Job ID = 1295827 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 48,729,799 reads read : 48,729,799 reads written : 48,729,799 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: 00:14:06 48729799 reads; of these: 48729799 (100.00%) were unpaired; of these: 1876822 (3.85%) aligned 0 times 41083862 (84.31%) aligned exactly 1 time 5769115 (11.84%) aligned >1 times 96.15% overall alignment rate Time searching: 00:14:06 Overall time: 00:14:06 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 20 files... [bam_rmdupse_core] 30756426 / 46852977 = 0.6564 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 16:11:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX457600/SRX457600.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX457600/SRX457600.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX457600/SRX457600.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX457600/SRX457600.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 16:11:21: #1 read tag files... INFO @ Mon, 03 Jun 2019 16:11:21: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 16:11:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX457600/SRX457600.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX457600/SRX457600.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX457600/SRX457600.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX457600/SRX457600.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 16:11:21: #1 read tag files... INFO @ Mon, 03 Jun 2019 16:11:21: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 16:11:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX457600/SRX457600.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX457600/SRX457600.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX457600/SRX457600.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX457600/SRX457600.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 16:11:21: #1 read tag files... INFO @ Mon, 03 Jun 2019 16:11:21: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 16:11:28: 1000000 INFO @ Mon, 03 Jun 2019 16:11:29: 1000000 INFO @ Mon, 03 Jun 2019 16:11:30: 1000000 INFO @ Mon, 03 Jun 2019 16:11:35: 2000000 INFO @ Mon, 03 Jun 2019 16:11:36: 2000000 INFO @ Mon, 03 Jun 2019 16:11:38: 2000000 INFO @ Mon, 03 Jun 2019 16:11:42: 3000000 INFO @ Mon, 03 Jun 2019 16:11:44: 3000000 INFO @ Mon, 03 Jun 2019 16:11:47: 3000000 INFO @ Mon, 03 Jun 2019 16:11:48: 4000000 INFO @ Mon, 03 Jun 2019 16:11:51: 4000000 INFO @ Mon, 03 Jun 2019 16:11:55: 5000000 INFO @ Mon, 03 Jun 2019 16:11:55: 4000000 INFO @ Mon, 03 Jun 2019 16:11:58: 5000000 INFO @ Mon, 03 Jun 2019 16:12:02: 6000000 INFO @ Mon, 03 Jun 2019 16:12:04: 5000000 INFO @ Mon, 03 Jun 2019 16:12:06: 6000000 INFO @ Mon, 03 Jun 2019 16:12:09: 7000000 INFO @ Mon, 03 Jun 2019 16:12:12: 6000000 INFO @ Mon, 03 Jun 2019 16:12:13: 7000000 INFO @ Mon, 03 Jun 2019 16:12:15: 8000000 INFO @ Mon, 03 Jun 2019 16:12:20: 7000000 INFO @ Mon, 03 Jun 2019 16:12:21: 8000000 INFO @ Mon, 03 Jun 2019 16:12:22: 9000000 INFO @ Mon, 03 Jun 2019 16:12:28: 9000000 INFO @ Mon, 03 Jun 2019 16:12:28: 8000000 INFO @ Mon, 03 Jun 2019 16:12:29: 10000000 INFO @ Mon, 03 Jun 2019 16:12:36: 11000000 INFO @ Mon, 03 Jun 2019 16:12:37: 10000000 INFO @ Mon, 03 Jun 2019 16:12:37: 9000000 INFO @ Mon, 03 Jun 2019 16:12:43: 12000000 INFO @ Mon, 03 Jun 2019 16:12:44: 11000000 INFO @ Mon, 03 Jun 2019 16:12:46: 10000000 INFO @ Mon, 03 Jun 2019 16:12:49: 13000000 INFO @ Mon, 03 Jun 2019 16:12:52: 12000000 INFO @ Mon, 03 Jun 2019 16:12:54: 11000000 INFO @ Mon, 03 Jun 2019 16:12:56: 14000000 INFO @ Mon, 03 Jun 2019 16:12:59: 13000000 INFO @ Mon, 03 Jun 2019 16:13:03: 12000000 INFO @ Mon, 03 Jun 2019 16:13:03: 15000000 INFO @ Mon, 03 Jun 2019 16:13:06: 14000000 INFO @ Mon, 03 Jun 2019 16:13:10: 16000000 INFO @ Mon, 03 Jun 2019 16:13:11: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 16:13:11: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 16:13:11: #1 total tags in treatment: 16096551 INFO @ Mon, 03 Jun 2019 16:13:11: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 16:13:11: #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 16:13:11: #1 tags after filtering in treatment: 16096551 INFO @ Mon, 03 Jun 2019 16:13:11: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 16:13:11: #1 finished! INFO @ Mon, 03 Jun 2019 16:13:11: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 16:13:11: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 16:13:11: 13000000 INFO @ Mon, 03 Jun 2019 16:13:13: #2 number of paired peaks: 4529 INFO @ Mon, 03 Jun 2019 16:13:13: start model_add_line... INFO @ Mon, 03 Jun 2019 16:13:14: start X-correlation... INFO @ Mon, 03 Jun 2019 16:13:14: end of X-cor INFO @ Mon, 03 Jun 2019 16:13:14: #2 finished! INFO @ Mon, 03 Jun 2019 16:13:14: #2 predicted fragment length is 167 bps INFO @ Mon, 03 Jun 2019 16:13:14: #2 alternative fragment length(s) may be 167 bps INFO @ Mon, 03 Jun 2019 16:13:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX457600/SRX457600.10_model.r INFO @ Mon, 03 Jun 2019 16:13:14: #3 Call peaks... INFO @ Mon, 03 Jun 2019 16:13:14: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 16:13:14: 15000000 INFO @ Mon, 03 Jun 2019 16:13:20: 14000000 INFO @ Mon, 03 Jun 2019 16:13:22: 16000000 INFO @ Mon, 03 Jun 2019 16:13:23: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 16:13:23: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 16:13:23: #1 total tags in treatment: 16096551 INFO @ Mon, 03 Jun 2019 16:13:23: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 16:13:23: #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 16:13:23: #1 tags after filtering in treatment: 16096551 INFO @ Mon, 03 Jun 2019 16:13:23: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 16:13:23: #1 finished! INFO @ Mon, 03 Jun 2019 16:13:23: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 16:13:23: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 16:13:25: #2 number of paired peaks: 4529 INFO @ Mon, 03 Jun 2019 16:13:25: start model_add_line... INFO @ Mon, 03 Jun 2019 16:13:25: start X-correlation... INFO @ Mon, 03 Jun 2019 16:13:25: end of X-cor INFO @ Mon, 03 Jun 2019 16:13:25: #2 finished! INFO @ Mon, 03 Jun 2019 16:13:25: #2 predicted fragment length is 167 bps INFO @ Mon, 03 Jun 2019 16:13:25: #2 alternative fragment length(s) may be 167 bps INFO @ Mon, 03 Jun 2019 16:13:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX457600/SRX457600.05_model.r INFO @ Mon, 03 Jun 2019 16:13:25: #3 Call peaks... INFO @ Mon, 03 Jun 2019 16:13:25: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 16:13:29: 15000000 INFO @ Mon, 03 Jun 2019 16:13:37: 16000000 INFO @ Mon, 03 Jun 2019 16:13:38: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 16:13:38: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 16:13:38: #1 total tags in treatment: 16096551 INFO @ Mon, 03 Jun 2019 16:13:38: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 16:13:38: #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 16:13:39: #1 tags after filtering in treatment: 16096551 INFO @ Mon, 03 Jun 2019 16:13:39: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 16:13:39: #1 finished! INFO @ Mon, 03 Jun 2019 16:13:39: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 16:13:39: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 16:13:41: #2 number of paired peaks: 4529 INFO @ Mon, 03 Jun 2019 16:13:41: start model_add_line... INFO @ Mon, 03 Jun 2019 16:13:41: start X-correlation... INFO @ Mon, 03 Jun 2019 16:13:41: end of X-cor INFO @ Mon, 03 Jun 2019 16:13:41: #2 finished! INFO @ Mon, 03 Jun 2019 16:13:41: #2 predicted fragment length is 167 bps INFO @ Mon, 03 Jun 2019 16:13:41: #2 alternative fragment length(s) may be 167 bps INFO @ Mon, 03 Jun 2019 16:13:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX457600/SRX457600.20_model.r INFO @ Mon, 03 Jun 2019 16:13:41: #3 Call peaks... INFO @ Mon, 03 Jun 2019 16:13:41: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 16:14:07: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 16:14:20: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 16:14:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX457600/SRX457600.10_peaks.xls INFO @ Mon, 03 Jun 2019 16:14:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX457600/SRX457600.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 16:14:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX457600/SRX457600.10_summits.bed INFO @ Mon, 03 Jun 2019 16:14:31: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (8374 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 16:14:34: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 16:14:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX457600/SRX457600.05_peaks.xls INFO @ Mon, 03 Jun 2019 16:14:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX457600/SRX457600.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 16:14:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX457600/SRX457600.05_summits.bed INFO @ Mon, 03 Jun 2019 16:14:44: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (10301 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 16:14:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX457600/SRX457600.20_peaks.xls INFO @ Mon, 03 Jun 2019 16:14:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX457600/SRX457600.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 16:14:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX457600/SRX457600.20_summits.bed INFO @ Mon, 03 Jun 2019 16:14:58: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6498 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。