Job ID = 10194798 sra ファイルのダウンロード中... Completed: 738772K bytes transferred in 11 seconds (529563K 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 14567681 spots for /home/okishinya/chipatlas/results/rn6/SRX1816856/SRR3621121.sra Written 14567681 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: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:37:20 14567681 reads; of these: 14567681 (100.00%) were unpaired; of these: 811377 (5.57%) aligned 0 times 10284652 (70.60%) aligned exactly 1 time 3471652 (23.83%) aligned >1 times 94.43% overall alignment rate Time searching: 00:37:24 Overall time: 00:37:24 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 8 files... [bam_rmdupse_core] 887364 / 13756304 = 0.0645 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 21:24:09: # Command line: callpeak -t SRX1816856.bam -f BAM -g 2.15e9 -n SRX1816856.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1816856.20 # format = BAM # ChIP-seq file = ['SRX1816856.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 21:24:09: #1 read tag files... INFO @ Fri, 10 Nov 2017 21:24:09: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 21:24:09: # Command line: callpeak -t SRX1816856.bam -f BAM -g 2.15e9 -n SRX1816856.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1816856.10 # format = BAM # ChIP-seq file = ['SRX1816856.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 21:24:09: #1 read tag files... INFO @ Fri, 10 Nov 2017 21:24:09: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 21:24:09: # Command line: callpeak -t SRX1816856.bam -f BAM -g 2.15e9 -n SRX1816856.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1816856.05 # format = BAM # ChIP-seq file = ['SRX1816856.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 21:24:09: #1 read tag files... INFO @ Fri, 10 Nov 2017 21:24:09: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 21:24:20: 1000000 INFO @ Fri, 10 Nov 2017 21:24:26: 1000000 INFO @ Fri, 10 Nov 2017 21:24:27: 1000000 INFO @ Fri, 10 Nov 2017 21:24:32: 2000000 INFO @ Fri, 10 Nov 2017 21:24:43: 3000000 INFO @ Fri, 10 Nov 2017 21:24:44: 2000000 INFO @ Fri, 10 Nov 2017 21:24:45: 2000000 INFO @ Fri, 10 Nov 2017 21:24:53: 4000000 INFO @ Fri, 10 Nov 2017 21:25:02: 3000000 INFO @ Fri, 10 Nov 2017 21:25:03: 3000000 INFO @ Fri, 10 Nov 2017 21:25:05: 5000000 INFO @ Fri, 10 Nov 2017 21:25:16: 6000000 INFO @ Fri, 10 Nov 2017 21:25:20: 4000000 INFO @ Fri, 10 Nov 2017 21:25:21: 4000000 INFO @ Fri, 10 Nov 2017 21:25:27: 7000000 INFO @ Fri, 10 Nov 2017 21:25:38: 5000000 INFO @ Fri, 10 Nov 2017 21:25:38: 8000000 INFO @ Fri, 10 Nov 2017 21:25:40: 5000000 INFO @ Fri, 10 Nov 2017 21:25:49: 9000000 INFO @ Fri, 10 Nov 2017 21:25:56: 6000000 INFO @ Fri, 10 Nov 2017 21:25:58: 6000000 INFO @ Fri, 10 Nov 2017 21:26:01: 10000000 INFO @ Fri, 10 Nov 2017 21:26:12: 11000000 INFO @ Fri, 10 Nov 2017 21:26:15: 7000000 INFO @ Fri, 10 Nov 2017 21:26:17: 7000000 INFO @ Fri, 10 Nov 2017 21:26:23: 12000000 INFO @ Fri, 10 Nov 2017 21:26:32: 8000000 INFO @ Fri, 10 Nov 2017 21:26:33: #1 tag size is determined as 75 bps INFO @ Fri, 10 Nov 2017 21:26:33: #1 tag size = 75 INFO @ Fri, 10 Nov 2017 21:26:33: #1 total tags in treatment: 12868940 INFO @ Fri, 10 Nov 2017 21:26:33: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 21:26:33: #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 21:26:34: #1 tags after filtering in treatment: 12868755 INFO @ Fri, 10 Nov 2017 21:26:34: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 21:26:34: #1 finished! INFO @ Fri, 10 Nov 2017 21:26:34: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 21:26:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 21:26:36: 8000000 INFO @ Fri, 10 Nov 2017 21:26:36: #2 number of paired peaks: 9842 INFO @ Fri, 10 Nov 2017 21:26:36: start model_add_line... INFO @ Fri, 10 Nov 2017 21:26:36: start X-correlation... INFO @ Fri, 10 Nov 2017 21:26:36: end of X-cor INFO @ Fri, 10 Nov 2017 21:26:36: #2 finished! INFO @ Fri, 10 Nov 2017 21:26:36: #2 predicted fragment length is 77 bps INFO @ Fri, 10 Nov 2017 21:26:36: #2 alternative fragment length(s) may be 77 bps INFO @ Fri, 10 Nov 2017 21:26:36: #2.2 Generate R script for model : SRX1816856.10_model.r WARNING @ Fri, 10 Nov 2017 21:26:36: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 21:26:36: #2 You may need to consider one of the other alternative d(s): 77 WARNING @ Fri, 10 Nov 2017 21:26:36: #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 21:26:36: #3 Call peaks... INFO @ Fri, 10 Nov 2017 21:26:36: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 21:26:50: 9000000 INFO @ Fri, 10 Nov 2017 21:26:54: 9000000 INFO @ Fri, 10 Nov 2017 21:27:08: 10000000 INFO @ Fri, 10 Nov 2017 21:27:13: 10000000 INFO @ Fri, 10 Nov 2017 21:27:19: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 21:27:26: 11000000 INFO @ Fri, 10 Nov 2017 21:27:32: 11000000 INFO @ Fri, 10 Nov 2017 21:27:44: #4 Write output xls file... SRX1816856.10_peaks.xls INFO @ Fri, 10 Nov 2017 21:27:44: #4 Write peak in narrowPeak format file... SRX1816856.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 21:27:44: #4 Write summits bed file... SRX1816856.10_summits.bed INFO @ Fri, 10 Nov 2017 21:27:44: Done! pass1 - making usageList (42 chroms): 1 millis pass2 - checking and writing primary data (660 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 21:27:45: 12000000 INFO @ Fri, 10 Nov 2017 21:27:50: 12000000 INFO @ Fri, 10 Nov 2017 21:28:01: #1 tag size is determined as 75 bps INFO @ Fri, 10 Nov 2017 21:28:01: #1 tag size = 75 INFO @ Fri, 10 Nov 2017 21:28:01: #1 total tags in treatment: 12868940 INFO @ Fri, 10 Nov 2017 21:28:01: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 21:28:01: #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 21:28:02: #1 tags after filtering in treatment: 12868755 INFO @ Fri, 10 Nov 2017 21:28:02: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 21:28:02: #1 finished! INFO @ Fri, 10 Nov 2017 21:28:02: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 21:28:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 21:28:04: #2 number of paired peaks: 9842 INFO @ Fri, 10 Nov 2017 21:28:04: start model_add_line... INFO @ Fri, 10 Nov 2017 21:28:04: start X-correlation... INFO @ Fri, 10 Nov 2017 21:28:04: end of X-cor INFO @ Fri, 10 Nov 2017 21:28:04: #2 finished! INFO @ Fri, 10 Nov 2017 21:28:04: #2 predicted fragment length is 77 bps INFO @ Fri, 10 Nov 2017 21:28:04: #2 alternative fragment length(s) may be 77 bps INFO @ Fri, 10 Nov 2017 21:28:04: #2.2 Generate R script for model : SRX1816856.05_model.r WARNING @ Fri, 10 Nov 2017 21:28:04: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 21:28:04: #2 You may need to consider one of the other alternative d(s): 77 WARNING @ Fri, 10 Nov 2017 21:28:04: #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 21:28:04: #3 Call peaks... INFO @ Fri, 10 Nov 2017 21:28:04: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 21:28:06: #1 tag size is determined as 75 bps INFO @ Fri, 10 Nov 2017 21:28:06: #1 tag size = 75 INFO @ Fri, 10 Nov 2017 21:28:06: #1 total tags in treatment: 12868940 INFO @ Fri, 10 Nov 2017 21:28:06: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 21:28:06: #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 21:28:07: #1 tags after filtering in treatment: 12868755 INFO @ Fri, 10 Nov 2017 21:28:07: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 21:28:07: #1 finished! INFO @ Fri, 10 Nov 2017 21:28:07: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 21:28:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 21:28:09: #2 number of paired peaks: 9842 INFO @ Fri, 10 Nov 2017 21:28:09: start model_add_line... INFO @ Fri, 10 Nov 2017 21:28:09: start X-correlation... INFO @ Fri, 10 Nov 2017 21:28:09: end of X-cor INFO @ Fri, 10 Nov 2017 21:28:09: #2 finished! INFO @ Fri, 10 Nov 2017 21:28:09: #2 predicted fragment length is 77 bps INFO @ Fri, 10 Nov 2017 21:28:09: #2 alternative fragment length(s) may be 77 bps INFO @ Fri, 10 Nov 2017 21:28:09: #2.2 Generate R script for model : SRX1816856.20_model.r WARNING @ Fri, 10 Nov 2017 21:28:09: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 21:28:09: #2 You may need to consider one of the other alternative d(s): 77 WARNING @ Fri, 10 Nov 2017 21:28:09: #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 21:28:09: #3 Call peaks... INFO @ Fri, 10 Nov 2017 21:28:09: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 21:28:42: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 21:28:48: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 21:29:03: #4 Write output xls file... SRX1816856.05_peaks.xls INFO @ Fri, 10 Nov 2017 21:29:03: #4 Write peak in narrowPeak format file... SRX1816856.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 21:29:03: #4 Write summits bed file... SRX1816856.05_summits.bed INFO @ Fri, 10 Nov 2017 21:29:03: Done! pass1 - making usageList (52 chroms): 2 millis pass2 - checking and writing primary data (1103 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 21:29:11: #4 Write output xls file... SRX1816856.20_peaks.xls INFO @ Fri, 10 Nov 2017 21:29:11: #4 Write peak in narrowPeak format file... SRX1816856.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 21:29:11: #4 Write summits bed file... SRX1816856.20_summits.bed INFO @ Fri, 10 Nov 2017 21:29:11: Done! pass1 - making usageList (34 chroms): 2 millis pass2 - checking and writing primary data (345 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。