Closed bbsunchen closed 10 years ago
Hi Jan, Recently I always encounter the following error information:
Stratify BAM file /gpfs/home/cxs1031/backup/data/socrates/sorted.bam with option values: threads = 4 min mapq = 5 min long sc length = 25 min avg soft clip base quality = 5 min aligned percent identity = 95 remove duplicates = true
Bowtie2 alignment, DB=/gpfs/home/cxs1031/backup/hg19/chr1_bowtie2
Add anchor information into re-alignment BAM file input BAM file: - output BAM file: sorted_long_sc_l25_q5_m5_i95.bam gzip: sorted_long_sc_l25_q5_m5_i95.fastq.gz: No such file or directory 0 reads 0.00% overall alignment rate sorted_long_sc_l25_q5_m5_i95.bai Required BAM file not found: sorted_short_sc.bam
These "sorted_long_sc_l25_q5_m5_i95.fastq.gz" and "sorted_short_sc.bam", as I suppose, are temp file of Socrates.
My running command is as follows: python BIN_PATH/Socrates-master/socrates.py all DATA_PATH/sorted.bam -t 4 --bowtie2_db DATA_PATH/hg19/chr1_bowtie2
BTW: I rename the "Socrates" program into "socrates.py" so that I can run it not using default "python" program
Hi Jan, Recently I always encounter the following error information:
Stratify BAM file /gpfs/home/cxs1031/backup/data/socrates/sorted.bam with option values: threads = 4 min mapq = 5 min long sc length = 25 min avg soft clip base quality = 5 min aligned percent identity = 95 remove duplicates = true
Bowtie2 alignment, DB=/gpfs/home/cxs1031/backup/hg19/chr1_bowtie2
Add anchor information into re-alignment BAM file input BAM file: - output BAM file: sorted_long_sc_l25_q5_m5_i95.bam gzip: sorted_long_sc_l25_q5_m5_i95.fastq.gz: No such file or directory 0 reads 0.00% overall alignment rate sorted_long_sc_l25_q5_m5_i95.bai Required BAM file not found: sorted_short_sc.bam
These "sorted_long_sc_l25_q5_m5_i95.fastq.gz" and "sorted_short_sc.bam", as I suppose, are temp file of Socrates.
My running command is as follows: python BIN_PATH/Socrates-master/socrates.py all DATA_PATH/sorted.bam -t 4 --bowtie2_db DATA_PATH/hg19/chr1_bowtie2
BTW: I rename the "Socrates" program into "socrates.py" so that I can run it not using default "python" program