Job ID = 1294258 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 50,624,300 reads read : 50,624,300 reads written : 50,624,300 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: 00:08:34 50624300 reads; of these: 50624300 (100.00%) were unpaired; of these: 21012408 (41.51%) aligned 0 times 25414713 (50.20%) aligned exactly 1 time 4197179 (8.29%) aligned >1 times 58.49% overall alignment rate Time searching: 00:08:34 Overall time: 00:08:34 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_sort_core] merging from 8 files... [bam_rmdupse_core] 17510937 / 29611892 = 0.5913 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 06:06:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX215502/SRX215502.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX215502/SRX215502.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX215502/SRX215502.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX215502/SRX215502.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 06:06:03: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:06:03: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:06:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX215502/SRX215502.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX215502/SRX215502.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX215502/SRX215502.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX215502/SRX215502.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 06:06:03: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:06:03: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:06:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX215502/SRX215502.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX215502/SRX215502.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX215502/SRX215502.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX215502/SRX215502.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 06:06:03: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:06:03: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:06:11: 1000000 INFO @ Mon, 03 Jun 2019 06:06:11: 1000000 INFO @ Mon, 03 Jun 2019 06:06:14: 1000000 INFO @ Mon, 03 Jun 2019 06:06:19: 2000000 INFO @ Mon, 03 Jun 2019 06:06:19: 2000000 INFO @ Mon, 03 Jun 2019 06:06:24: 2000000 INFO @ Mon, 03 Jun 2019 06:06:26: 3000000 INFO @ Mon, 03 Jun 2019 06:06:27: 3000000 INFO @ Mon, 03 Jun 2019 06:06:34: 4000000 INFO @ Mon, 03 Jun 2019 06:06:34: 3000000 INFO @ Mon, 03 Jun 2019 06:06:34: 4000000 INFO @ Mon, 03 Jun 2019 06:06:42: 5000000 INFO @ Mon, 03 Jun 2019 06:06:42: 5000000 INFO @ Mon, 03 Jun 2019 06:06:44: 4000000 INFO @ Mon, 03 Jun 2019 06:06:49: 6000000 INFO @ Mon, 03 Jun 2019 06:06:50: 6000000 INFO @ Mon, 03 Jun 2019 06:06:55: 5000000 INFO @ Mon, 03 Jun 2019 06:06:57: 7000000 INFO @ Mon, 03 Jun 2019 06:06:57: 7000000 INFO @ Mon, 03 Jun 2019 06:07:05: 8000000 INFO @ Mon, 03 Jun 2019 06:07:05: 6000000 INFO @ Mon, 03 Jun 2019 06:07:05: 8000000 INFO @ Mon, 03 Jun 2019 06:07:12: 9000000 INFO @ Mon, 03 Jun 2019 06:07:13: 9000000 INFO @ Mon, 03 Jun 2019 06:07:15: 7000000 INFO @ Mon, 03 Jun 2019 06:07:20: 10000000 INFO @ Mon, 03 Jun 2019 06:07:21: 10000000 INFO @ Mon, 03 Jun 2019 06:07:26: 8000000 INFO @ Mon, 03 Jun 2019 06:07:28: 11000000 INFO @ Mon, 03 Jun 2019 06:07:29: 11000000 INFO @ Mon, 03 Jun 2019 06:07:36: 9000000 INFO @ Mon, 03 Jun 2019 06:07:36: 12000000 INFO @ Mon, 03 Jun 2019 06:07:36: 12000000 INFO @ Mon, 03 Jun 2019 06:07:37: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 06:07:37: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 06:07:37: #1 total tags in treatment: 12100955 INFO @ Mon, 03 Jun 2019 06:07:37: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:07:37: #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 06:07:37: #1 tags after filtering in treatment: 12100955 INFO @ Mon, 03 Jun 2019 06:07:37: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:07:37: #1 finished! INFO @ Mon, 03 Jun 2019 06:07:37: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:07:37: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:07:37: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 06:07:37: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 06:07:37: #1 total tags in treatment: 12100955 INFO @ Mon, 03 Jun 2019 06:07:37: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:07:37: #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 06:07:37: #1 tags after filtering in treatment: 12100955 INFO @ Mon, 03 Jun 2019 06:07:37: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:07:37: #1 finished! INFO @ Mon, 03 Jun 2019 06:07:37: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:07:37: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:07:39: #2 number of paired peaks: 7082 INFO @ Mon, 03 Jun 2019 06:07:39: start model_add_line... INFO @ Mon, 03 Jun 2019 06:07:39: start X-correlation... INFO @ Mon, 03 Jun 2019 06:07:39: end of X-cor INFO @ Mon, 03 Jun 2019 06:07:39: #2 finished! INFO @ Mon, 03 Jun 2019 06:07:39: #2 predicted fragment length is 330 bps INFO @ Mon, 03 Jun 2019 06:07:39: #2 alternative fragment length(s) may be 330 bps INFO @ Mon, 03 Jun 2019 06:07:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX215502/SRX215502.05_model.r INFO @ Mon, 03 Jun 2019 06:07:39: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:07:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:07:39: #2 number of paired peaks: 7082 INFO @ Mon, 03 Jun 2019 06:07:39: start model_add_line... INFO @ Mon, 03 Jun 2019 06:07:40: start X-correlation... INFO @ Mon, 03 Jun 2019 06:07:40: end of X-cor INFO @ Mon, 03 Jun 2019 06:07:40: #2 finished! INFO @ Mon, 03 Jun 2019 06:07:40: #2 predicted fragment length is 330 bps INFO @ Mon, 03 Jun 2019 06:07:40: #2 alternative fragment length(s) may be 330 bps INFO @ Mon, 03 Jun 2019 06:07:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX215502/SRX215502.10_model.r INFO @ Mon, 03 Jun 2019 06:07:40: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:07:40: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:07:46: 10000000 INFO @ Mon, 03 Jun 2019 06:07:55: 11000000 INFO @ Mon, 03 Jun 2019 06:08:05: 12000000 INFO @ Mon, 03 Jun 2019 06:08:05: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 06:08:05: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 06:08:05: #1 total tags in treatment: 12100955 INFO @ Mon, 03 Jun 2019 06:08:05: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:08:05: #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 06:08:06: #1 tags after filtering in treatment: 12100955 INFO @ Mon, 03 Jun 2019 06:08:06: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:08:06: #1 finished! INFO @ Mon, 03 Jun 2019 06:08:06: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:08:06: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:08:07: #2 number of paired peaks: 7082 INFO @ Mon, 03 Jun 2019 06:08:07: start model_add_line... INFO @ Mon, 03 Jun 2019 06:08:08: start X-correlation... INFO @ Mon, 03 Jun 2019 06:08:08: end of X-cor INFO @ Mon, 03 Jun 2019 06:08:08: #2 finished! INFO @ Mon, 03 Jun 2019 06:08:08: #2 predicted fragment length is 330 bps INFO @ Mon, 03 Jun 2019 06:08:08: #2 alternative fragment length(s) may be 330 bps INFO @ Mon, 03 Jun 2019 06:08:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX215502/SRX215502.20_model.r INFO @ Mon, 03 Jun 2019 06:08:08: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:08:08: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:08:27: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:08:28: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:08:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX215502/SRX215502.05_peaks.xls INFO @ Mon, 03 Jun 2019 06:08:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX215502/SRX215502.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:08:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX215502/SRX215502.05_summits.bed INFO @ Mon, 03 Jun 2019 06:08:46: Done! INFO @ Mon, 03 Jun 2019 06:08:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX215502/SRX215502.10_peaks.xls INFO @ Mon, 03 Jun 2019 06:08:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX215502/SRX215502.10_peaks.narrowPeak pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7231 records, 4 fields): 11 millis INFO @ Mon, 03 Jun 2019 06:08:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX215502/SRX215502.10_summits.bed CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 06:08:46: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6743 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 06:08:56: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:09:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX215502/SRX215502.20_peaks.xls INFO @ Mon, 03 Jun 2019 06:09:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX215502/SRX215502.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:09:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX215502/SRX215502.20_summits.bed INFO @ Mon, 03 Jun 2019 06:09:14: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6069 records, 4 fields): 17 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。