS/BCL2FASTQ_WITH_SAMPLESHEET/fork0/chnk0-u4cc631f273/_stderr|less
2020-08-10 18:20:51 [189d880] INFO:     Barcode: 'GTGTATTA'
2020-08-10 18:20:51 [189d880] INFO:   Sample: #34 'MM_399_2' 'MM_399' [HCHLFAFX2]
2020-08-10 18:20:51 [189d880] INFO:     Barcode: 'TGTGCGGG'
biomystery commented 4 years ago
Sequencing ID i7index
MM_396 SI-NA-C5
MM_399 SI-GA-B3
biomystery commented 4 years ago

bcl2fastq --minimum-trimmed-read-length 8 --mask-short-adapter-reads 8 --create-fastq-for-index-reads --ignore-missing-positions --ignore-missing-filter --ignore-missing-bcls --use-bases-ma sk=Y50,I8,Y16,Y93 -R /projects/ps-epigen/nextSeq/200809_NB501692_0027_AHCHLFAFX2 --output-dir=/projects/ps-epigen/nextSeq/200809_NB501692_0027_AHCHLFAFX2/HCHLFAFX2/MAKE_FASTQS_CS/MAKE_FASTQS/BCL2FASTQ_WITH_SAMPLESHEET/fork0/chnk0-u4cc631f273/fi les/fastq_path --interop-dir=/projects/ps-epigen/nextSeq/200809_NB501692_0027_AHCHLFAFX2/HCHLFAFX2/MAKE_FASTQS_CS/MAKE_FASTQS/BCL2FASTQ_WITH_SAMPLESHEET/fork0/chnk0-u4cc631f273/files/interop_path --sample-sheet=/projects/ps-epigen/nextSeq/20080 9_NB501692_0027_AHCHLFAFX2/HCHLFAFX2/MAKE_FASTQS_CS/MAKE_FASTQS/PREPARE_SAMPLESHEET/fork0/chnk0-u4cc631f26f/files/samplesheet.csv -p 6 -r 6 -w 6

biomystery commented 4 years ago

0248f65 http://epigenomics.sdsc.edu:8000/nextseq/266/ http://epigenomics.sdsc.edu:8000/nextseq/276/