haowenz
commented
1 year ago Please use the issue template and fill in all the information to get help on your problem. It is hard to know what happen without those information.
Closed taotaoyuan closed 1 year ago
haowenz
commented
1 year ago Please use the issue template and fill in all the information to get help on your problem. It is hard to know what happen without those information.
Preset parameters for Hi-C are used. Start to map reads. Parameters: error threshold: 4, min-num-seeds: 2, max-seed-frequency: 500,1000, max-num-best-mappings: 1, max-insert-size: 1000, MAPQ-threshold: 1, min-read-length: 30, bc-error-threshold: 1, bc-probability-threshold: 0.90 Number of threads: 48 Analyze bulk data. Won't try to remove adapters on 3'. Will remove PCR duplicates after mapping. Will remove PCR duplicates at bulk level. Won't allocate multi-mappings after mapping. Only output unique mappings after mapping. Only output mappings of which barcodes are in whitelist. Allow split alignment. Output mappings in SAM format. Reference file: /home/lx_sky6/yt/20230106_baimaike/0105_YC_hifi/4-chromap_yahs/purge_haplotigs.fa Index file: purge_haplotigs.fa.index 1th read 1 file: /home/lx_sky6/yt/20230106_baimaike/0106_hic/Unknown_BB398-05H0001_good_1.fq.gz 1th read 2 file: /home/lx_sky6/yt/20230106_baimaike/0106_hic/Unknown_BB398-05H0001_good_2.fq.gz Output file: aligned.sam Loaded all sequences successfully in 0.84s, number of sequences: 85, number of bases: 591963067. Kmer size: 17, window size: 7. Lookup table size: 47988402, occurrence table size: 110090456. Loaded index successfully in 1.18s. Mapped 500000 read pairs in 93.96s. Mapped 500000 read pairs in 14.48s ...... Mapped 500000 read pairs in 6.74s. Mapped 500000 read pairs in 10.41s. Numbers of reads and barcodes don't match!