Job ID = 10194740 sra ファイルのダウンロード中... Completed: 577665K bytes transferred in 8 seconds (557306K 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 22819435 spots for /home/okishinya/chipatlas/results/rn6/SRX1068229/SRR2073188.sra Written 22819435 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: 00:00:00 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:25:39 22819435 reads; of these: 22819435 (100.00%) were unpaired; of these: 482666 (2.12%) aligned 0 times 16336411 (71.59%) aligned exactly 1 time 6000358 (26.29%) aligned >1 times 97.88% overall alignment rate Time searching: 00:25:42 Overall time: 00:25:42 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 12 files... [bam_rmdupse_core] 997602 / 22336769 = 0.0447 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 @ Fri, 10 Nov 2017 23:43:43: # Command line: callpeak -t SRX1068229.bam -f BAM -g 2.15e9 -n SRX1068229.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1068229.10 # format = BAM # ChIP-seq file = ['SRX1068229.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 @ Fri, 10 Nov 2017 23:43:43: #1 read tag files... INFO @ Fri, 10 Nov 2017 23:43:43: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 23:43:43: # Command line: callpeak -t SRX1068229.bam -f BAM -g 2.15e9 -n SRX1068229.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1068229.20 # format = BAM # ChIP-seq file = ['SRX1068229.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 @ Fri, 10 Nov 2017 23:43:43: #1 read tag files... INFO @ Fri, 10 Nov 2017 23:43:43: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 23:43:43: # Command line: callpeak -t SRX1068229.bam -f BAM -g 2.15e9 -n SRX1068229.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1068229.05 # format = BAM # ChIP-seq file = ['SRX1068229.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 @ Fri, 10 Nov 2017 23:43:43: #1 read tag files... INFO @ Fri, 10 Nov 2017 23:43:43: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 23:43:50: 1000000 INFO @ Fri, 10 Nov 2017 23:43:50: 1000000 INFO @ Fri, 10 Nov 2017 23:43:50: 1000000 INFO @ Fri, 10 Nov 2017 23:43:56: 2000000 INFO @ Fri, 10 Nov 2017 23:43:56: 2000000 INFO @ Fri, 10 Nov 2017 23:43:56: 2000000 INFO @ Fri, 10 Nov 2017 23:44:02: 3000000 INFO @ Fri, 10 Nov 2017 23:44:02: 3000000 INFO @ Fri, 10 Nov 2017 23:44:03: 3000000 INFO @ Fri, 10 Nov 2017 23:44:09: 4000000 INFO @ Fri, 10 Nov 2017 23:44:09: 4000000 INFO @ Fri, 10 Nov 2017 23:44:10: 4000000 INFO @ Fri, 10 Nov 2017 23:44:15: 5000000 INFO @ Fri, 10 Nov 2017 23:44:15: 5000000 INFO @ Fri, 10 Nov 2017 23:44:16: 5000000 INFO @ Fri, 10 Nov 2017 23:44:21: 6000000 INFO @ Fri, 10 Nov 2017 23:44:21: 6000000 INFO @ Fri, 10 Nov 2017 23:44:23: 6000000 INFO @ Fri, 10 Nov 2017 23:44:28: 7000000 INFO @ Fri, 10 Nov 2017 23:44:28: 7000000 INFO @ Fri, 10 Nov 2017 23:44:29: 7000000 INFO @ Fri, 10 Nov 2017 23:44:34: 8000000 INFO @ Fri, 10 Nov 2017 23:44:34: 8000000 INFO @ Fri, 10 Nov 2017 23:44:36: 8000000 INFO @ Fri, 10 Nov 2017 23:44:40: 9000000 INFO @ Fri, 10 Nov 2017 23:44:40: 9000000 INFO @ Fri, 10 Nov 2017 23:44:42: 9000000 INFO @ Fri, 10 Nov 2017 23:44:47: 10000000 INFO @ Fri, 10 Nov 2017 23:44:47: 10000000 INFO @ Fri, 10 Nov 2017 23:44:49: 10000000 INFO @ Fri, 10 Nov 2017 23:44:53: 11000000 INFO @ Fri, 10 Nov 2017 23:44:53: 11000000 INFO @ Fri, 10 Nov 2017 23:44:55: 11000000 INFO @ Fri, 10 Nov 2017 23:44:59: 12000000 INFO @ Fri, 10 Nov 2017 23:45:00: 12000000 INFO @ Fri, 10 Nov 2017 23:45:02: 12000000 INFO @ Fri, 10 Nov 2017 23:45:06: 13000000 INFO @ Fri, 10 Nov 2017 23:45:06: 13000000 INFO @ Fri, 10 Nov 2017 23:45:08: 13000000 INFO @ Fri, 10 Nov 2017 23:45:12: 14000000 INFO @ Fri, 10 Nov 2017 23:45:12: 14000000 INFO @ Fri, 10 Nov 2017 23:45:15: 14000000 INFO @ Fri, 10 Nov 2017 23:45:19: 15000000 INFO @ Fri, 10 Nov 2017 23:45:19: 15000000 INFO @ Fri, 10 Nov 2017 23:45:21: 15000000 INFO @ Fri, 10 Nov 2017 23:45:25: 16000000 INFO @ Fri, 10 Nov 2017 23:45:25: 16000000 INFO @ Fri, 10 Nov 2017 23:45:28: 16000000 INFO @ Fri, 10 Nov 2017 23:45:31: 17000000 INFO @ Fri, 10 Nov 2017 23:45:31: 17000000 INFO @ Fri, 10 Nov 2017 23:45:34: 17000000 INFO @ Fri, 10 Nov 2017 23:45:38: 18000000 INFO @ Fri, 10 Nov 2017 23:45:38: 18000000 INFO @ Fri, 10 Nov 2017 23:45:41: 18000000 INFO @ Fri, 10 Nov 2017 23:45:44: 19000000 INFO @ Fri, 10 Nov 2017 23:45:44: 19000000 INFO @ Fri, 10 Nov 2017 23:45:48: 19000000 INFO @ Fri, 10 Nov 2017 23:45:51: 20000000 INFO @ Fri, 10 Nov 2017 23:45:51: 20000000 INFO @ Fri, 10 Nov 2017 23:45:54: 20000000 INFO @ Fri, 10 Nov 2017 23:45:57: 21000000 INFO @ Fri, 10 Nov 2017 23:45:57: 21000000 INFO @ Fri, 10 Nov 2017 23:45:59: #1 tag size is determined as 64 bps INFO @ Fri, 10 Nov 2017 23:45:59: #1 tag size = 64 INFO @ Fri, 10 Nov 2017 23:45:59: #1 total tags in treatment: 21339167 INFO @ Fri, 10 Nov 2017 23:45:59: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 23:45:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 23:46:00: #1 tag size is determined as 64 bps INFO @ Fri, 10 Nov 2017 23:46:00: #1 tag size = 64 INFO @ Fri, 10 Nov 2017 23:46:00: #1 total tags in treatment: 21339167 INFO @ Fri, 10 Nov 2017 23:46:00: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 23:46:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 23:46:00: #1 tags after filtering in treatment: 21339037 INFO @ Fri, 10 Nov 2017 23:46:00: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 23:46:00: #1 finished! INFO @ Fri, 10 Nov 2017 23:46:00: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 23:46:00: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 23:46:00: #1 tags after filtering in treatment: 21339037 INFO @ Fri, 10 Nov 2017 23:46:00: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 23:46:00: #1 finished! INFO @ Fri, 10 Nov 2017 23:46:00: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 23:46:00: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 23:46:01: 21000000 INFO @ Fri, 10 Nov 2017 23:46:02: #2 number of paired peaks: 5507 INFO @ Fri, 10 Nov 2017 23:46:02: start model_add_line... INFO @ Fri, 10 Nov 2017 23:46:02: #2 number of paired peaks: 5507 INFO @ Fri, 10 Nov 2017 23:46:02: start model_add_line... INFO @ Fri, 10 Nov 2017 23:46:03: start X-correlation... INFO @ Fri, 10 Nov 2017 23:46:03: end of X-cor INFO @ Fri, 10 Nov 2017 23:46:03: #2 finished! INFO @ Fri, 10 Nov 2017 23:46:03: #2 predicted fragment length is 65 bps INFO @ Fri, 10 Nov 2017 23:46:03: #2 alternative fragment length(s) may be 65,416 bps INFO @ Fri, 10 Nov 2017 23:46:03: #2.2 Generate R script for model : SRX1068229.10_model.r INFO @ Fri, 10 Nov 2017 23:46:03: start X-correlation... INFO @ Fri, 10 Nov 2017 23:46:03: end of X-cor INFO @ Fri, 10 Nov 2017 23:46:03: #2 finished! INFO @ Fri, 10 Nov 2017 23:46:03: #2 predicted fragment length is 65 bps INFO @ Fri, 10 Nov 2017 23:46:03: #2 alternative fragment length(s) may be 65,416 bps INFO @ Fri, 10 Nov 2017 23:46:03: #2.2 Generate R script for model : SRX1068229.20_model.r WARNING @ Fri, 10 Nov 2017 23:46:03: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 23:46:03: #2 You may need to consider one of the other alternative d(s): 65,416 WARNING @ Fri, 10 Nov 2017 23:46:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Nov 2017 23:46:03: #3 Call peaks... INFO @ Fri, 10 Nov 2017 23:46:03: #3 Pre-compute pvalue-qvalue table... WARNING @ Fri, 10 Nov 2017 23:46:03: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 23:46:03: #2 You may need to consider one of the other alternative d(s): 65,416 WARNING @ Fri, 10 Nov 2017 23:46:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Nov 2017 23:46:03: #3 Call peaks... INFO @ Fri, 10 Nov 2017 23:46:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 23:46:03: #1 tag size is determined as 64 bps INFO @ Fri, 10 Nov 2017 23:46:03: #1 tag size = 64 INFO @ Fri, 10 Nov 2017 23:46:03: #1 total tags in treatment: 21339167 INFO @ Fri, 10 Nov 2017 23:46:03: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 23:46:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 23:46:04: #1 tags after filtering in treatment: 21339037 INFO @ Fri, 10 Nov 2017 23:46:04: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 23:46:04: #1 finished! INFO @ Fri, 10 Nov 2017 23:46:04: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 23:46:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 23:46:06: #2 number of paired peaks: 5507 INFO @ Fri, 10 Nov 2017 23:46:06: start model_add_line... INFO @ Fri, 10 Nov 2017 23:46:06: start X-correlation... INFO @ Fri, 10 Nov 2017 23:46:06: end of X-cor INFO @ Fri, 10 Nov 2017 23:46:06: #2 finished! INFO @ Fri, 10 Nov 2017 23:46:06: #2 predicted fragment length is 65 bps INFO @ Fri, 10 Nov 2017 23:46:06: #2 alternative fragment length(s) may be 65,416 bps INFO @ Fri, 10 Nov 2017 23:46:06: #2.2 Generate R script for model : SRX1068229.05_model.r WARNING @ Fri, 10 Nov 2017 23:46:06: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 23:46:06: #2 You may need to consider one of the other alternative d(s): 65,416 WARNING @ Fri, 10 Nov 2017 23:46:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Nov 2017 23:46:06: #3 Call peaks... INFO @ Fri, 10 Nov 2017 23:46:06: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 23:46:52: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 23:46:54: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 23:46:56: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 23:47:20: #4 Write output xls file... SRX1068229.10_peaks.xls INFO @ Fri, 10 Nov 2017 23:47:20: #4 Write peak in narrowPeak format file... SRX1068229.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 23:47:20: #4 Write summits bed file... SRX1068229.10_summits.bed INFO @ Fri, 10 Nov 2017 23:47:20: Done! pass1 - making usageList (34 chroms): 1 millis pass2 - checking and writing primary data (846 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 23:47:21: #4 Write output xls file... SRX1068229.20_peaks.xls INFO @ Fri, 10 Nov 2017 23:47:21: #4 Write peak in narrowPeak format file... SRX1068229.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 23:47:21: #4 Write summits bed file... SRX1068229.20_summits.bed INFO @ Fri, 10 Nov 2017 23:47:21: Done! pass1 - making usageList (30 chroms): 0 millis pass2 - checking and writing primary data (429 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 23:47:28: #4 Write output xls file... SRX1068229.05_peaks.xls INFO @ Fri, 10 Nov 2017 23:47:28: #4 Write peak in narrowPeak format file... SRX1068229.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 23:47:28: #4 Write summits bed file... SRX1068229.05_summits.bed INFO @ Fri, 10 Nov 2017 23:47:28: Done! pass1 - making usageList (40 chroms): 1 millis pass2 - checking and writing primary data (1383 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。