Job ID = 1293983 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 1,692,051 reads read : 1,692,051 reads written : 1,692,051 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:00:31 1692051 reads; of these: 1692051 (100.00%) were unpaired; of these: 478807 (28.30%) aligned 0 times 1033274 (61.07%) aligned exactly 1 time 179970 (10.64%) aligned >1 times 71.70% overall alignment rate Time searching: 00:00:31 Overall time: 00:00:31 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 132711 / 1213244 = 0.1094 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Mon, 03 Jun 2019 03:44:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1550617/SRX1550617.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1550617/SRX1550617.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1550617/SRX1550617.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1550617/SRX1550617.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Mon, 03 Jun 2019 03:44:48: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:44:48: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:44:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1550617/SRX1550617.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1550617/SRX1550617.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1550617/SRX1550617.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1550617/SRX1550617.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Mon, 03 Jun 2019 03:44:48: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:44:48: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:44:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1550617/SRX1550617.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1550617/SRX1550617.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1550617/SRX1550617.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1550617/SRX1550617.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Mon, 03 Jun 2019 03:44:48: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:44:48: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:44:56: 1000000 INFO @ Mon, 03 Jun 2019 03:44:57: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 03:44:57: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 03:44:57: #1 total tags in treatment: 1080533 INFO @ Mon, 03 Jun 2019 03:44:57: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:44:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 03:44:57: #1 tags after filtering in treatment: 1080533 INFO @ Mon, 03 Jun 2019 03:44:57: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:44:57: #1 finished! INFO @ Mon, 03 Jun 2019 03:44:57: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:44:57: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:44:57: #2 number of paired peaks: 3626 INFO @ Mon, 03 Jun 2019 03:44:57: start model_add_line... INFO @ Mon, 03 Jun 2019 03:44:57: start X-correlation... INFO @ Mon, 03 Jun 2019 03:44:57: 1000000 INFO @ Mon, 03 Jun 2019 03:44:57: end of X-cor INFO @ Mon, 03 Jun 2019 03:44:57: #2 finished! INFO @ Mon, 03 Jun 2019 03:44:57: #2 predicted fragment length is 137 bps INFO @ Mon, 03 Jun 2019 03:44:57: #2 alternative fragment length(s) may be 137 bps INFO @ Mon, 03 Jun 2019 03:44:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1550617/SRX1550617.20_model.r INFO @ Mon, 03 Jun 2019 03:44:57: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:44:57: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:44:57: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 03:44:57: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 03:44:57: #1 total tags in treatment: 1080533 INFO @ Mon, 03 Jun 2019 03:44:57: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:44:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 03:44:57: #1 tags after filtering in treatment: 1080533 INFO @ Mon, 03 Jun 2019 03:44:57: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:44:57: #1 finished! INFO @ Mon, 03 Jun 2019 03:44:57: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:44:57: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:44:58: #2 number of paired peaks: 3626 INFO @ Mon, 03 Jun 2019 03:44:58: start model_add_line... INFO @ Mon, 03 Jun 2019 03:44:58: start X-correlation... INFO @ Mon, 03 Jun 2019 03:44:58: end of X-cor INFO @ Mon, 03 Jun 2019 03:44:58: #2 finished! INFO @ Mon, 03 Jun 2019 03:44:58: #2 predicted fragment length is 137 bps INFO @ Mon, 03 Jun 2019 03:44:58: #2 alternative fragment length(s) may be 137 bps INFO @ Mon, 03 Jun 2019 03:44:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1550617/SRX1550617.10_model.r INFO @ Mon, 03 Jun 2019 03:44:58: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:44:58: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:44:58: 1000000 INFO @ Mon, 03 Jun 2019 03:44:59: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 03:44:59: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 03:44:59: #1 total tags in treatment: 1080533 INFO @ Mon, 03 Jun 2019 03:44:59: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:44:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 03:44:59: #1 tags after filtering in treatment: 1080533 INFO @ Mon, 03 Jun 2019 03:44:59: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:44:59: #1 finished! INFO @ Mon, 03 Jun 2019 03:44:59: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:44:59: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:44:59: #2 number of paired peaks: 3626 INFO @ Mon, 03 Jun 2019 03:44:59: start model_add_line... INFO @ Mon, 03 Jun 2019 03:44:59: start X-correlation... INFO @ Mon, 03 Jun 2019 03:44:59: end of X-cor INFO @ Mon, 03 Jun 2019 03:44:59: #2 finished! INFO @ Mon, 03 Jun 2019 03:44:59: #2 predicted fragment length is 137 bps INFO @ Mon, 03 Jun 2019 03:44:59: #2 alternative fragment length(s) may be 137 bps INFO @ Mon, 03 Jun 2019 03:44:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1550617/SRX1550617.05_model.r INFO @ Mon, 03 Jun 2019 03:44:59: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:44:59: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:45:00: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:45:01: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:45:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1550617/SRX1550617.20_peaks.xls INFO @ Mon, 03 Jun 2019 03:45:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1550617/SRX1550617.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:45:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1550617/SRX1550617.20_summits.bed INFO @ Mon, 03 Jun 2019 03:45:02: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (936 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 03:45:03: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:45:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1550617/SRX1550617.10_peaks.xls INFO @ Mon, 03 Jun 2019 03:45:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1550617/SRX1550617.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:45:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1550617/SRX1550617.10_summits.bed INFO @ Mon, 03 Jun 2019 03:45:03: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1886 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 03 Jun 2019 03:45:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1550617/SRX1550617.05_peaks.xls INFO @ Mon, 03 Jun 2019 03:45:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1550617/SRX1550617.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:45:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1550617/SRX1550617.05_summits.bed INFO @ Mon, 03 Jun 2019 03:45:05: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (3111 records, 4 fields): 9 millis CompletedMACS2peakCalling BigWig に変換しました。