bs3

bs3 copied to clipboard

bs3-build error - std::bad_alloc ??

1

Hi, I am trying to index this genome: ftp://ftp.ensembl.org/pub/release-91/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz I am using this command line: `./bs3-build -f /mnt/data/Genomes/hg38/Homo_sapiens.GRCh38.dna.primary_assembly.fa -s 20 -L 8` I get this error: ``` Bias computation: 6000000000...

ghost

Hi, I ran bs3 with your test data without any problem. But when I'm trying to index hg38, indexing done without any error ([Done] Build Whole genome preprocessing) while align...

fanghe0720

"[Error] Cannot open input file : %s" % read_file

1

command used ./bs3-align -1 test_data/pair1.fq -2 test_data/pair2.fq -o WGBC -f sam -g reference_genome/genome.fa -d reference_genome/ error I got: File "bs3-align.py", line 149 print "[Error] Cannot open input file : %s"...

sunta3iouxos

ktang

TabError: inconsistent use of tabs and spaces in indentation

1

The command ran was: python bs3-build.py -f /file/location/hg38.fa The error received: File "bs3-build.py", line 5, in from bs_index.wg_build import * File "/gpfs/home/jmm498/software/bs3-dev1/bs_index/wg_build.py", line 49 chrom_num += 1 ^ TabError: inconsistent...

joseemayo

when i run the ./bs3-call_methylation using test data, there have a question. please tell me why? thanks Samtools-htslib-API: bam_index_build2() not yet implemented Traceback (most recent call last): File "/TJNAS01/CANCER/RD/TEST/chendongdong/bs3/bs3-call_methylation.py", line...

Dongdong-Chen

i have a question: when i run bs3-align.py, a bug will open python: can't open file 'bs_align/bs_single_end3.py': [Errno 2] No such file or directory python: can't open file 'bs_align/bs_single_end3.py': [Errno...

Dongdong-Chen

bs3-align printing version only

7

Hi, I built the genome without any issues and am now trying to align some reads. Unfortunately, bs3-align is just printing the version and exiting. Is there a verbose option...

nsmackler

enormandeau

enormandeau