Job ID = 11192581 sra ファイルのダウンロード中... Completed: 339994K bytes transferred in 6 seconds (449567K 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 33169024 spots for /home/okishinya/chipatlas/results/rn6/SRX4014802/SRR7085051.sra Written 33169024 spots for /home/okishinya/chipatlas/results/rn6/SRX4014802/SRR7085051.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: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:41:22 33169024 reads; of these: 33169024 (100.00%) were unpaired; of these: 999402 (3.01%) aligned 0 times 23837845 (71.87%) aligned exactly 1 time 8331777 (25.12%) aligned >1 times 96.99% overall alignment rate Time searching: 00:41:24 Overall time: 00:41:24 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 2810116 / 32169622 = 0.0874 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, 15 Sep 2018 11:48:44: # Command line: callpeak -t SRX4014802.bam -f BAM -g 2.15e9 -n SRX4014802.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4014802.20 # format = BAM # ChIP-seq file = ['SRX4014802.bam'] # control file = None # effective genome size = 2.15e+09 # 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, 15 Sep 2018 11:48:44: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:48:44: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:48:44: # Command line: callpeak -t SRX4014802.bam -f BAM -g 2.15e9 -n SRX4014802.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4014802.05 # format = BAM # ChIP-seq file = ['SRX4014802.bam'] # control file = None # effective genome size = 2.15e+09 # 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, 15 Sep 2018 11:48:44: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:48:44: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:48:44: # Command line: callpeak -t SRX4014802.bam -f BAM -g 2.15e9 -n SRX4014802.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4014802.10 # format = BAM # ChIP-seq file = ['SRX4014802.bam'] # control file = None # effective genome size = 2.15e+09 # 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, 15 Sep 2018 11:48:44: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:48:44: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:48:51: 1000000 INFO @ Sat, 15 Sep 2018 11:48:51: 1000000 INFO @ Sat, 15 Sep 2018 11:48:54: 1000000 INFO @ Sat, 15 Sep 2018 11:48:58: 2000000 INFO @ Sat, 15 Sep 2018 11:48:58: 2000000 INFO @ Sat, 15 Sep 2018 11:49:03: 2000000 INFO @ Sat, 15 Sep 2018 11:49:05: 3000000 INFO @ Sat, 15 Sep 2018 11:49:05: 3000000 INFO @ Sat, 15 Sep 2018 11:49:12: 4000000 INFO @ Sat, 15 Sep 2018 11:49:12: 4000000 INFO @ Sat, 15 Sep 2018 11:49:13: 3000000 INFO @ Sat, 15 Sep 2018 11:49:19: 5000000 INFO @ Sat, 15 Sep 2018 11:49:19: 5000000 INFO @ Sat, 15 Sep 2018 11:49:21: 4000000 INFO @ Sat, 15 Sep 2018 11:49:26: 6000000 INFO @ Sat, 15 Sep 2018 11:49:26: 6000000 INFO @ Sat, 15 Sep 2018 11:49:29: 5000000 INFO @ Sat, 15 Sep 2018 11:49:33: 7000000 INFO @ Sat, 15 Sep 2018 11:49:34: 7000000 INFO @ Sat, 15 Sep 2018 11:49:36: 6000000 INFO @ Sat, 15 Sep 2018 11:49:40: 8000000 INFO @ Sat, 15 Sep 2018 11:49:41: 8000000 INFO @ Sat, 15 Sep 2018 11:49:44: 7000000 INFO @ Sat, 15 Sep 2018 11:49:47: 9000000 INFO @ Sat, 15 Sep 2018 11:49:48: 9000000 INFO @ Sat, 15 Sep 2018 11:49:51: 8000000 INFO @ Sat, 15 Sep 2018 11:49:54: 10000000 INFO @ Sat, 15 Sep 2018 11:49:55: 10000000 INFO @ Sat, 15 Sep 2018 11:49:58: 9000000 INFO @ Sat, 15 Sep 2018 11:50:01: 11000000 INFO @ Sat, 15 Sep 2018 11:50:02: 11000000 INFO @ Sat, 15 Sep 2018 11:50:05: 10000000 INFO @ Sat, 15 Sep 2018 11:50:08: 12000000 INFO @ Sat, 15 Sep 2018 11:50:09: 12000000 INFO @ Sat, 15 Sep 2018 11:50:13: 11000000 INFO @ Sat, 15 Sep 2018 11:50:15: 13000000 INFO @ Sat, 15 Sep 2018 11:50:17: 13000000 INFO @ Sat, 15 Sep 2018 11:50:20: 12000000 INFO @ Sat, 15 Sep 2018 11:50:22: 14000000 INFO @ Sat, 15 Sep 2018 11:50:24: 14000000 INFO @ Sat, 15 Sep 2018 11:50:27: 13000000 INFO @ Sat, 15 Sep 2018 11:50:29: 15000000 INFO @ Sat, 15 Sep 2018 11:50:31: 15000000 INFO @ Sat, 15 Sep 2018 11:50:35: 14000000 INFO @ Sat, 15 Sep 2018 11:50:36: 16000000 INFO @ Sat, 15 Sep 2018 11:50:38: 16000000 INFO @ Sat, 15 Sep 2018 11:50:42: 15000000 INFO @ Sat, 15 Sep 2018 11:50:43: 17000000 INFO @ Sat, 15 Sep 2018 11:50:45: 17000000 INFO @ Sat, 15 Sep 2018 11:50:49: 16000000 INFO @ Sat, 15 Sep 2018 11:50:50: 18000000 INFO @ Sat, 15 Sep 2018 11:50:52: 18000000 INFO @ Sat, 15 Sep 2018 11:50:57: 17000000 INFO @ Sat, 15 Sep 2018 11:50:57: 19000000 INFO @ Sat, 15 Sep 2018 11:50:59: 19000000 INFO @ Sat, 15 Sep 2018 11:51:04: 20000000 INFO @ Sat, 15 Sep 2018 11:51:04: 18000000 INFO @ Sat, 15 Sep 2018 11:51:07: 20000000 INFO @ Sat, 15 Sep 2018 11:51:11: 21000000 INFO @ Sat, 15 Sep 2018 11:51:11: 19000000 INFO @ Sat, 15 Sep 2018 11:51:14: 21000000 INFO @ Sat, 15 Sep 2018 11:51:18: 22000000 INFO @ Sat, 15 Sep 2018 11:51:19: 20000000 INFO @ Sat, 15 Sep 2018 11:51:21: 22000000 INFO @ Sat, 15 Sep 2018 11:51:25: 23000000 INFO @ Sat, 15 Sep 2018 11:51:26: 21000000 INFO @ Sat, 15 Sep 2018 11:51:28: 23000000 INFO @ Sat, 15 Sep 2018 11:51:32: 24000000 INFO @ Sat, 15 Sep 2018 11:51:34: 22000000 INFO @ Sat, 15 Sep 2018 11:51:35: 24000000 INFO @ Sat, 15 Sep 2018 11:51:39: 25000000 INFO @ Sat, 15 Sep 2018 11:51:42: 23000000 INFO @ Sat, 15 Sep 2018 11:51:42: 25000000 INFO @ Sat, 15 Sep 2018 11:51:46: 26000000 INFO @ Sat, 15 Sep 2018 11:51:49: 24000000 INFO @ Sat, 15 Sep 2018 11:51:50: 26000000 INFO @ Sat, 15 Sep 2018 11:51:53: 27000000 INFO @ Sat, 15 Sep 2018 11:51:57: 27000000 INFO @ Sat, 15 Sep 2018 11:51:57: 25000000 INFO @ Sat, 15 Sep 2018 11:52:00: 28000000 INFO @ Sat, 15 Sep 2018 11:52:04: 28000000 INFO @ Sat, 15 Sep 2018 11:52:05: 26000000 INFO @ Sat, 15 Sep 2018 11:52:07: 29000000 INFO @ Sat, 15 Sep 2018 11:52:10: #1 tag size is determined as 75 bps INFO @ Sat, 15 Sep 2018 11:52:10: #1 tag size = 75 INFO @ Sat, 15 Sep 2018 11:52:10: #1 total tags in treatment: 29359506 INFO @ Sat, 15 Sep 2018 11:52:10: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:52:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 11:52:10: #1 tags after filtering in treatment: 29359417 INFO @ Sat, 15 Sep 2018 11:52:10: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 11:52:10: #1 finished! INFO @ Sat, 15 Sep 2018 11:52:10: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:52:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:52:11: 29000000 INFO @ Sat, 15 Sep 2018 11:52:13: 27000000 INFO @ Sat, 15 Sep 2018 11:52:13: #2 number of paired peaks: 5894 INFO @ Sat, 15 Sep 2018 11:52:13: start model_add_line... INFO @ Sat, 15 Sep 2018 11:52:14: start X-correlation... INFO @ Sat, 15 Sep 2018 11:52:14: end of X-cor INFO @ Sat, 15 Sep 2018 11:52:14: #2 finished! INFO @ Sat, 15 Sep 2018 11:52:14: #2 predicted fragment length is 75 bps INFO @ Sat, 15 Sep 2018 11:52:14: #2 alternative fragment length(s) may be 75 bps INFO @ Sat, 15 Sep 2018 11:52:14: #2.2 Generate R script for model : SRX4014802.05_model.r WARNING @ Sat, 15 Sep 2018 11:52:14: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Sep 2018 11:52:14: #2 You may need to consider one of the other alternative d(s): 75 WARNING @ Sat, 15 Sep 2018 11:52:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Sep 2018 11:52:14: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:52:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:52:14: #1 tag size is determined as 75 bps INFO @ Sat, 15 Sep 2018 11:52:14: #1 tag size = 75 INFO @ Sat, 15 Sep 2018 11:52:14: #1 total tags in treatment: 29359506 INFO @ Sat, 15 Sep 2018 11:52:14: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:52:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 11:52:15: #1 tags after filtering in treatment: 29359417 INFO @ Sat, 15 Sep 2018 11:52:15: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 11:52:15: #1 finished! INFO @ Sat, 15 Sep 2018 11:52:15: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:52:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:52:18: #2 number of paired peaks: 5894 INFO @ Sat, 15 Sep 2018 11:52:18: start model_add_line... INFO @ Sat, 15 Sep 2018 11:52:18: start X-correlation... INFO @ Sat, 15 Sep 2018 11:52:18: end of X-cor INFO @ Sat, 15 Sep 2018 11:52:18: #2 finished! INFO @ Sat, 15 Sep 2018 11:52:18: #2 predicted fragment length is 75 bps INFO @ Sat, 15 Sep 2018 11:52:18: #2 alternative fragment length(s) may be 75 bps INFO @ Sat, 15 Sep 2018 11:52:18: #2.2 Generate R script for model : SRX4014802.20_model.r WARNING @ Sat, 15 Sep 2018 11:52:18: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Sep 2018 11:52:18: #2 You may need to consider one of the other alternative d(s): 75 WARNING @ Sat, 15 Sep 2018 11:52:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Sep 2018 11:52:18: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:52:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:52:21: 28000000 INFO @ Sat, 15 Sep 2018 11:52:28: 29000000 INFO @ Sat, 15 Sep 2018 11:52:31: #1 tag size is determined as 75 bps INFO @ Sat, 15 Sep 2018 11:52:31: #1 tag size = 75 INFO @ Sat, 15 Sep 2018 11:52:31: #1 total tags in treatment: 29359506 INFO @ Sat, 15 Sep 2018 11:52:31: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:52:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 11:52:32: #1 tags after filtering in treatment: 29359417 INFO @ Sat, 15 Sep 2018 11:52:32: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 11:52:32: #1 finished! INFO @ Sat, 15 Sep 2018 11:52:32: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:52:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:52:35: #2 number of paired peaks: 5894 INFO @ Sat, 15 Sep 2018 11:52:35: start model_add_line... INFO @ Sat, 15 Sep 2018 11:52:35: start X-correlation... INFO @ Sat, 15 Sep 2018 11:52:35: end of X-cor INFO @ Sat, 15 Sep 2018 11:52:35: #2 finished! INFO @ Sat, 15 Sep 2018 11:52:35: #2 predicted fragment length is 75 bps INFO @ Sat, 15 Sep 2018 11:52:35: #2 alternative fragment length(s) may be 75 bps INFO @ Sat, 15 Sep 2018 11:52:35: #2.2 Generate R script for model : SRX4014802.10_model.r WARNING @ Sat, 15 Sep 2018 11:52:35: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Sep 2018 11:52:35: #2 You may need to consider one of the other alternative d(s): 75 WARNING @ Sat, 15 Sep 2018 11:52:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Sep 2018 11:52:35: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:52:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:53:24: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:53:34: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:53:48: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:54:06: #4 Write output xls file... SRX4014802.05_peaks.xls INFO @ Sat, 15 Sep 2018 11:54:06: #4 Write peak in narrowPeak format file... SRX4014802.05_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:54:06: #4 Write summits bed file... SRX4014802.05_summits.bed INFO @ Sat, 15 Sep 2018 11:54:06: Done! pass1 - making usageList (60 chroms): 1 millis pass2 - checking and writing primary data (1891 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 11:54:15: #4 Write output xls file... SRX4014802.20_peaks.xls INFO @ Sat, 15 Sep 2018 11:54:15: #4 Write peak in narrowPeak format file... SRX4014802.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:54:15: #4 Write summits bed file... SRX4014802.20_summits.bed INFO @ Sat, 15 Sep 2018 11:54:15: Done! pass1 - making usageList (36 chroms): 1 millis pass2 - checking and writing primary data (501 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 11:54:26: #4 Write output xls file... SRX4014802.10_peaks.xls INFO @ Sat, 15 Sep 2018 11:54:26: #4 Write peak in narrowPeak format file... SRX4014802.10_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:54:26: #4 Write summits bed file... SRX4014802.10_summits.bed INFO @ Sat, 15 Sep 2018 11:54:26: Done! pass1 - making usageList (46 chroms): 1 millis pass2 - checking and writing primary data (1020 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。