Job ID = 2590377 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 13,555,808 reads read : 27,111,616 reads written : 13,555,808 reads 0-length : 13,555,808 spots read : 13,441,102 reads read : 26,882,204 reads written : 13,441,102 reads 0-length : 13,441,102 spots read : 13,427,000 reads read : 26,854,000 reads written : 13,427,000 reads 0-length : 13,427,000 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: 00:10:49 40423910 reads; of these: 40423910 (100.00%) were unpaired; of these: 1053637 (2.61%) aligned 0 times 33797956 (83.61%) aligned exactly 1 time 5572317 (13.78%) aligned >1 times 97.39% overall alignment rate Time searching: 00:10:49 Overall time: 00:10:49 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] 8921063 / 39370273 = 0.2266 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 21:39:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981647/SRX3981647.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981647/SRX3981647.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981647/SRX3981647.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981647/SRX3981647.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 21:39:44: #1 read tag files... INFO @ Mon, 12 Aug 2019 21:39:44: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 21:39:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981647/SRX3981647.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981647/SRX3981647.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981647/SRX3981647.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981647/SRX3981647.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 21:39:45: #1 read tag files... INFO @ Mon, 12 Aug 2019 21:39:45: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 21:39:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981647/SRX3981647.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981647/SRX3981647.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981647/SRX3981647.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981647/SRX3981647.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 21:39:46: #1 read tag files... INFO @ Mon, 12 Aug 2019 21:39:46: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 21:39:54: 1000000 INFO @ Mon, 12 Aug 2019 21:39:54: 1000000 INFO @ Mon, 12 Aug 2019 21:39:54: 1000000 INFO @ Mon, 12 Aug 2019 21:40:02: 2000000 INFO @ Mon, 12 Aug 2019 21:40:02: 2000000 INFO @ Mon, 12 Aug 2019 21:40:03: 2000000 INFO @ Mon, 12 Aug 2019 21:40:10: 3000000 INFO @ Mon, 12 Aug 2019 21:40:10: 3000000 INFO @ Mon, 12 Aug 2019 21:40:13: 3000000 INFO @ Mon, 12 Aug 2019 21:40:17: 4000000 INFO @ Mon, 12 Aug 2019 21:40:18: 4000000 INFO @ Mon, 12 Aug 2019 21:40:22: 4000000 INFO @ Mon, 12 Aug 2019 21:40:25: 5000000 INFO @ Mon, 12 Aug 2019 21:40:26: 5000000 INFO @ Mon, 12 Aug 2019 21:40:31: 5000000 INFO @ Mon, 12 Aug 2019 21:40:33: 6000000 INFO @ Mon, 12 Aug 2019 21:40:34: 6000000 INFO @ Mon, 12 Aug 2019 21:40:40: 7000000 INFO @ Mon, 12 Aug 2019 21:40:41: 6000000 INFO @ Mon, 12 Aug 2019 21:40:42: 7000000 INFO @ Mon, 12 Aug 2019 21:40:47: 8000000 INFO @ Mon, 12 Aug 2019 21:40:49: 8000000 INFO @ Mon, 12 Aug 2019 21:40:50: 7000000 INFO @ Mon, 12 Aug 2019 21:40:54: 9000000 INFO @ Mon, 12 Aug 2019 21:40:57: 9000000 INFO @ Mon, 12 Aug 2019 21:41:00: 8000000 INFO @ Mon, 12 Aug 2019 21:41:01: 10000000 INFO @ Mon, 12 Aug 2019 21:41:05: 10000000 INFO @ Mon, 12 Aug 2019 21:41:08: 11000000 INFO @ Mon, 12 Aug 2019 21:41:09: 9000000 INFO @ Mon, 12 Aug 2019 21:41:13: 11000000 INFO @ Mon, 12 Aug 2019 21:41:16: 12000000 INFO @ Mon, 12 Aug 2019 21:41:19: 10000000 INFO @ Mon, 12 Aug 2019 21:41:21: 12000000 INFO @ Mon, 12 Aug 2019 21:41:23: 13000000 INFO @ Mon, 12 Aug 2019 21:41:28: 11000000 INFO @ Mon, 12 Aug 2019 21:41:29: 13000000 INFO @ Mon, 12 Aug 2019 21:41:30: 14000000 INFO @ Mon, 12 Aug 2019 21:41:37: 14000000 INFO @ Mon, 12 Aug 2019 21:41:37: 15000000 INFO @ Mon, 12 Aug 2019 21:41:38: 12000000 INFO @ Mon, 12 Aug 2019 21:41:44: 16000000 INFO @ Mon, 12 Aug 2019 21:41:45: 15000000 INFO @ Mon, 12 Aug 2019 21:41:47: 13000000 INFO @ Mon, 12 Aug 2019 21:41:51: 17000000 INFO @ Mon, 12 Aug 2019 21:41:52: 16000000 INFO @ Mon, 12 Aug 2019 21:41:57: 14000000 INFO @ Mon, 12 Aug 2019 21:41:58: 18000000 INFO @ Mon, 12 Aug 2019 21:42:00: 17000000 INFO @ Mon, 12 Aug 2019 21:42:05: 19000000 INFO @ Mon, 12 Aug 2019 21:42:06: 15000000 INFO @ Mon, 12 Aug 2019 21:42:08: 18000000 INFO @ Mon, 12 Aug 2019 21:42:13: 20000000 INFO @ Mon, 12 Aug 2019 21:42:15: 16000000 INFO @ Mon, 12 Aug 2019 21:42:16: 19000000 INFO @ Mon, 12 Aug 2019 21:42:20: 21000000 INFO @ Mon, 12 Aug 2019 21:42:24: 20000000 INFO @ Mon, 12 Aug 2019 21:42:24: 17000000 INFO @ Mon, 12 Aug 2019 21:42:27: 22000000 INFO @ Mon, 12 Aug 2019 21:42:31: 21000000 INFO @ Mon, 12 Aug 2019 21:42:34: 18000000 INFO @ Mon, 12 Aug 2019 21:42:34: 23000000 INFO @ Mon, 12 Aug 2019 21:42:39: 22000000 INFO @ Mon, 12 Aug 2019 21:42:41: 24000000 INFO @ Mon, 12 Aug 2019 21:42:43: 19000000 INFO @ Mon, 12 Aug 2019 21:42:47: 23000000 INFO @ Mon, 12 Aug 2019 21:42:48: 25000000 INFO @ Mon, 12 Aug 2019 21:42:52: 20000000 INFO @ Mon, 12 Aug 2019 21:42:55: 24000000 INFO @ Mon, 12 Aug 2019 21:42:55: 26000000 INFO @ Mon, 12 Aug 2019 21:43:02: 21000000 INFO @ Mon, 12 Aug 2019 21:43:02: 25000000 INFO @ Mon, 12 Aug 2019 21:43:03: 27000000 INFO @ Mon, 12 Aug 2019 21:43:10: 28000000 INFO @ Mon, 12 Aug 2019 21:43:10: 26000000 INFO @ Mon, 12 Aug 2019 21:43:11: 22000000 INFO @ Mon, 12 Aug 2019 21:43:17: 29000000 INFO @ Mon, 12 Aug 2019 21:43:18: 27000000 INFO @ Mon, 12 Aug 2019 21:43:20: 23000000 INFO @ Mon, 12 Aug 2019 21:43:24: 30000000 INFO @ Mon, 12 Aug 2019 21:43:26: 28000000 INFO @ Mon, 12 Aug 2019 21:43:27: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 21:43:27: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 21:43:27: #1 total tags in treatment: 30449210 INFO @ Mon, 12 Aug 2019 21:43:27: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:43:27: #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 21:43:28: #1 tags after filtering in treatment: 30449210 INFO @ Mon, 12 Aug 2019 21:43:28: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:43:28: #1 finished! INFO @ Mon, 12 Aug 2019 21:43:28: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:43:28: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:43:30: 24000000 INFO @ Mon, 12 Aug 2019 21:43:31: #2 number of paired peaks: 1452 INFO @ Mon, 12 Aug 2019 21:43:31: start model_add_line... INFO @ Mon, 12 Aug 2019 21:43:31: start X-correlation... INFO @ Mon, 12 Aug 2019 21:43:31: end of X-cor INFO @ Mon, 12 Aug 2019 21:43:31: #2 finished! INFO @ Mon, 12 Aug 2019 21:43:31: #2 predicted fragment length is 87 bps INFO @ Mon, 12 Aug 2019 21:43:31: #2 alternative fragment length(s) may be 2,87,103 bps INFO @ Mon, 12 Aug 2019 21:43:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981647/SRX3981647.20_model.r WARNING @ Mon, 12 Aug 2019 21:43:31: #2 Since the d (87) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 21:43:31: #2 You may need to consider one of the other alternative d(s): 2,87,103 WARNING @ Mon, 12 Aug 2019 21:43:31: #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 21:43:31: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:43:31: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:43:34: 29000000 INFO @ Mon, 12 Aug 2019 21:43:39: 25000000 INFO @ Mon, 12 Aug 2019 21:43:42: 30000000 INFO @ Mon, 12 Aug 2019 21:43:45: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 21:43:45: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 21:43:45: #1 total tags in treatment: 30449210 INFO @ Mon, 12 Aug 2019 21:43:45: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:43:45: #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 21:43:46: #1 tags after filtering in treatment: 30449210 INFO @ Mon, 12 Aug 2019 21:43:46: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:43:46: #1 finished! INFO @ Mon, 12 Aug 2019 21:43:46: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:43:46: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:43:48: 26000000 INFO @ Mon, 12 Aug 2019 21:43:49: #2 number of paired peaks: 1452 INFO @ Mon, 12 Aug 2019 21:43:49: start model_add_line... INFO @ Mon, 12 Aug 2019 21:43:49: start X-correlation... INFO @ Mon, 12 Aug 2019 21:43:49: end of X-cor INFO @ Mon, 12 Aug 2019 21:43:49: #2 finished! INFO @ Mon, 12 Aug 2019 21:43:49: #2 predicted fragment length is 87 bps INFO @ Mon, 12 Aug 2019 21:43:49: #2 alternative fragment length(s) may be 2,87,103 bps INFO @ Mon, 12 Aug 2019 21:43:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981647/SRX3981647.10_model.r WARNING @ Mon, 12 Aug 2019 21:43:49: #2 Since the d (87) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 21:43:49: #2 You may need to consider one of the other alternative d(s): 2,87,103 WARNING @ Mon, 12 Aug 2019 21:43:49: #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 21:43:49: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:43:49: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:43:58: 27000000 INFO @ Mon, 12 Aug 2019 21:44:07: 28000000 INFO @ Mon, 12 Aug 2019 21:44:16: 29000000 INFO @ Mon, 12 Aug 2019 21:44:25: 30000000 INFO @ Mon, 12 Aug 2019 21:44:29: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 21:44:29: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 21:44:29: #1 total tags in treatment: 30449210 INFO @ Mon, 12 Aug 2019 21:44:29: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:44:29: #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 21:44:30: #1 tags after filtering in treatment: 30449210 INFO @ Mon, 12 Aug 2019 21:44:30: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:44:30: #1 finished! INFO @ Mon, 12 Aug 2019 21:44:30: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:44:30: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:44:32: #2 number of paired peaks: 1452 INFO @ Mon, 12 Aug 2019 21:44:32: start model_add_line... INFO @ Mon, 12 Aug 2019 21:44:33: start X-correlation... INFO @ Mon, 12 Aug 2019 21:44:33: end of X-cor INFO @ Mon, 12 Aug 2019 21:44:33: #2 finished! INFO @ Mon, 12 Aug 2019 21:44:33: #2 predicted fragment length is 87 bps INFO @ Mon, 12 Aug 2019 21:44:33: #2 alternative fragment length(s) may be 2,87,103 bps INFO @ Mon, 12 Aug 2019 21:44:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981647/SRX3981647.05_model.r WARNING @ Mon, 12 Aug 2019 21:44:33: #2 Since the d (87) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 21:44:33: #2 You may need to consider one of the other alternative d(s): 2,87,103 WARNING @ Mon, 12 Aug 2019 21:44:33: #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 21:44:33: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:44:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:44:41: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:44:58: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:45:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981647/SRX3981647.20_peaks.xls INFO @ Mon, 12 Aug 2019 21:45:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981647/SRX3981647.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:45:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981647/SRX3981647.20_summits.bed INFO @ Mon, 12 Aug 2019 21:45:16: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (889 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 21:45:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981647/SRX3981647.10_peaks.xls INFO @ Mon, 12 Aug 2019 21:45:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981647/SRX3981647.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:45:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981647/SRX3981647.10_summits.bed INFO @ Mon, 12 Aug 2019 21:45:33: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3990 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 21:45:43: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:46:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981647/SRX3981647.05_peaks.xls INFO @ Mon, 12 Aug 2019 21:46:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981647/SRX3981647.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:46:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981647/SRX3981647.05_summits.bed INFO @ Mon, 12 Aug 2019 21:46:17: Done! pass1 - making usageList (14 chroms): 5 millis pass2 - checking and writing primary data (11065 records, 4 fields): 15 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。