mehdiborji / nanoranger Goto Github PK

...<lines above cut>...
TRA chains: 156 (55.12%)
TRB chains: 127 (44.88%)
TCR_out/TCR_testrun_bcreads.fasta
TCR_out/TCR_testrun_ref/
Feb 19 22:24:35 ..... started STAR run
Feb 19 22:24:35 ... starting to generate Genome files

genomeGenerate.cpp:150:genomeGenerate: exiting because of *OUTPUT FILE* error: could not create output file TCR_out/TCR_testrun_ref//genomeParameters.txt
Solution: check that the path exists and you have write permission for this file

alignment to genome and generation of BC-UMI-Transcript tagged BAM 


cores = 20
ref = /home/user/nanoranger/FUSION_SEQUENCE.fa
infile= FUSION_TEST/fusion_deconcat.fastq.gz
outdir = FUSION_TEST
sample = fusion
[M::mm_idx_gen::0.001*1.50] collected minimizers
[M::mm_idx_gen::0.001*5.99] sorted minimizers
[M::main::0.001*5.96] loaded/built the index for 1 target sequence(s)
[M::mm_mapopt_update::0.001*5.82] mid_occ = 15
[M::mm_idx_stat] kmer size: 15; skip: 5; is_hpc: 0; #seq: 1
[M::mm_idx_stat::0.002*5.70] distinct minimizers: 626 (98.72% are singletons); average occurrences: 1.032; average spacing: 2.913; total length: 1882
[M::worker_pipeline::0.734*16.79] mapped 103327 sequences
[M::main] Version: 2.26-r1175
[M::main] CMD: minimap2 -aY --eqx -x splice -t 20 --secondary=no --sam-hit-only /home/user/nanoranger/FUSION_SEQUENCE.fa FUSION_TEST/fusion_deconcat.fastq.gz
[M::main] Real time: 0.738 sec; CPU: 12.330 sec; Peak RSS: 0.053 GB
[bam_sort_core] merging from 0 files and 20 in-memory blocks...
number of genome aligned reads =  4693
10000 barcode candidates processed
20000 barcode candidates processed
30000 barcode candidates processed
40000 barcode candidates processed
50000 barcode candidates processed
60000 barcode candidates processed
70000 barcode candidates processed
80000 barcode candidates processed
number of short UMI reads =  250
20000 Read-BC-UMI-Transcript tuples saved
40000 Read-BC-UMI-Transcript tuples saved
60000 Read-BC-UMI-Transcript tuples saved
rm: cannot remove 'FUSION_TEST/fusion_matching_*': No such file or directory
`

 alignment to genome and generation of BC-UMI-Transcript tagged BAM 


cores = 8
ref = /home/user/nanoranger/data/RUNX1_RUNX1T1_ABL1_BCR.fa
infile= K562_Kasumi1/fusion_deconcat.fastq.gz
outdir = K562_Kasumi1
sample = fusion
[M::mm_idx_gen::0.001*1.89] collected minimizers
[M::mm_idx_gen::0.001*2.31] sorted minimizers
[M::main::0.001*2.30] loaded/built the index for 7 target sequence(s)
[M::mm_mapopt_update::0.002*2.22] mid_occ = 10
[M::mm_idx_stat] kmer size: 15; skip: 5; is_hpc: 0; #seq: 7
[M::mm_idx_stat::0.002*2.17] distinct minimizers: 2164 (96.63% are singletons); average occurrences: 1.035; average spacing: 2.973; total length: 6656
[M::worker_pipeline::0.050*6.04] mapped 3152 sequences
[M::main] Version: 2.26-r1175
[M::main] CMD: minimap2 -aY --eqx -x splice -t 8 --secondary=no --sam-hit-only /home/user/nanoranger/data/RUNX1_RUNX1T1_ABL1_BCR.fa K562_Kasumi1/fusion_deconcat.fastq.gz
[M::main] Real time: 0.050 sec; CPU: 0.303 sec; Peak RSS: 0.010 GB
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
number of genome aligned reads =  2883
number of short UMI reads =  4
rm: cannot remove 'K562_Kasumi1/fusion_matching_*': No such file or directory