Job ID = 2590368 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 13,362,062 reads read : 26,724,124 reads written : 13,362,062 reads 0-length : 13,362,062 spots read : 13,252,955 reads read : 26,505,910 reads written : 13,252,955 reads 0-length : 13,252,955 spots read : 13,239,239 reads read : 26,478,478 reads written : 13,239,239 reads 0-length : 13,239,239 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: 00:10:33 39854256 reads; of these: 39854256 (100.00%) were unpaired; of these: 1157529 (2.90%) aligned 0 times 33222641 (83.36%) aligned exactly 1 time 5474086 (13.74%) aligned >1 times 97.10% overall alignment rate Time searching: 00:10:33 Overall time: 00:10:33 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 16 files... [bam_rmdupse_core] 9710952 / 38696727 = 0.2510 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, 12 Aug 2019 21:34:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981640/SRX3981640.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981640/SRX3981640.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981640/SRX3981640.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981640/SRX3981640.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, 12 Aug 2019 21:34:57: #1 read tag files... INFO @ Mon, 12 Aug 2019 21:34:57: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 21:34:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981640/SRX3981640.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981640/SRX3981640.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981640/SRX3981640.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981640/SRX3981640.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, 12 Aug 2019 21:34:58: #1 read tag files... INFO @ Mon, 12 Aug 2019 21:34:58: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 21:34:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981640/SRX3981640.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981640/SRX3981640.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981640/SRX3981640.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981640/SRX3981640.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, 12 Aug 2019 21:34:59: #1 read tag files... INFO @ Mon, 12 Aug 2019 21:34:59: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 21:35:04: 1000000 INFO @ Mon, 12 Aug 2019 21:35:05: 1000000 INFO @ Mon, 12 Aug 2019 21:35:07: 1000000 INFO @ Mon, 12 Aug 2019 21:35:11: 2000000 INFO @ Mon, 12 Aug 2019 21:35:12: 2000000 INFO @ Mon, 12 Aug 2019 21:35:15: 2000000 INFO @ Mon, 12 Aug 2019 21:35:18: 3000000 INFO @ Mon, 12 Aug 2019 21:35:19: 3000000 INFO @ Mon, 12 Aug 2019 21:35:22: 3000000 INFO @ Mon, 12 Aug 2019 21:35:25: 4000000 INFO @ Mon, 12 Aug 2019 21:35:26: 4000000 INFO @ Mon, 12 Aug 2019 21:35:30: 4000000 INFO @ Mon, 12 Aug 2019 21:35:32: 5000000 INFO @ Mon, 12 Aug 2019 21:35:33: 5000000 INFO @ Mon, 12 Aug 2019 21:35:38: 5000000 INFO @ Mon, 12 Aug 2019 21:35:40: 6000000 INFO @ Mon, 12 Aug 2019 21:35:40: 6000000 INFO @ Mon, 12 Aug 2019 21:35:45: 6000000 INFO @ Mon, 12 Aug 2019 21:35:47: 7000000 INFO @ Mon, 12 Aug 2019 21:35:47: 7000000 INFO @ Mon, 12 Aug 2019 21:35:53: 7000000 INFO @ Mon, 12 Aug 2019 21:35:53: 8000000 INFO @ Mon, 12 Aug 2019 21:35:54: 8000000 INFO @ Mon, 12 Aug 2019 21:36:00: 9000000 INFO @ Mon, 12 Aug 2019 21:36:00: 8000000 INFO @ Mon, 12 Aug 2019 21:36:00: 9000000 INFO @ Mon, 12 Aug 2019 21:36:07: 10000000 INFO @ Mon, 12 Aug 2019 21:36:07: 10000000 INFO @ Mon, 12 Aug 2019 21:36:08: 9000000 INFO @ Mon, 12 Aug 2019 21:36:14: 11000000 INFO @ Mon, 12 Aug 2019 21:36:14: 11000000 INFO @ Mon, 12 Aug 2019 21:36:15: 10000000 INFO @ Mon, 12 Aug 2019 21:36:21: 12000000 INFO @ Mon, 12 Aug 2019 21:36:21: 12000000 INFO @ Mon, 12 Aug 2019 21:36:23: 11000000 INFO @ Mon, 12 Aug 2019 21:36:27: 13000000 INFO @ Mon, 12 Aug 2019 21:36:28: 13000000 INFO @ Mon, 12 Aug 2019 21:36:30: 12000000 INFO @ Mon, 12 Aug 2019 21:36:34: 14000000 INFO @ Mon, 12 Aug 2019 21:36:35: 14000000 INFO @ Mon, 12 Aug 2019 21:36:38: 13000000 INFO @ Mon, 12 Aug 2019 21:36:41: 15000000 INFO @ Mon, 12 Aug 2019 21:36:41: 15000000 INFO @ Mon, 12 Aug 2019 21:36:45: 14000000 INFO @ Mon, 12 Aug 2019 21:36:48: 16000000 INFO @ Mon, 12 Aug 2019 21:36:48: 16000000 INFO @ Mon, 12 Aug 2019 21:36:53: 15000000 INFO @ Mon, 12 Aug 2019 21:36:55: 17000000 INFO @ Mon, 12 Aug 2019 21:36:55: 17000000 INFO @ Mon, 12 Aug 2019 21:37:00: 16000000 INFO @ Mon, 12 Aug 2019 21:37:01: 18000000 INFO @ Mon, 12 Aug 2019 21:37:02: 18000000 INFO @ Mon, 12 Aug 2019 21:37:08: 17000000 INFO @ Mon, 12 Aug 2019 21:37:08: 19000000 INFO @ Mon, 12 Aug 2019 21:37:09: 19000000 INFO @ Mon, 12 Aug 2019 21:37:15: 20000000 INFO @ Mon, 12 Aug 2019 21:37:15: 18000000 INFO @ Mon, 12 Aug 2019 21:37:15: 20000000 INFO @ Mon, 12 Aug 2019 21:37:22: 21000000 INFO @ Mon, 12 Aug 2019 21:37:22: 21000000 INFO @ Mon, 12 Aug 2019 21:37:23: 19000000 INFO @ Mon, 12 Aug 2019 21:37:29: 22000000 INFO @ Mon, 12 Aug 2019 21:37:29: 22000000 INFO @ Mon, 12 Aug 2019 21:37:30: 20000000 INFO @ Mon, 12 Aug 2019 21:37:35: 23000000 INFO @ Mon, 12 Aug 2019 21:37:36: 23000000 INFO @ Mon, 12 Aug 2019 21:37:38: 21000000 INFO @ Mon, 12 Aug 2019 21:37:42: 24000000 INFO @ Mon, 12 Aug 2019 21:37:43: 24000000 INFO @ Mon, 12 Aug 2019 21:37:45: 22000000 INFO @ Mon, 12 Aug 2019 21:37:49: 25000000 INFO @ Mon, 12 Aug 2019 21:37:50: 25000000 INFO @ Mon, 12 Aug 2019 21:37:53: 23000000 INFO @ Mon, 12 Aug 2019 21:37:56: 26000000 INFO @ Mon, 12 Aug 2019 21:37:56: 26000000 INFO @ Mon, 12 Aug 2019 21:38:00: 24000000 INFO @ Mon, 12 Aug 2019 21:38:03: 27000000 INFO @ Mon, 12 Aug 2019 21:38:03: 27000000 INFO @ Mon, 12 Aug 2019 21:38:08: 25000000 INFO @ Mon, 12 Aug 2019 21:38:10: 28000000 INFO @ Mon, 12 Aug 2019 21:38:10: 28000000 INFO @ Mon, 12 Aug 2019 21:38:15: 26000000 INFO @ Mon, 12 Aug 2019 21:38:17: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 21:38:17: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 21:38:17: #1 total tags in treatment: 28985775 INFO @ Mon, 12 Aug 2019 21:38:17: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:38:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 21:38:17: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 21:38:17: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 21:38:17: #1 total tags in treatment: 28985775 INFO @ Mon, 12 Aug 2019 21:38:17: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:38:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 21:38:17: #1 tags after filtering in treatment: 28985775 INFO @ Mon, 12 Aug 2019 21:38:17: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:38:17: #1 finished! INFO @ Mon, 12 Aug 2019 21:38:17: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:38:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:38:18: #1 tags after filtering in treatment: 28985775 INFO @ Mon, 12 Aug 2019 21:38:18: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:38:18: #1 finished! INFO @ Mon, 12 Aug 2019 21:38:18: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:38:18: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:38:20: #2 number of paired peaks: 2990 INFO @ Mon, 12 Aug 2019 21:38:20: start model_add_line... INFO @ Mon, 12 Aug 2019 21:38:21: start X-correlation... INFO @ Mon, 12 Aug 2019 21:38:21: end of X-cor INFO @ Mon, 12 Aug 2019 21:38:21: #2 finished! INFO @ Mon, 12 Aug 2019 21:38:21: #2 predicted fragment length is 89 bps INFO @ Mon, 12 Aug 2019 21:38:21: #2 alternative fragment length(s) may be 2,89,93,114 bps INFO @ Mon, 12 Aug 2019 21:38:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981640/SRX3981640.10_model.r WARNING @ Mon, 12 Aug 2019 21:38:21: #2 Since the d (89) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 21:38:21: #2 You may need to consider one of the other alternative d(s): 2,89,93,114 WARNING @ Mon, 12 Aug 2019 21:38:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 21:38:21: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:38:21: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:38:21: #2 number of paired peaks: 2990 INFO @ Mon, 12 Aug 2019 21:38:21: start model_add_line... INFO @ Mon, 12 Aug 2019 21:38:21: start X-correlation... INFO @ Mon, 12 Aug 2019 21:38:21: end of X-cor INFO @ Mon, 12 Aug 2019 21:38:21: #2 finished! INFO @ Mon, 12 Aug 2019 21:38:21: #2 predicted fragment length is 89 bps INFO @ Mon, 12 Aug 2019 21:38:21: #2 alternative fragment length(s) may be 2,89,93,114 bps INFO @ Mon, 12 Aug 2019 21:38:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981640/SRX3981640.05_model.r WARNING @ Mon, 12 Aug 2019 21:38:21: #2 Since the d (89) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 21:38:21: #2 You may need to consider one of the other alternative d(s): 2,89,93,114 WARNING @ Mon, 12 Aug 2019 21:38:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 21:38:21: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:38:21: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:38:23: 27000000 INFO @ Mon, 12 Aug 2019 21:38:30: 28000000 INFO @ Mon, 12 Aug 2019 21:38:38: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 21:38:38: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 21:38:38: #1 total tags in treatment: 28985775 INFO @ Mon, 12 Aug 2019 21:38:38: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:38:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 21:38:38: #1 tags after filtering in treatment: 28985775 INFO @ Mon, 12 Aug 2019 21:38:38: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:38:38: #1 finished! INFO @ Mon, 12 Aug 2019 21:38:38: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:38:38: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:38:41: #2 number of paired peaks: 2990 INFO @ Mon, 12 Aug 2019 21:38:41: start model_add_line... INFO @ Mon, 12 Aug 2019 21:38:42: start X-correlation... INFO @ Mon, 12 Aug 2019 21:38:42: end of X-cor INFO @ Mon, 12 Aug 2019 21:38:42: #2 finished! INFO @ Mon, 12 Aug 2019 21:38:42: #2 predicted fragment length is 89 bps INFO @ Mon, 12 Aug 2019 21:38:42: #2 alternative fragment length(s) may be 2,89,93,114 bps INFO @ Mon, 12 Aug 2019 21:38:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981640/SRX3981640.20_model.r WARNING @ Mon, 12 Aug 2019 21:38:42: #2 Since the d (89) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 21:38:42: #2 You may need to consider one of the other alternative d(s): 2,89,93,114 WARNING @ Mon, 12 Aug 2019 21:38:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 21:38:42: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:38:42: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:39:26: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:39:26: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:39:47: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:39:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981640/SRX3981640.10_peaks.xls INFO @ Mon, 12 Aug 2019 21:39:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981640/SRX3981640.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:39:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981640/SRX3981640.10_summits.bed INFO @ Mon, 12 Aug 2019 21:39:54: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (4873 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 21:39:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981640/SRX3981640.05_peaks.xls INFO @ Mon, 12 Aug 2019 21:39:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981640/SRX3981640.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:39:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981640/SRX3981640.05_summits.bed INFO @ Mon, 12 Aug 2019 21:39:55: Done! pass1 - making usageList (14 chroms): 5 millis pass2 - checking and writing primary data (11729 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 21:40:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981640/SRX3981640.20_peaks.xls INFO @ Mon, 12 Aug 2019 21:40:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981640/SRX3981640.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:40:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981640/SRX3981640.20_summits.bed INFO @ Mon, 12 Aug 2019 21:40:15: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1285 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。