Job ID = 11171370 sra ファイルのダウンロード中... Completed: 637607K bytes transferred in 7 seconds (681968K 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 40096891 spots for /home/okishinya/chipatlas/results/dm3/SRX4315043/SRR7444504.sra Written 40096891 spots for /home/okishinya/chipatlas/results/dm3/SRX4315043/SRR7444504.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: 00:12:03 40096891 reads; of these: 40096891 (100.00%) were unpaired; of these: 4090 (0.01%) aligned 0 times 36633353 (91.36%) aligned exactly 1 time 3459448 (8.63%) aligned >1 times 99.99% overall alignment rate Time searching: 00:12:03 Overall time: 00:12:03 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] 19399056 / 40092801 = 0.4839 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 14:26:40: # Command line: callpeak -t SRX4315043.bam -f BAM -g dm -n SRX4315043.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4315043.10 # format = BAM # ChIP-seq file = ['SRX4315043.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 14:26:40: #1 read tag files... INFO @ Sat, 08 Sep 2018 14:26:40: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 14:26:40: # Command line: callpeak -t SRX4315043.bam -f BAM -g dm -n SRX4315043.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4315043.05 # format = BAM # ChIP-seq file = ['SRX4315043.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 14:26:40: #1 read tag files... INFO @ Sat, 08 Sep 2018 14:26:40: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 14:26:40: # Command line: callpeak -t SRX4315043.bam -f BAM -g dm -n SRX4315043.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4315043.20 # format = BAM # ChIP-seq file = ['SRX4315043.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 14:26:40: #1 read tag files... INFO @ Sat, 08 Sep 2018 14:26:40: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 14:26:48: 1000000 INFO @ Sat, 08 Sep 2018 14:26:49: 1000000 INFO @ Sat, 08 Sep 2018 14:26:49: 1000000 INFO @ Sat, 08 Sep 2018 14:26:55: 2000000 INFO @ Sat, 08 Sep 2018 14:26:57: 2000000 INFO @ Sat, 08 Sep 2018 14:26:57: 2000000 INFO @ Sat, 08 Sep 2018 14:27:03: 3000000 INFO @ Sat, 08 Sep 2018 14:27:05: 3000000 INFO @ Sat, 08 Sep 2018 14:27:05: 3000000 INFO @ Sat, 08 Sep 2018 14:27:10: 4000000 INFO @ Sat, 08 Sep 2018 14:27:13: 4000000 INFO @ Sat, 08 Sep 2018 14:27:13: 4000000 INFO @ Sat, 08 Sep 2018 14:27:18: 5000000 INFO @ Sat, 08 Sep 2018 14:27:21: 5000000 INFO @ Sat, 08 Sep 2018 14:27:21: 5000000 INFO @ Sat, 08 Sep 2018 14:27:25: 6000000 INFO @ Sat, 08 Sep 2018 14:27:29: 6000000 INFO @ Sat, 08 Sep 2018 14:27:29: 6000000 INFO @ Sat, 08 Sep 2018 14:27:33: 7000000 INFO @ Sat, 08 Sep 2018 14:27:37: 7000000 INFO @ Sat, 08 Sep 2018 14:27:37: 7000000 INFO @ Sat, 08 Sep 2018 14:27:40: 8000000 INFO @ Sat, 08 Sep 2018 14:27:46: 8000000 INFO @ Sat, 08 Sep 2018 14:27:46: 8000000 INFO @ Sat, 08 Sep 2018 14:27:48: 9000000 INFO @ Sat, 08 Sep 2018 14:27:54: 9000000 INFO @ Sat, 08 Sep 2018 14:27:54: 9000000 INFO @ Sat, 08 Sep 2018 14:27:55: 10000000 INFO @ Sat, 08 Sep 2018 14:28:02: 10000000 INFO @ Sat, 08 Sep 2018 14:28:02: 10000000 INFO @ Sat, 08 Sep 2018 14:28:02: 11000000 INFO @ Sat, 08 Sep 2018 14:28:10: 12000000 INFO @ Sat, 08 Sep 2018 14:28:10: 11000000 INFO @ Sat, 08 Sep 2018 14:28:10: 11000000 INFO @ Sat, 08 Sep 2018 14:28:17: 13000000 INFO @ Sat, 08 Sep 2018 14:28:18: 12000000 INFO @ Sat, 08 Sep 2018 14:28:18: 12000000 INFO @ Sat, 08 Sep 2018 14:28:25: 14000000 INFO @ Sat, 08 Sep 2018 14:28:26: 13000000 INFO @ Sat, 08 Sep 2018 14:28:27: 13000000 INFO @ Sat, 08 Sep 2018 14:28:32: 15000000 INFO @ Sat, 08 Sep 2018 14:28:35: 14000000 INFO @ Sat, 08 Sep 2018 14:28:35: 14000000 INFO @ Sat, 08 Sep 2018 14:28:40: 16000000 INFO @ Sat, 08 Sep 2018 14:28:43: 15000000 INFO @ Sat, 08 Sep 2018 14:28:43: 15000000 INFO @ Sat, 08 Sep 2018 14:28:47: 17000000 INFO @ Sat, 08 Sep 2018 14:28:51: 16000000 INFO @ Sat, 08 Sep 2018 14:28:51: 16000000 INFO @ Sat, 08 Sep 2018 14:28:55: 18000000 INFO @ Sat, 08 Sep 2018 14:29:00: 17000000 INFO @ Sat, 08 Sep 2018 14:29:00: 17000000 INFO @ Sat, 08 Sep 2018 14:29:02: 19000000 INFO @ Sat, 08 Sep 2018 14:29:08: 18000000 INFO @ Sat, 08 Sep 2018 14:29:08: 18000000 INFO @ Sat, 08 Sep 2018 14:29:10: 20000000 INFO @ Sat, 08 Sep 2018 14:29:15: #1 tag size is determined as 75 bps INFO @ Sat, 08 Sep 2018 14:29:15: #1 tag size = 75 INFO @ Sat, 08 Sep 2018 14:29:15: #1 total tags in treatment: 20693745 INFO @ Sat, 08 Sep 2018 14:29:15: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 14:29:15: #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 14:29:15: #1 tags after filtering in treatment: 20693745 INFO @ Sat, 08 Sep 2018 14:29:15: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 14:29:15: #1 finished! INFO @ Sat, 08 Sep 2018 14:29:15: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 14:29:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 14:29:16: 19000000 INFO @ Sat, 08 Sep 2018 14:29:17: 19000000 INFO @ Sat, 08 Sep 2018 14:29:18: #2 number of paired peaks: 5510 INFO @ Sat, 08 Sep 2018 14:29:18: start model_add_line... INFO @ Sat, 08 Sep 2018 14:29:18: start X-correlation... INFO @ Sat, 08 Sep 2018 14:29:18: end of X-cor INFO @ Sat, 08 Sep 2018 14:29:18: #2 finished! INFO @ Sat, 08 Sep 2018 14:29:18: #2 predicted fragment length is 135 bps INFO @ Sat, 08 Sep 2018 14:29:18: #2 alternative fragment length(s) may be 135 bps INFO @ Sat, 08 Sep 2018 14:29:18: #2.2 Generate R script for model : SRX4315043.10_model.r WARNING @ Sat, 08 Sep 2018 14:29:18: #2 Since the d (135) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 14:29:18: #2 You may need to consider one of the other alternative d(s): 135 WARNING @ Sat, 08 Sep 2018 14:29:18: #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 14:29:18: #3 Call peaks... INFO @ Sat, 08 Sep 2018 14:29:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 14:29:25: 20000000 INFO @ Sat, 08 Sep 2018 14:29:25: 20000000 INFO @ Sat, 08 Sep 2018 14:29:30: #1 tag size is determined as 75 bps INFO @ Sat, 08 Sep 2018 14:29:30: #1 tag size = 75 INFO @ Sat, 08 Sep 2018 14:29:30: #1 total tags in treatment: 20693745 INFO @ Sat, 08 Sep 2018 14:29:30: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 14:29:30: #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 14:29:31: #1 tags after filtering in treatment: 20693745 INFO @ Sat, 08 Sep 2018 14:29:31: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 14:29:31: #1 finished! INFO @ Sat, 08 Sep 2018 14:29:31: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 14:29:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 14:29:31: #1 tag size is determined as 75 bps INFO @ Sat, 08 Sep 2018 14:29:31: #1 tag size = 75 INFO @ Sat, 08 Sep 2018 14:29:31: #1 total tags in treatment: 20693745 INFO @ Sat, 08 Sep 2018 14:29:31: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 14:29:31: #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 14:29:31: #1 tags after filtering in treatment: 20693745 INFO @ Sat, 08 Sep 2018 14:29:31: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 14:29:31: #1 finished! INFO @ Sat, 08 Sep 2018 14:29:31: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 14:29:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 14:29:33: #2 number of paired peaks: 5510 INFO @ Sat, 08 Sep 2018 14:29:33: start model_add_line... INFO @ Sat, 08 Sep 2018 14:29:33: start X-correlation... INFO @ Sat, 08 Sep 2018 14:29:33: end of X-cor INFO @ Sat, 08 Sep 2018 14:29:33: #2 finished! INFO @ Sat, 08 Sep 2018 14:29:33: #2 predicted fragment length is 135 bps INFO @ Sat, 08 Sep 2018 14:29:33: #2 alternative fragment length(s) may be 135 bps INFO @ Sat, 08 Sep 2018 14:29:33: #2.2 Generate R script for model : SRX4315043.05_model.r WARNING @ Sat, 08 Sep 2018 14:29:33: #2 Since the d (135) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 14:29:33: #2 You may need to consider one of the other alternative d(s): 135 WARNING @ Sat, 08 Sep 2018 14:29:33: #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 14:29:33: #3 Call peaks... INFO @ Sat, 08 Sep 2018 14:29:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 14:29:34: #2 number of paired peaks: 5510 INFO @ Sat, 08 Sep 2018 14:29:34: start model_add_line... INFO @ Sat, 08 Sep 2018 14:29:34: start X-correlation... INFO @ Sat, 08 Sep 2018 14:29:34: end of X-cor INFO @ Sat, 08 Sep 2018 14:29:34: #2 finished! INFO @ Sat, 08 Sep 2018 14:29:34: #2 predicted fragment length is 135 bps INFO @ Sat, 08 Sep 2018 14:29:34: #2 alternative fragment length(s) may be 135 bps INFO @ Sat, 08 Sep 2018 14:29:34: #2.2 Generate R script for model : SRX4315043.20_model.r WARNING @ Sat, 08 Sep 2018 14:29:34: #2 Since the d (135) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 14:29:34: #2 You may need to consider one of the other alternative d(s): 135 WARNING @ Sat, 08 Sep 2018 14:29:34: #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 14:29:34: #3 Call peaks... INFO @ Sat, 08 Sep 2018 14:29:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 14:30:17: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 14:30:30: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 14:30:32: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 14:30:47: #4 Write output xls file... SRX4315043.10_peaks.xls INFO @ Sat, 08 Sep 2018 14:30:47: #4 Write peak in narrowPeak format file... SRX4315043.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 14:30:47: #4 Write summits bed file... SRX4315043.10_summits.bed INFO @ Sat, 08 Sep 2018 14:30:48: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (10963 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 14:30:55: #4 Write output xls file... SRX4315043.05_peaks.xls INFO @ Sat, 08 Sep 2018 14:30:56: #4 Write peak in narrowPeak format file... SRX4315043.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 14:30:56: #4 Write summits bed file... SRX4315043.05_summits.bed INFO @ Sat, 08 Sep 2018 14:30:56: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (12798 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 14:30:58: #4 Write output xls file... SRX4315043.20_peaks.xls INFO @ Sat, 08 Sep 2018 14:30:58: #4 Write peak in narrowPeak format file... SRX4315043.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 14:30:58: #4 Write summits bed file... SRX4315043.20_summits.bed INFO @ Sat, 08 Sep 2018 14:30:58: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (8742 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。