Job ID = 1293861 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 8,414,719 reads read : 8,414,719 reads written : 8,414,719 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: 00:03:10 8414719 reads; of these: 8414719 (100.00%) were unpaired; of these: 1053742 (12.52%) aligned 0 times 5389803 (64.05%) aligned exactly 1 time 1971174 (23.43%) aligned >1 times 87.48% overall alignment rate Time searching: 00:03:10 Overall time: 00:03:10 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] 2477702 / 7360977 = 0.3366 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 02:54:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1299939/SRX1299939.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1299939/SRX1299939.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1299939/SRX1299939.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1299939/SRX1299939.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 02:54:46: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:54:46: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:54:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1299939/SRX1299939.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1299939/SRX1299939.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1299939/SRX1299939.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1299939/SRX1299939.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 02:54:46: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:54:46: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:54:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1299939/SRX1299939.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1299939/SRX1299939.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1299939/SRX1299939.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1299939/SRX1299939.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 02:54:46: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:54:46: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:54:56: 1000000 INFO @ Mon, 03 Jun 2019 02:54:56: 1000000 INFO @ Mon, 03 Jun 2019 02:54:56: 1000000 INFO @ Mon, 03 Jun 2019 02:55:05: 2000000 INFO @ Mon, 03 Jun 2019 02:55:06: 2000000 INFO @ Mon, 03 Jun 2019 02:55:06: 2000000 INFO @ Mon, 03 Jun 2019 02:55:13: 3000000 INFO @ Mon, 03 Jun 2019 02:55:15: 3000000 INFO @ Mon, 03 Jun 2019 02:55:15: 3000000 INFO @ Mon, 03 Jun 2019 02:55:22: 4000000 INFO @ Mon, 03 Jun 2019 02:55:25: 4000000 INFO @ Mon, 03 Jun 2019 02:55:25: 4000000 INFO @ Mon, 03 Jun 2019 02:55:30: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 02:55:30: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 02:55:30: #1 total tags in treatment: 4883275 INFO @ Mon, 03 Jun 2019 02:55:30: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:55:30: #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 02:55:30: #1 tags after filtering in treatment: 4883275 INFO @ Mon, 03 Jun 2019 02:55:30: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:55:30: #1 finished! INFO @ Mon, 03 Jun 2019 02:55:30: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:55:30: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:55:31: #2 number of paired peaks: 3881 INFO @ Mon, 03 Jun 2019 02:55:31: start model_add_line... INFO @ Mon, 03 Jun 2019 02:55:31: start X-correlation... INFO @ Mon, 03 Jun 2019 02:55:31: end of X-cor INFO @ Mon, 03 Jun 2019 02:55:31: #2 finished! INFO @ Mon, 03 Jun 2019 02:55:31: #2 predicted fragment length is 139 bps INFO @ Mon, 03 Jun 2019 02:55:31: #2 alternative fragment length(s) may be 4,139 bps INFO @ Mon, 03 Jun 2019 02:55:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1299939/SRX1299939.10_model.r INFO @ Mon, 03 Jun 2019 02:55:31: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:55:31: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:55:33: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 02:55:33: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 02:55:33: #1 total tags in treatment: 4883275 INFO @ Mon, 03 Jun 2019 02:55:33: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:55:33: #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 02:55:33: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 02:55:33: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 02:55:33: #1 total tags in treatment: 4883275 INFO @ Mon, 03 Jun 2019 02:55:33: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:55:33: #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 02:55:33: #1 tags after filtering in treatment: 4883275 INFO @ Mon, 03 Jun 2019 02:55:33: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:55:33: #1 finished! INFO @ Mon, 03 Jun 2019 02:55:33: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:55:33: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:55:33: #1 tags after filtering in treatment: 4883275 INFO @ Mon, 03 Jun 2019 02:55:33: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:55:33: #1 finished! INFO @ Mon, 03 Jun 2019 02:55:33: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:55:33: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:55:34: #2 number of paired peaks: 3881 INFO @ Mon, 03 Jun 2019 02:55:34: start model_add_line... INFO @ Mon, 03 Jun 2019 02:55:34: start X-correlation... INFO @ Mon, 03 Jun 2019 02:55:34: end of X-cor INFO @ Mon, 03 Jun 2019 02:55:34: #2 finished! INFO @ Mon, 03 Jun 2019 02:55:34: #2 predicted fragment length is 139 bps INFO @ Mon, 03 Jun 2019 02:55:34: #2 alternative fragment length(s) may be 4,139 bps INFO @ Mon, 03 Jun 2019 02:55:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1299939/SRX1299939.05_model.r INFO @ Mon, 03 Jun 2019 02:55:34: #2 number of paired peaks: 3881 INFO @ Mon, 03 Jun 2019 02:55:34: start model_add_line... INFO @ Mon, 03 Jun 2019 02:55:34: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:55:34: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:55:34: start X-correlation... INFO @ Mon, 03 Jun 2019 02:55:34: end of X-cor INFO @ Mon, 03 Jun 2019 02:55:34: #2 finished! INFO @ Mon, 03 Jun 2019 02:55:34: #2 predicted fragment length is 139 bps INFO @ Mon, 03 Jun 2019 02:55:34: #2 alternative fragment length(s) may be 4,139 bps INFO @ Mon, 03 Jun 2019 02:55:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1299939/SRX1299939.20_model.r INFO @ Mon, 03 Jun 2019 02:55:34: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:55:34: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:55:46: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:55:49: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:55:50: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:55:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1299939/SRX1299939.10_peaks.xls INFO @ Mon, 03 Jun 2019 02:55:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1299939/SRX1299939.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:55:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1299939/SRX1299939.10_summits.bed INFO @ Mon, 03 Jun 2019 02:55:54: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1703 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 02:55:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1299939/SRX1299939.05_peaks.xls INFO @ Mon, 03 Jun 2019 02:55:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1299939/SRX1299939.20_peaks.xls INFO @ Mon, 03 Jun 2019 02:55:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1299939/SRX1299939.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:55:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1299939/SRX1299939.20_summits.bed INFO @ Mon, 03 Jun 2019 02:55:57: Done! INFO @ Mon, 03 Jun 2019 02:55:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1299939/SRX1299939.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:55:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1299939/SRX1299939.05_summits.bed INFO @ Mon, 03 Jun 2019 02:55:57: Done! pass1 - making usageList (11 chroms): 2 millis pass2 - checking and writing primary data (655 records, 4 fields): 3 millis CompletedMACS2peakCalling pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3426 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。