Job ID = 10195040 sra ファイルのダウンロード中... Completed: 613004K bytes transferred in 7 seconds (694559K bits/sec), in 1 file. Completed: 665466K bytes transferred in 9 seconds (552029K 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... Written 18370115 spots for /home/okishinya/chipatlas/results/rn6/SRX913509/SRR1870954.sra Written 18370115 spots total Written 19733304 spots for /home/okishinya/chipatlas/results/rn6/SRX913509/SRR1870955.sra Written 19733304 spots total 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 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: 00:23:18 38103419 reads; of these: 38103419 (100.00%) were unpaired; of these: 2077973 (5.45%) aligned 0 times 25856034 (67.86%) aligned exactly 1 time 10169412 (26.69%) aligned >1 times 94.55% overall alignment rate Time searching: 00:23:20 Overall time: 00:23:20 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] 11119109 / 36025446 = 0.3086 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, 11 Nov 2017 07:44:07: # Command line: callpeak -t SRX913509.bam -f BAM -g 2.15e9 -n SRX913509.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX913509.20 # format = BAM # ChIP-seq file = ['SRX913509.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, 11 Nov 2017 07:44:07: # Command line: callpeak -t SRX913509.bam -f BAM -g 2.15e9 -n SRX913509.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX913509.05 # format = BAM # ChIP-seq file = ['SRX913509.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, 11 Nov 2017 07:44:07: # Command line: callpeak -t SRX913509.bam -f BAM -g 2.15e9 -n SRX913509.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX913509.10 # format = BAM # ChIP-seq file = ['SRX913509.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, 11 Nov 2017 07:44:07: #1 read tag files... INFO @ Sat, 11 Nov 2017 07:44:07: #1 read tag files... INFO @ Sat, 11 Nov 2017 07:44:07: #1 read tag files... INFO @ Sat, 11 Nov 2017 07:44:07: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 07:44:07: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 07:44:07: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 07:44:14: 1000000 INFO @ Sat, 11 Nov 2017 07:44:14: 1000000 INFO @ Sat, 11 Nov 2017 07:44:14: 1000000 INFO @ Sat, 11 Nov 2017 07:44:21: 2000000 INFO @ Sat, 11 Nov 2017 07:44:21: 2000000 INFO @ Sat, 11 Nov 2017 07:44:21: 2000000 INFO @ Sat, 11 Nov 2017 07:44:28: 3000000 INFO @ Sat, 11 Nov 2017 07:44:29: 3000000 INFO @ Sat, 11 Nov 2017 07:44:29: 3000000 INFO @ Sat, 11 Nov 2017 07:44:35: 4000000 INFO @ Sat, 11 Nov 2017 07:44:36: 4000000 INFO @ Sat, 11 Nov 2017 07:44:36: 4000000 INFO @ Sat, 11 Nov 2017 07:44:42: 5000000 INFO @ Sat, 11 Nov 2017 07:44:43: 5000000 INFO @ Sat, 11 Nov 2017 07:44:43: 5000000 INFO @ Sat, 11 Nov 2017 07:44:50: 6000000 INFO @ Sat, 11 Nov 2017 07:44:50: 6000000 INFO @ Sat, 11 Nov 2017 07:44:51: 6000000 INFO @ Sat, 11 Nov 2017 07:44:57: 7000000 INFO @ Sat, 11 Nov 2017 07:44:58: 7000000 INFO @ Sat, 11 Nov 2017 07:44:58: 7000000 INFO @ Sat, 11 Nov 2017 07:45:04: 8000000 INFO @ Sat, 11 Nov 2017 07:45:05: 8000000 INFO @ Sat, 11 Nov 2017 07:45:05: 8000000 INFO @ Sat, 11 Nov 2017 07:45:11: 9000000 INFO @ Sat, 11 Nov 2017 07:45:12: 9000000 INFO @ Sat, 11 Nov 2017 07:45:13: 9000000 INFO @ Sat, 11 Nov 2017 07:45:18: 10000000 INFO @ Sat, 11 Nov 2017 07:45:20: 10000000 INFO @ Sat, 11 Nov 2017 07:45:20: 10000000 INFO @ Sat, 11 Nov 2017 07:45:25: 11000000 INFO @ Sat, 11 Nov 2017 07:45:27: 11000000 INFO @ Sat, 11 Nov 2017 07:45:28: 11000000 INFO @ Sat, 11 Nov 2017 07:45:33: 12000000 INFO @ Sat, 11 Nov 2017 07:45:34: 12000000 INFO @ Sat, 11 Nov 2017 07:45:35: 12000000 INFO @ Sat, 11 Nov 2017 07:45:41: 13000000 INFO @ Sat, 11 Nov 2017 07:45:42: 13000000 INFO @ Sat, 11 Nov 2017 07:45:44: 13000000 INFO @ Sat, 11 Nov 2017 07:45:49: 14000000 INFO @ Sat, 11 Nov 2017 07:45:50: 14000000 INFO @ Sat, 11 Nov 2017 07:45:52: 14000000 INFO @ Sat, 11 Nov 2017 07:45:56: 15000000 INFO @ Sat, 11 Nov 2017 07:45:57: 15000000 INFO @ Sat, 11 Nov 2017 07:46:00: 15000000 INFO @ Sat, 11 Nov 2017 07:46:05: 16000000 INFO @ Sat, 11 Nov 2017 07:46:05: 16000000 INFO @ Sat, 11 Nov 2017 07:46:09: 16000000 INFO @ Sat, 11 Nov 2017 07:46:12: 17000000 INFO @ Sat, 11 Nov 2017 07:46:13: 17000000 INFO @ Sat, 11 Nov 2017 07:46:16: 17000000 INFO @ Sat, 11 Nov 2017 07:46:20: 18000000 INFO @ Sat, 11 Nov 2017 07:46:21: 18000000 INFO @ Sat, 11 Nov 2017 07:46:23: 18000000 INFO @ Sat, 11 Nov 2017 07:46:27: 19000000 INFO @ Sat, 11 Nov 2017 07:46:28: 19000000 INFO @ Sat, 11 Nov 2017 07:46:30: 19000000 INFO @ Sat, 11 Nov 2017 07:46:34: 20000000 INFO @ Sat, 11 Nov 2017 07:46:35: 20000000 INFO @ Sat, 11 Nov 2017 07:46:37: 20000000 INFO @ Sat, 11 Nov 2017 07:46:42: 21000000 INFO @ Sat, 11 Nov 2017 07:46:43: 21000000 INFO @ Sat, 11 Nov 2017 07:46:45: 21000000 INFO @ Sat, 11 Nov 2017 07:46:50: 22000000 INFO @ Sat, 11 Nov 2017 07:46:51: 22000000 INFO @ Sat, 11 Nov 2017 07:46:53: 22000000 INFO @ Sat, 11 Nov 2017 07:46:57: 23000000 INFO @ Sat, 11 Nov 2017 07:46:59: 23000000 INFO @ Sat, 11 Nov 2017 07:47:01: 23000000 INFO @ Sat, 11 Nov 2017 07:47:05: 24000000 INFO @ Sat, 11 Nov 2017 07:47:06: 24000000 INFO @ Sat, 11 Nov 2017 07:47:08: 24000000 INFO @ Sat, 11 Nov 2017 07:47:11: #1 tag size is determined as 46 bps INFO @ Sat, 11 Nov 2017 07:47:11: #1 tag size = 46 INFO @ Sat, 11 Nov 2017 07:47:11: #1 total tags in treatment: 24906337 INFO @ Sat, 11 Nov 2017 07:47:11: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 07:47:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 07:47:12: #1 tags after filtering in treatment: 24906228 INFO @ Sat, 11 Nov 2017 07:47:12: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 07:47:12: #1 finished! INFO @ Sat, 11 Nov 2017 07:47:12: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 07:47:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 07:47:13: #1 tag size is determined as 46 bps INFO @ Sat, 11 Nov 2017 07:47:13: #1 tag size = 46 INFO @ Sat, 11 Nov 2017 07:47:13: #1 total tags in treatment: 24906337 INFO @ Sat, 11 Nov 2017 07:47:13: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 07:47:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 07:47:14: #1 tags after filtering in treatment: 24906228 INFO @ Sat, 11 Nov 2017 07:47:14: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 07:47:14: #1 finished! INFO @ Sat, 11 Nov 2017 07:47:14: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 07:47:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 07:47:14: #2 number of paired peaks: 8011 INFO @ Sat, 11 Nov 2017 07:47:14: start model_add_line... INFO @ Sat, 11 Nov 2017 07:47:15: start X-correlation... INFO @ Sat, 11 Nov 2017 07:47:15: end of X-cor INFO @ Sat, 11 Nov 2017 07:47:15: #2 finished! INFO @ Sat, 11 Nov 2017 07:47:15: #2 predicted fragment length is 52 bps INFO @ Sat, 11 Nov 2017 07:47:15: #2 alternative fragment length(s) may be 52 bps INFO @ Sat, 11 Nov 2017 07:47:15: #2.2 Generate R script for model : SRX913509.10_model.r WARNING @ Sat, 11 Nov 2017 07:47:15: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 07:47:15: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Sat, 11 Nov 2017 07:47:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Nov 2017 07:47:15: #3 Call peaks... INFO @ Sat, 11 Nov 2017 07:47:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 07:47:15: #1 tag size is determined as 46 bps INFO @ Sat, 11 Nov 2017 07:47:15: #1 tag size = 46 INFO @ Sat, 11 Nov 2017 07:47:15: #1 total tags in treatment: 24906337 INFO @ Sat, 11 Nov 2017 07:47:15: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 07:47:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 07:47:16: #1 tags after filtering in treatment: 24906228 INFO @ Sat, 11 Nov 2017 07:47:16: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 07:47:16: #1 finished! INFO @ Sat, 11 Nov 2017 07:47:16: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 07:47:16: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 07:47:17: #2 number of paired peaks: 8011 INFO @ Sat, 11 Nov 2017 07:47:17: start model_add_line... INFO @ Sat, 11 Nov 2017 07:47:17: start X-correlation... INFO @ Sat, 11 Nov 2017 07:47:17: end of X-cor INFO @ Sat, 11 Nov 2017 07:47:17: #2 finished! INFO @ Sat, 11 Nov 2017 07:47:17: #2 predicted fragment length is 52 bps INFO @ Sat, 11 Nov 2017 07:47:17: #2 alternative fragment length(s) may be 52 bps INFO @ Sat, 11 Nov 2017 07:47:17: #2.2 Generate R script for model : SRX913509.05_model.r WARNING @ Sat, 11 Nov 2017 07:47:17: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 07:47:17: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Sat, 11 Nov 2017 07:47:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Nov 2017 07:47:17: #3 Call peaks... INFO @ Sat, 11 Nov 2017 07:47:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 07:47:18: #2 number of paired peaks: 8011 INFO @ Sat, 11 Nov 2017 07:47:18: start model_add_line... INFO @ Sat, 11 Nov 2017 07:47:19: start X-correlation... INFO @ Sat, 11 Nov 2017 07:47:19: end of X-cor INFO @ Sat, 11 Nov 2017 07:47:19: #2 finished! INFO @ Sat, 11 Nov 2017 07:47:19: #2 predicted fragment length is 52 bps INFO @ Sat, 11 Nov 2017 07:47:19: #2 alternative fragment length(s) may be 52 bps INFO @ Sat, 11 Nov 2017 07:47:19: #2.2 Generate R script for model : SRX913509.20_model.r WARNING @ Sat, 11 Nov 2017 07:47:19: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 07:47:19: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Sat, 11 Nov 2017 07:47:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Nov 2017 07:47:19: #3 Call peaks... INFO @ Sat, 11 Nov 2017 07:47:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 07:48:13: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 07:48:17: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 07:48:21: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 07:48:45: #4 Write output xls file... SRX913509.10_peaks.xls INFO @ Sat, 11 Nov 2017 07:48:45: #4 Write peak in narrowPeak format file... SRX913509.10_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 07:48:45: #4 Write summits bed file... SRX913509.10_summits.bed INFO @ Sat, 11 Nov 2017 07:48:45: Done! pass1 - making usageList (40 chroms): 1 millis pass2 - checking and writing primary data (608 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 07:48:49: #4 Write output xls file... SRX913509.05_peaks.xls INFO @ Sat, 11 Nov 2017 07:48:49: #4 Write peak in narrowPeak format file... SRX913509.05_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 07:48:49: #4 Write summits bed file... SRX913509.05_summits.bed INFO @ Sat, 11 Nov 2017 07:48:49: Done! pass1 - making usageList (52 chroms): 1 millis pass2 - checking and writing primary data (1256 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 07:48:58: #4 Write output xls file... SRX913509.20_peaks.xls INFO @ Sat, 11 Nov 2017 07:48:58: #4 Write peak in narrowPeak format file... SRX913509.20_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 07:48:58: #4 Write summits bed file... SRX913509.20_summits.bed INFO @ Sat, 11 Nov 2017 07:48:58: Done! pass1 - making usageList (26 chroms): 1 millis pass2 - checking and writing primary data (219 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。