Job ID = 11171413 sra ファイルのダウンロード中... Completed: 487935K bytes transferred in 7 seconds (542153K bits/sec), in 1 file. sra ファイルのダウンロードが完了しました。 Read layout: SINGLE fastq に変換中... Read 33635931 spots for /home/okishinya/chipatlas/results/dm3/SRX4315049/SRR7444510.sra Written 33635931 spots for /home/okishinya/chipatlas/results/dm3/SRX4315049/SRR7444510.sra rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません rm: cannot remove `[DSE]RR*.fastq': そのようなファイルやディレクトリはありません 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: 00:08:48 33635931 reads; of these: 33635931 (100.00%) were unpaired; of these: 1856 (0.01%) aligned 0 times 31651070 (94.10%) aligned exactly 1 time 1983005 (5.90%) aligned >1 times 99.99% overall alignment rate Time searching: 00:08:48 Overall time: 00:08:48 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] 8932687 / 33634075 = 0.2656 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 @ Sat, 08 Sep 2018 14:37:55: # Command line: callpeak -t SRX4315049.bam -f BAM -g dm -n SRX4315049.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4315049.10 # format = BAM # ChIP-seq file = ['SRX4315049.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 @ Sat, 08 Sep 2018 14:37:55: # Command line: callpeak -t SRX4315049.bam -f BAM -g dm -n SRX4315049.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4315049.20 # format = BAM # ChIP-seq file = ['SRX4315049.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 @ Sat, 08 Sep 2018 14:37:55: # Command line: callpeak -t SRX4315049.bam -f BAM -g dm -n SRX4315049.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4315049.05 # format = BAM # ChIP-seq file = ['SRX4315049.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 @ Sat, 08 Sep 2018 14:37:55: #1 read tag files... INFO @ Sat, 08 Sep 2018 14:37:55: #1 read tag files... INFO @ Sat, 08 Sep 2018 14:37:55: #1 read tag files... INFO @ Sat, 08 Sep 2018 14:37:55: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 14:37:55: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 14:37:55: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 14:38:02: 1000000 INFO @ Sat, 08 Sep 2018 14:38:02: 1000000 INFO @ Sat, 08 Sep 2018 14:38:02: 1000000 INFO @ Sat, 08 Sep 2018 14:38:08: 2000000 INFO @ Sat, 08 Sep 2018 14:38:09: 2000000 INFO @ Sat, 08 Sep 2018 14:38:09: 2000000 INFO @ Sat, 08 Sep 2018 14:38:15: 3000000 INFO @ Sat, 08 Sep 2018 14:38:15: 3000000 INFO @ Sat, 08 Sep 2018 14:38:15: 3000000 INFO @ Sat, 08 Sep 2018 14:38:21: 4000000 INFO @ Sat, 08 Sep 2018 14:38:22: 4000000 INFO @ Sat, 08 Sep 2018 14:38:22: 4000000 INFO @ Sat, 08 Sep 2018 14:38:28: 5000000 INFO @ Sat, 08 Sep 2018 14:38:29: 5000000 INFO @ Sat, 08 Sep 2018 14:38:29: 5000000 INFO @ Sat, 08 Sep 2018 14:38:34: 6000000 INFO @ Sat, 08 Sep 2018 14:38:36: 6000000 INFO @ Sat, 08 Sep 2018 14:38:36: 6000000 INFO @ Sat, 08 Sep 2018 14:38:41: 7000000 INFO @ Sat, 08 Sep 2018 14:38:42: 7000000 INFO @ Sat, 08 Sep 2018 14:38:43: 7000000 INFO @ Sat, 08 Sep 2018 14:38:47: 8000000 INFO @ Sat, 08 Sep 2018 14:38:49: 8000000 INFO @ Sat, 08 Sep 2018 14:38:50: 8000000 INFO @ Sat, 08 Sep 2018 14:38:54: 9000000 INFO @ Sat, 08 Sep 2018 14:38:56: 9000000 INFO @ Sat, 08 Sep 2018 14:38:56: 9000000 INFO @ Sat, 08 Sep 2018 14:39:00: 10000000 INFO @ Sat, 08 Sep 2018 14:39:03: 10000000 INFO @ Sat, 08 Sep 2018 14:39:03: 10000000 INFO @ Sat, 08 Sep 2018 14:39:07: 11000000 INFO @ Sat, 08 Sep 2018 14:39:10: 11000000 INFO @ Sat, 08 Sep 2018 14:39:10: 11000000 INFO @ Sat, 08 Sep 2018 14:39:13: 12000000 INFO @ Sat, 08 Sep 2018 14:39:17: 12000000 INFO @ Sat, 08 Sep 2018 14:39:17: 12000000 INFO @ Sat, 08 Sep 2018 14:39:20: 13000000 INFO @ Sat, 08 Sep 2018 14:39:23: 13000000 INFO @ Sat, 08 Sep 2018 14:39:24: 13000000 INFO @ Sat, 08 Sep 2018 14:39:26: 14000000 INFO @ Sat, 08 Sep 2018 14:39:30: 14000000 INFO @ Sat, 08 Sep 2018 14:39:31: 14000000 INFO @ Sat, 08 Sep 2018 14:39:33: 15000000 INFO @ Sat, 08 Sep 2018 14:39:37: 15000000 INFO @ Sat, 08 Sep 2018 14:39:39: 15000000 INFO @ Sat, 08 Sep 2018 14:39:40: 16000000 INFO @ Sat, 08 Sep 2018 14:39:43: 16000000 INFO @ Sat, 08 Sep 2018 14:39:46: 16000000 INFO @ Sat, 08 Sep 2018 14:39:47: 17000000 INFO @ Sat, 08 Sep 2018 14:39:50: 17000000 INFO @ Sat, 08 Sep 2018 14:39:53: 17000000 INFO @ Sat, 08 Sep 2018 14:39:53: 18000000 INFO @ Sat, 08 Sep 2018 14:39:57: 18000000 INFO @ Sat, 08 Sep 2018 14:40:00: 18000000 INFO @ Sat, 08 Sep 2018 14:40:00: 19000000 INFO @ Sat, 08 Sep 2018 14:40:03: 19000000 INFO @ Sat, 08 Sep 2018 14:40:07: 20000000 INFO @ Sat, 08 Sep 2018 14:40:07: 19000000 INFO @ Sat, 08 Sep 2018 14:40:10: 20000000 INFO @ Sat, 08 Sep 2018 14:40:14: 21000000 INFO @ Sat, 08 Sep 2018 14:40:15: 20000000 INFO @ Sat, 08 Sep 2018 14:40:17: 21000000 INFO @ Sat, 08 Sep 2018 14:40:21: 22000000 INFO @ Sat, 08 Sep 2018 14:40:22: 21000000 INFO @ Sat, 08 Sep 2018 14:40:23: 22000000 INFO @ Sat, 08 Sep 2018 14:40:28: 23000000 INFO @ Sat, 08 Sep 2018 14:40:29: 22000000 INFO @ Sat, 08 Sep 2018 14:40:30: 23000000 INFO @ Sat, 08 Sep 2018 14:40:35: 24000000 INFO @ Sat, 08 Sep 2018 14:40:37: 24000000 INFO @ Sat, 08 Sep 2018 14:40:37: 23000000 INFO @ Sat, 08 Sep 2018 14:40:39: #1 tag size is determined as 75 bps INFO @ Sat, 08 Sep 2018 14:40:39: #1 tag size = 75 INFO @ Sat, 08 Sep 2018 14:40:39: #1 total tags in treatment: 24701388 INFO @ Sat, 08 Sep 2018 14:40:39: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 14:40:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 14:40:40: #1 tags after filtering in treatment: 24701388 INFO @ Sat, 08 Sep 2018 14:40:40: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 14:40:40: #1 finished! INFO @ Sat, 08 Sep 2018 14:40:40: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 14:40:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 14:40:41: #1 tag size is determined as 75 bps INFO @ Sat, 08 Sep 2018 14:40:41: #1 tag size = 75 INFO @ Sat, 08 Sep 2018 14:40:41: #1 total tags in treatment: 24701388 INFO @ Sat, 08 Sep 2018 14:40:41: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 14:40:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 14:40:42: #1 tags after filtering in treatment: 24701388 INFO @ Sat, 08 Sep 2018 14:40:42: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 14:40:42: #1 finished! INFO @ Sat, 08 Sep 2018 14:40:42: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 14:40:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 14:40:43: #2 number of paired peaks: 9426 INFO @ Sat, 08 Sep 2018 14:40:43: start model_add_line... INFO @ Sat, 08 Sep 2018 14:40:43: start X-correlation... INFO @ Sat, 08 Sep 2018 14:40:43: end of X-cor INFO @ Sat, 08 Sep 2018 14:40:43: #2 finished! INFO @ Sat, 08 Sep 2018 14:40:43: #2 predicted fragment length is 97 bps INFO @ Sat, 08 Sep 2018 14:40:43: #2 alternative fragment length(s) may be 97 bps INFO @ Sat, 08 Sep 2018 14:40:43: #2.2 Generate R script for model : SRX4315049.10_model.r WARNING @ Sat, 08 Sep 2018 14:40:43: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 14:40:43: #2 You may need to consider one of the other alternative d(s): 97 WARNING @ Sat, 08 Sep 2018 14:40:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 14:40:43: #3 Call peaks... INFO @ Sat, 08 Sep 2018 14:40:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 14:40:43: 24000000 INFO @ Sat, 08 Sep 2018 14:40:45: #2 number of paired peaks: 9426 INFO @ Sat, 08 Sep 2018 14:40:45: start model_add_line... INFO @ Sat, 08 Sep 2018 14:40:46: start X-correlation... INFO @ Sat, 08 Sep 2018 14:40:46: end of X-cor INFO @ Sat, 08 Sep 2018 14:40:46: #2 finished! INFO @ Sat, 08 Sep 2018 14:40:46: #2 predicted fragment length is 97 bps INFO @ Sat, 08 Sep 2018 14:40:46: #2 alternative fragment length(s) may be 97 bps INFO @ Sat, 08 Sep 2018 14:40:46: #2.2 Generate R script for model : SRX4315049.20_model.r WARNING @ Sat, 08 Sep 2018 14:40:46: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 14:40:46: #2 You may need to consider one of the other alternative d(s): 97 WARNING @ Sat, 08 Sep 2018 14:40:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 14:40:46: #3 Call peaks... INFO @ Sat, 08 Sep 2018 14:40:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 14:40:48: #1 tag size is determined as 75 bps INFO @ Sat, 08 Sep 2018 14:40:48: #1 tag size = 75 INFO @ Sat, 08 Sep 2018 14:40:48: #1 total tags in treatment: 24701388 INFO @ Sat, 08 Sep 2018 14:40:48: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 14:40:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 14:40:49: #1 tags after filtering in treatment: 24701388 INFO @ Sat, 08 Sep 2018 14:40:49: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 14:40:49: #1 finished! INFO @ Sat, 08 Sep 2018 14:40:49: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 14:40:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 14:40:52: #2 number of paired peaks: 9426 INFO @ Sat, 08 Sep 2018 14:40:52: start model_add_line... INFO @ Sat, 08 Sep 2018 14:40:53: start X-correlation... INFO @ Sat, 08 Sep 2018 14:40:53: end of X-cor INFO @ Sat, 08 Sep 2018 14:40:53: #2 finished! INFO @ Sat, 08 Sep 2018 14:40:53: #2 predicted fragment length is 97 bps INFO @ Sat, 08 Sep 2018 14:40:53: #2 alternative fragment length(s) may be 97 bps INFO @ Sat, 08 Sep 2018 14:40:53: #2.2 Generate R script for model : SRX4315049.05_model.r WARNING @ Sat, 08 Sep 2018 14:40:53: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 14:40:53: #2 You may need to consider one of the other alternative d(s): 97 WARNING @ Sat, 08 Sep 2018 14:40:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 14:40:53: #3 Call peaks... INFO @ Sat, 08 Sep 2018 14:40:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 14:41:38: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 14:41:42: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 14:41:49: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 14:42:03: #4 Write output xls file... SRX4315049.10_peaks.xls INFO @ Sat, 08 Sep 2018 14:42:03: #4 Write peak in narrowPeak format file... SRX4315049.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 14:42:03: #4 Write summits bed file... SRX4315049.10_summits.bed INFO @ Sat, 08 Sep 2018 14:42:03: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (9892 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 14:42:08: #4 Write output xls file... SRX4315049.20_peaks.xls INFO @ Sat, 08 Sep 2018 14:42:08: #4 Write peak in narrowPeak format file... SRX4315049.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 14:42:08: #4 Write summits bed file... SRX4315049.20_summits.bed INFO @ Sat, 08 Sep 2018 14:42:08: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (7689 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 14:42:14: #4 Write output xls file... SRX4315049.05_peaks.xls INFO @ Sat, 08 Sep 2018 14:42:14: #4 Write peak in narrowPeak format file... SRX4315049.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 14:42:15: #4 Write summits bed file... SRX4315049.05_summits.bed INFO @ Sat, 08 Sep 2018 14:42:15: Done! pass1 - making usageList (15 chroms): 7 millis pass2 - checking and writing primary data (11725 records, 4 fields): 16 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。