Job ID = 10194751 sra ファイルのダウンロード中... Completed: 448091K bytes transferred in 7 seconds (463001K 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 33183791 spots for /home/okishinya/chipatlas/results/rn6/SRX1091089/SRR2095966.sra Written 33183791 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 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: 00:00:01 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:25:37 33183791 reads; of these: 33183791 (100.00%) were unpaired; of these: 1668264 (5.03%) aligned 0 times 22704272 (68.42%) aligned exactly 1 time 8811255 (26.55%) aligned >1 times 94.97% overall alignment rate Time searching: 00:25:40 Overall time: 00:25:40 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] 1311902 / 31515527 = 0.0416 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 00:52:14: # Command line: callpeak -t SRX1091089.bam -f BAM -g 2.15e9 -n SRX1091089.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1091089.20 # format = BAM # ChIP-seq file = ['SRX1091089.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 00:52:14: # Command line: callpeak -t SRX1091089.bam -f BAM -g 2.15e9 -n SRX1091089.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1091089.05 # format = BAM # ChIP-seq file = ['SRX1091089.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 00:52:14: #1 read tag files... INFO @ Sat, 11 Nov 2017 00:52:14: # Command line: callpeak -t SRX1091089.bam -f BAM -g 2.15e9 -n SRX1091089.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1091089.10 # format = BAM # ChIP-seq file = ['SRX1091089.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 00:52:14: #1 read tag files... INFO @ Sat, 11 Nov 2017 00:52:14: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 00:52:14: #1 read tag files... INFO @ Sat, 11 Nov 2017 00:52:14: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 00:52:14: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 00:52:22: 1000000 INFO @ Sat, 11 Nov 2017 00:52:22: 1000000 INFO @ Sat, 11 Nov 2017 00:52:22: 1000000 INFO @ Sat, 11 Nov 2017 00:52:29: 2000000 INFO @ Sat, 11 Nov 2017 00:52:30: 2000000 INFO @ Sat, 11 Nov 2017 00:52:30: 2000000 INFO @ Sat, 11 Nov 2017 00:52:37: 3000000 INFO @ Sat, 11 Nov 2017 00:52:37: 3000000 INFO @ Sat, 11 Nov 2017 00:52:38: 3000000 INFO @ Sat, 11 Nov 2017 00:52:44: 4000000 INFO @ Sat, 11 Nov 2017 00:52:45: 4000000 INFO @ Sat, 11 Nov 2017 00:52:45: 4000000 INFO @ Sat, 11 Nov 2017 00:52:52: 5000000 INFO @ Sat, 11 Nov 2017 00:52:53: 5000000 INFO @ Sat, 11 Nov 2017 00:52:53: 5000000 INFO @ Sat, 11 Nov 2017 00:52:59: 6000000 INFO @ Sat, 11 Nov 2017 00:53:01: 6000000 INFO @ Sat, 11 Nov 2017 00:53:01: 6000000 INFO @ Sat, 11 Nov 2017 00:53:07: 7000000 INFO @ Sat, 11 Nov 2017 00:53:08: 7000000 INFO @ Sat, 11 Nov 2017 00:53:08: 7000000 INFO @ Sat, 11 Nov 2017 00:53:14: 8000000 INFO @ Sat, 11 Nov 2017 00:53:16: 8000000 INFO @ Sat, 11 Nov 2017 00:53:16: 8000000 INFO @ Sat, 11 Nov 2017 00:53:21: 9000000 INFO @ Sat, 11 Nov 2017 00:53:24: 9000000 INFO @ Sat, 11 Nov 2017 00:53:24: 9000000 INFO @ Sat, 11 Nov 2017 00:53:29: 10000000 INFO @ Sat, 11 Nov 2017 00:53:32: 10000000 INFO @ Sat, 11 Nov 2017 00:53:32: 10000000 INFO @ Sat, 11 Nov 2017 00:53:36: 11000000 INFO @ Sat, 11 Nov 2017 00:53:40: 11000000 INFO @ Sat, 11 Nov 2017 00:53:40: 11000000 INFO @ Sat, 11 Nov 2017 00:53:43: 12000000 INFO @ Sat, 11 Nov 2017 00:53:48: 12000000 INFO @ Sat, 11 Nov 2017 00:53:48: 12000000 INFO @ Sat, 11 Nov 2017 00:53:51: 13000000 INFO @ Sat, 11 Nov 2017 00:53:56: 13000000 INFO @ Sat, 11 Nov 2017 00:53:56: 13000000 INFO @ Sat, 11 Nov 2017 00:53:58: 14000000 INFO @ Sat, 11 Nov 2017 00:54:04: 14000000 INFO @ Sat, 11 Nov 2017 00:54:04: 14000000 INFO @ Sat, 11 Nov 2017 00:54:05: 15000000 INFO @ Sat, 11 Nov 2017 00:54:12: 15000000 INFO @ Sat, 11 Nov 2017 00:54:12: 15000000 INFO @ Sat, 11 Nov 2017 00:54:13: 16000000 INFO @ Sat, 11 Nov 2017 00:54:20: 16000000 INFO @ Sat, 11 Nov 2017 00:54:20: 16000000 INFO @ Sat, 11 Nov 2017 00:54:20: 17000000 INFO @ Sat, 11 Nov 2017 00:54:28: 17000000 INFO @ Sat, 11 Nov 2017 00:54:28: 17000000 INFO @ Sat, 11 Nov 2017 00:54:30: 18000000 INFO @ Sat, 11 Nov 2017 00:54:36: 18000000 INFO @ Sat, 11 Nov 2017 00:54:37: 18000000 INFO @ Sat, 11 Nov 2017 00:54:39: 19000000 INFO @ Sat, 11 Nov 2017 00:54:44: 19000000 INFO @ Sat, 11 Nov 2017 00:54:45: 19000000 INFO @ Sat, 11 Nov 2017 00:54:48: 20000000 INFO @ Sat, 11 Nov 2017 00:54:52: 20000000 INFO @ Sat, 11 Nov 2017 00:54:53: 20000000 INFO @ Sat, 11 Nov 2017 00:54:57: 21000000 INFO @ Sat, 11 Nov 2017 00:55:00: 21000000 INFO @ Sat, 11 Nov 2017 00:55:01: 21000000 INFO @ Sat, 11 Nov 2017 00:55:06: 22000000 INFO @ Sat, 11 Nov 2017 00:55:09: 22000000 INFO @ Sat, 11 Nov 2017 00:55:09: 22000000 INFO @ Sat, 11 Nov 2017 00:55:15: 23000000 INFO @ Sat, 11 Nov 2017 00:55:17: 23000000 INFO @ Sat, 11 Nov 2017 00:55:17: 23000000 INFO @ Sat, 11 Nov 2017 00:55:24: 24000000 INFO @ Sat, 11 Nov 2017 00:55:24: 24000000 INFO @ Sat, 11 Nov 2017 00:55:25: 24000000 INFO @ Sat, 11 Nov 2017 00:55:32: 25000000 INFO @ Sat, 11 Nov 2017 00:55:33: 25000000 INFO @ Sat, 11 Nov 2017 00:55:33: 25000000 INFO @ Sat, 11 Nov 2017 00:55:40: 26000000 INFO @ Sat, 11 Nov 2017 00:55:40: 26000000 INFO @ Sat, 11 Nov 2017 00:55:41: 26000000 INFO @ Sat, 11 Nov 2017 00:55:48: 27000000 INFO @ Sat, 11 Nov 2017 00:55:48: 27000000 INFO @ Sat, 11 Nov 2017 00:55:50: 27000000 INFO @ Sat, 11 Nov 2017 00:55:55: 28000000 INFO @ Sat, 11 Nov 2017 00:55:56: 28000000 INFO @ Sat, 11 Nov 2017 00:55:58: 28000000 INFO @ Sat, 11 Nov 2017 00:56:03: 29000000 INFO @ Sat, 11 Nov 2017 00:56:04: 29000000 INFO @ Sat, 11 Nov 2017 00:56:07: 29000000 INFO @ Sat, 11 Nov 2017 00:56:12: 30000000 INFO @ Sat, 11 Nov 2017 00:56:12: 30000000 INFO @ Sat, 11 Nov 2017 00:56:13: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 00:56:13: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 00:56:13: #1 total tags in treatment: 30203625 INFO @ Sat, 11 Nov 2017 00:56:13: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 00:56:13: #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 00:56:14: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 00:56:14: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 00:56:14: #1 total tags in treatment: 30203625 INFO @ Sat, 11 Nov 2017 00:56:14: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 00:56:14: #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 00:56:14: #1 tags after filtering in treatment: 30203523 INFO @ Sat, 11 Nov 2017 00:56:14: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 00:56:14: #1 finished! INFO @ Sat, 11 Nov 2017 00:56:14: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 00:56:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 00:56:15: #1 tags after filtering in treatment: 30203523 INFO @ Sat, 11 Nov 2017 00:56:15: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 00:56:15: #1 finished! INFO @ Sat, 11 Nov 2017 00:56:15: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 00:56:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 00:56:16: 30000000 INFO @ Sat, 11 Nov 2017 00:56:17: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 00:56:17: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 00:56:17: #1 total tags in treatment: 30203625 INFO @ Sat, 11 Nov 2017 00:56:17: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 00:56:17: #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 00:56:17: #2 number of paired peaks: 5732 INFO @ Sat, 11 Nov 2017 00:56:17: start model_add_line... INFO @ Sat, 11 Nov 2017 00:56:17: #2 number of paired peaks: 5732 INFO @ Sat, 11 Nov 2017 00:56:17: start model_add_line... INFO @ Sat, 11 Nov 2017 00:56:18: start X-correlation... INFO @ Sat, 11 Nov 2017 00:56:18: end of X-cor INFO @ Sat, 11 Nov 2017 00:56:18: #2 finished! INFO @ Sat, 11 Nov 2017 00:56:18: #2 predicted fragment length is 52 bps INFO @ Sat, 11 Nov 2017 00:56:18: #2 alternative fragment length(s) may be 52 bps INFO @ Sat, 11 Nov 2017 00:56:18: #2.2 Generate R script for model : SRX1091089.20_model.r INFO @ Sat, 11 Nov 2017 00:56:18: start X-correlation... WARNING @ Sat, 11 Nov 2017 00:56:18: #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 00:56:18: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Sat, 11 Nov 2017 00:56:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Nov 2017 00:56:18: #3 Call peaks... INFO @ Sat, 11 Nov 2017 00:56:18: end of X-cor INFO @ Sat, 11 Nov 2017 00:56:18: #2 finished! INFO @ Sat, 11 Nov 2017 00:56:18: #2 predicted fragment length is 52 bps INFO @ Sat, 11 Nov 2017 00:56:18: #2 alternative fragment length(s) may be 52 bps INFO @ Sat, 11 Nov 2017 00:56:18: #2.2 Generate R script for model : SRX1091089.05_model.r INFO @ Sat, 11 Nov 2017 00:56:18: #3 Pre-compute pvalue-qvalue table... WARNING @ Sat, 11 Nov 2017 00:56:18: #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 00:56:18: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Sat, 11 Nov 2017 00:56:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Nov 2017 00:56:18: #3 Call peaks... INFO @ Sat, 11 Nov 2017 00:56:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 00:56:18: #1 tags after filtering in treatment: 30203523 INFO @ Sat, 11 Nov 2017 00:56:18: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 00:56:18: #1 finished! INFO @ Sat, 11 Nov 2017 00:56:18: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 00:56:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 00:56:21: #2 number of paired peaks: 5732 INFO @ Sat, 11 Nov 2017 00:56:21: start model_add_line... INFO @ Sat, 11 Nov 2017 00:56:21: start X-correlation... INFO @ Sat, 11 Nov 2017 00:56:21: end of X-cor INFO @ Sat, 11 Nov 2017 00:56:21: #2 finished! INFO @ Sat, 11 Nov 2017 00:56:21: #2 predicted fragment length is 52 bps INFO @ Sat, 11 Nov 2017 00:56:21: #2 alternative fragment length(s) may be 52 bps INFO @ Sat, 11 Nov 2017 00:56:21: #2.2 Generate R script for model : SRX1091089.10_model.r WARNING @ Sat, 11 Nov 2017 00:56:21: #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 00:56:21: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Sat, 11 Nov 2017 00:56:21: #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 00:56:21: #3 Call peaks... INFO @ Sat, 11 Nov 2017 00:56:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 00:57:30: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 00:57:32: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 00:57:35: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 00:58:09: #4 Write output xls file... SRX1091089.05_peaks.xls INFO @ Sat, 11 Nov 2017 00:58:09: #4 Write peak in narrowPeak format file... SRX1091089.05_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 00:58:09: #4 Write summits bed file... SRX1091089.05_summits.bed INFO @ Sat, 11 Nov 2017 00:58:09: Done! pass1 - making usageList (57 chroms): 1 millis pass2 - checking and writing primary data (2159 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 00:58:11: #4 Write output xls file... SRX1091089.20_peaks.xls INFO @ Sat, 11 Nov 2017 00:58:11: #4 Write peak in narrowPeak format file... SRX1091089.20_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 00:58:11: #4 Write summits bed file... SRX1091089.20_summits.bed INFO @ Sat, 11 Nov 2017 00:58:11: Done! pass1 - making usageList (40 chroms): 1 millis pass2 - checking and writing primary data (541 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 00:58:15: #4 Write output xls file... SRX1091089.10_peaks.xls INFO @ Sat, 11 Nov 2017 00:58:15: #4 Write peak in narrowPeak format file... SRX1091089.10_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 00:58:15: #4 Write summits bed file... SRX1091089.10_summits.bed INFO @ Sat, 11 Nov 2017 00:58:15: Done! pass1 - making usageList (44 chroms): 1 millis pass2 - checking and writing primary data (1131 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。