Job ID = 1294980 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 24,477,501 reads read : 24,477,501 reads written : 24,477,501 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: 00:09:12 24477501 reads; of these: 24477501 (100.00%) were unpaired; of these: 1744944 (7.13%) aligned 0 times 16708620 (68.26%) aligned exactly 1 time 6023937 (24.61%) aligned >1 times 92.87% overall alignment rate Time searching: 00:09:12 Overall time: 00:09:12 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 12 files... [bam_rmdupse_core] 3944444 / 22732557 = 0.1735 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 11:29:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288037/SRX288037.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288037/SRX288037.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288037/SRX288037.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288037/SRX288037.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 11:29:09: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:29:09: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:29:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288037/SRX288037.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288037/SRX288037.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288037/SRX288037.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288037/SRX288037.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 11:29:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288037/SRX288037.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288037/SRX288037.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288037/SRX288037.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288037/SRX288037.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 11:29:09: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:29:09: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:29:09: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:29:09: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:29:16: 1000000 INFO @ Mon, 03 Jun 2019 11:29:17: 1000000 INFO @ Mon, 03 Jun 2019 11:29:17: 1000000 INFO @ Mon, 03 Jun 2019 11:29:23: 2000000 INFO @ Mon, 03 Jun 2019 11:29:25: 2000000 INFO @ Mon, 03 Jun 2019 11:29:25: 2000000 INFO @ Mon, 03 Jun 2019 11:29:30: 3000000 INFO @ Mon, 03 Jun 2019 11:29:33: 3000000 INFO @ Mon, 03 Jun 2019 11:29:33: 3000000 INFO @ Mon, 03 Jun 2019 11:29:37: 4000000 INFO @ Mon, 03 Jun 2019 11:29:40: 4000000 INFO @ Mon, 03 Jun 2019 11:29:40: 4000000 INFO @ Mon, 03 Jun 2019 11:29:44: 5000000 INFO @ Mon, 03 Jun 2019 11:29:48: 5000000 INFO @ Mon, 03 Jun 2019 11:29:48: 5000000 INFO @ Mon, 03 Jun 2019 11:29:51: 6000000 INFO @ Mon, 03 Jun 2019 11:29:56: 6000000 INFO @ Mon, 03 Jun 2019 11:29:56: 6000000 INFO @ Mon, 03 Jun 2019 11:29:58: 7000000 INFO @ Mon, 03 Jun 2019 11:30:04: 7000000 INFO @ Mon, 03 Jun 2019 11:30:04: 7000000 INFO @ Mon, 03 Jun 2019 11:30:05: 8000000 INFO @ Mon, 03 Jun 2019 11:30:11: 8000000 INFO @ Mon, 03 Jun 2019 11:30:11: 8000000 INFO @ Mon, 03 Jun 2019 11:30:12: 9000000 INFO @ Mon, 03 Jun 2019 11:30:19: 10000000 INFO @ Mon, 03 Jun 2019 11:30:19: 9000000 INFO @ Mon, 03 Jun 2019 11:30:19: 9000000 INFO @ Mon, 03 Jun 2019 11:30:26: 11000000 INFO @ Mon, 03 Jun 2019 11:30:27: 10000000 INFO @ Mon, 03 Jun 2019 11:30:27: 10000000 INFO @ Mon, 03 Jun 2019 11:30:33: 12000000 INFO @ Mon, 03 Jun 2019 11:30:34: 11000000 INFO @ Mon, 03 Jun 2019 11:30:34: 11000000 INFO @ Mon, 03 Jun 2019 11:30:40: 13000000 INFO @ Mon, 03 Jun 2019 11:30:41: 12000000 INFO @ Mon, 03 Jun 2019 11:30:42: 12000000 INFO @ Mon, 03 Jun 2019 11:30:48: 14000000 INFO @ Mon, 03 Jun 2019 11:30:48: 13000000 INFO @ Mon, 03 Jun 2019 11:30:49: 13000000 INFO @ Mon, 03 Jun 2019 11:30:54: 14000000 INFO @ Mon, 03 Jun 2019 11:30:55: 15000000 INFO @ Mon, 03 Jun 2019 11:30:57: 14000000 INFO @ Mon, 03 Jun 2019 11:31:01: 15000000 INFO @ Mon, 03 Jun 2019 11:31:02: 16000000 INFO @ Mon, 03 Jun 2019 11:31:04: 15000000 INFO @ Mon, 03 Jun 2019 11:31:08: 16000000 INFO @ Mon, 03 Jun 2019 11:31:10: 17000000 INFO @ Mon, 03 Jun 2019 11:31:11: 16000000 INFO @ Mon, 03 Jun 2019 11:31:15: 17000000 INFO @ Mon, 03 Jun 2019 11:31:17: 18000000 INFO @ Mon, 03 Jun 2019 11:31:19: 17000000 INFO @ Mon, 03 Jun 2019 11:31:22: 18000000 INFO @ Mon, 03 Jun 2019 11:31:23: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:31:23: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:31:23: #1 total tags in treatment: 18788113 INFO @ Mon, 03 Jun 2019 11:31:23: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:31:23: #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 11:31:24: #1 tags after filtering in treatment: 18788113 INFO @ Mon, 03 Jun 2019 11:31:24: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:31:24: #1 finished! INFO @ Mon, 03 Jun 2019 11:31:24: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:31:24: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:31:25: #2 number of paired peaks: 408 WARNING @ Mon, 03 Jun 2019 11:31:25: Fewer paired peaks (408) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 408 pairs to build model! INFO @ Mon, 03 Jun 2019 11:31:25: start model_add_line... INFO @ Mon, 03 Jun 2019 11:31:25: start X-correlation... INFO @ Mon, 03 Jun 2019 11:31:25: end of X-cor INFO @ Mon, 03 Jun 2019 11:31:25: #2 finished! INFO @ Mon, 03 Jun 2019 11:31:25: #2 predicted fragment length is 221 bps INFO @ Mon, 03 Jun 2019 11:31:25: #2 alternative fragment length(s) may be 221 bps INFO @ Mon, 03 Jun 2019 11:31:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288037/SRX288037.10_model.r INFO @ Mon, 03 Jun 2019 11:31:25: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:31:25: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:31:26: 18000000 INFO @ Mon, 03 Jun 2019 11:31:27: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:31:27: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:31:27: #1 total tags in treatment: 18788113 INFO @ Mon, 03 Jun 2019 11:31:27: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:31:27: #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 11:31:28: #1 tags after filtering in treatment: 18788113 INFO @ Mon, 03 Jun 2019 11:31:28: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:31:28: #1 finished! INFO @ Mon, 03 Jun 2019 11:31:28: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:31:28: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:31:29: #2 number of paired peaks: 408 WARNING @ Mon, 03 Jun 2019 11:31:29: Fewer paired peaks (408) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 408 pairs to build model! INFO @ Mon, 03 Jun 2019 11:31:29: start model_add_line... INFO @ Mon, 03 Jun 2019 11:31:30: start X-correlation... INFO @ Mon, 03 Jun 2019 11:31:30: end of X-cor INFO @ Mon, 03 Jun 2019 11:31:30: #2 finished! INFO @ Mon, 03 Jun 2019 11:31:30: #2 predicted fragment length is 221 bps INFO @ Mon, 03 Jun 2019 11:31:30: #2 alternative fragment length(s) may be 221 bps INFO @ Mon, 03 Jun 2019 11:31:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288037/SRX288037.20_model.r INFO @ Mon, 03 Jun 2019 11:31:30: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:31:30: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:31:31: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:31:31: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:31:31: #1 total tags in treatment: 18788113 INFO @ Mon, 03 Jun 2019 11:31:31: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:31:31: #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 11:31:32: #1 tags after filtering in treatment: 18788113 INFO @ Mon, 03 Jun 2019 11:31:32: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:31:32: #1 finished! INFO @ Mon, 03 Jun 2019 11:31:32: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:31:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:31:33: #2 number of paired peaks: 408 WARNING @ Mon, 03 Jun 2019 11:31:33: Fewer paired peaks (408) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 408 pairs to build model! INFO @ Mon, 03 Jun 2019 11:31:33: start model_add_line... INFO @ Mon, 03 Jun 2019 11:31:33: start X-correlation... INFO @ Mon, 03 Jun 2019 11:31:33: end of X-cor INFO @ Mon, 03 Jun 2019 11:31:33: #2 finished! INFO @ Mon, 03 Jun 2019 11:31:33: #2 predicted fragment length is 221 bps INFO @ Mon, 03 Jun 2019 11:31:33: #2 alternative fragment length(s) may be 221 bps INFO @ Mon, 03 Jun 2019 11:31:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288037/SRX288037.05_model.r INFO @ Mon, 03 Jun 2019 11:31:33: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:31:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:32:20: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:32:24: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:32:28: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:32:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288037/SRX288037.10_peaks.xls INFO @ Mon, 03 Jun 2019 11:32:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288037/SRX288037.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:32:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288037/SRX288037.10_summits.bed INFO @ Mon, 03 Jun 2019 11:32:45: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (5068 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:32:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288037/SRX288037.20_peaks.xls INFO @ Mon, 03 Jun 2019 11:32:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288037/SRX288037.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:32:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288037/SRX288037.20_summits.bed INFO @ Mon, 03 Jun 2019 11:32:49: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2959 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:32:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288037/SRX288037.05_peaks.xls INFO @ Mon, 03 Jun 2019 11:32:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288037/SRX288037.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:32:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288037/SRX288037.05_summits.bed INFO @ Mon, 03 Jun 2019 11:32:54: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7369 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。