Job ID = 10320341 sra ファイルのダウンロード中... Completed: 624534K bytes transferred in 39 seconds (129876K 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 40733662 spots for /home/okishinya/chipatlas/results/dm3/SRX3166317/SRR6012936.sra Written 40733662 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:17:47 40733662 reads; of these: 40733662 (100.00%) were unpaired; of these: 9258369 (22.73%) aligned 0 times 11724780 (28.78%) aligned exactly 1 time 19750513 (48.49%) aligned >1 times 77.27% overall alignment rate Time searching: 00:17:47 Overall time: 00:17:47 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 11792352 / 31475293 = 0.3747 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 @ Thu, 11 Jan 2018 02:31:23: # Command line: callpeak -t SRX3166317.bam -f BAM -g dm -n SRX3166317.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3166317.20 # format = BAM # ChIP-seq file = ['SRX3166317.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Thu, 11 Jan 2018 02:31:23: # Command line: callpeak -t SRX3166317.bam -f BAM -g dm -n SRX3166317.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3166317.05 # format = BAM # ChIP-seq file = ['SRX3166317.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Thu, 11 Jan 2018 02:31:23: # Command line: callpeak -t SRX3166317.bam -f BAM -g dm -n SRX3166317.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3166317.10 # format = BAM # ChIP-seq file = ['SRX3166317.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Thu, 11 Jan 2018 02:31:23: #1 read tag files... INFO @ Thu, 11 Jan 2018 02:31:23: #1 read tag files... INFO @ Thu, 11 Jan 2018 02:31:23: #1 read tag files... INFO @ Thu, 11 Jan 2018 02:31:23: #1 read treatment tags... INFO @ Thu, 11 Jan 2018 02:31:23: #1 read treatment tags... INFO @ Thu, 11 Jan 2018 02:31:23: #1 read treatment tags... INFO @ Thu, 11 Jan 2018 02:31:30: 1000000 INFO @ Thu, 11 Jan 2018 02:31:30: 1000000 INFO @ Thu, 11 Jan 2018 02:31:30: 1000000 INFO @ Thu, 11 Jan 2018 02:31:36: 2000000 INFO @ Thu, 11 Jan 2018 02:31:36: 2000000 INFO @ Thu, 11 Jan 2018 02:31:37: 2000000 INFO @ Thu, 11 Jan 2018 02:31:43: 3000000 INFO @ Thu, 11 Jan 2018 02:31:43: 3000000 INFO @ Thu, 11 Jan 2018 02:31:44: 3000000 INFO @ Thu, 11 Jan 2018 02:31:49: 4000000 INFO @ Thu, 11 Jan 2018 02:31:50: 4000000 INFO @ Thu, 11 Jan 2018 02:31:51: 4000000 INFO @ Thu, 11 Jan 2018 02:31:56: 5000000 INFO @ Thu, 11 Jan 2018 02:31:57: 5000000 INFO @ Thu, 11 Jan 2018 02:31:58: 5000000 INFO @ Thu, 11 Jan 2018 02:32:03: 6000000 INFO @ Thu, 11 Jan 2018 02:32:04: 6000000 INFO @ Thu, 11 Jan 2018 02:32:05: 6000000 INFO @ Thu, 11 Jan 2018 02:32:09: 7000000 INFO @ Thu, 11 Jan 2018 02:32:11: 7000000 INFO @ Thu, 11 Jan 2018 02:32:12: 7000000 INFO @ Thu, 11 Jan 2018 02:32:16: 8000000 INFO @ Thu, 11 Jan 2018 02:32:18: 8000000 INFO @ Thu, 11 Jan 2018 02:32:19: 8000000 INFO @ Thu, 11 Jan 2018 02:32:23: 9000000 INFO @ Thu, 11 Jan 2018 02:32:25: 9000000 INFO @ Thu, 11 Jan 2018 02:32:25: 9000000 INFO @ Thu, 11 Jan 2018 02:32:30: 10000000 INFO @ Thu, 11 Jan 2018 02:32:32: 10000000 INFO @ Thu, 11 Jan 2018 02:32:32: 10000000 INFO @ Thu, 11 Jan 2018 02:32:37: 11000000 INFO @ Thu, 11 Jan 2018 02:32:39: 11000000 INFO @ Thu, 11 Jan 2018 02:32:39: 11000000 INFO @ Thu, 11 Jan 2018 02:32:43: 12000000 INFO @ Thu, 11 Jan 2018 02:32:46: 12000000 INFO @ Thu, 11 Jan 2018 02:32:46: 12000000 INFO @ Thu, 11 Jan 2018 02:32:50: 13000000 INFO @ Thu, 11 Jan 2018 02:32:53: 13000000 INFO @ Thu, 11 Jan 2018 02:32:53: 13000000 INFO @ Thu, 11 Jan 2018 02:32:57: 14000000 INFO @ Thu, 11 Jan 2018 02:33:00: 14000000 INFO @ Thu, 11 Jan 2018 02:33:00: 14000000 INFO @ Thu, 11 Jan 2018 02:33:04: 15000000 INFO @ Thu, 11 Jan 2018 02:33:07: 15000000 INFO @ Thu, 11 Jan 2018 02:33:07: 15000000 INFO @ Thu, 11 Jan 2018 02:33:11: 16000000 INFO @ Thu, 11 Jan 2018 02:33:13: 16000000 INFO @ Thu, 11 Jan 2018 02:33:14: 16000000 INFO @ Thu, 11 Jan 2018 02:33:17: 17000000 INFO @ Thu, 11 Jan 2018 02:33:20: 17000000 INFO @ Thu, 11 Jan 2018 02:33:21: 17000000 INFO @ Thu, 11 Jan 2018 02:33:24: 18000000 INFO @ Thu, 11 Jan 2018 02:33:27: 18000000 INFO @ Thu, 11 Jan 2018 02:33:29: 18000000 INFO @ Thu, 11 Jan 2018 02:33:31: 19000000 INFO @ Thu, 11 Jan 2018 02:33:34: 19000000 INFO @ Thu, 11 Jan 2018 02:33:36: 19000000 INFO @ Thu, 11 Jan 2018 02:33:36: #1 tag size is determined as 51 bps INFO @ Thu, 11 Jan 2018 02:33:36: #1 tag size = 51 INFO @ Thu, 11 Jan 2018 02:33:36: #1 total tags in treatment: 19682941 INFO @ Thu, 11 Jan 2018 02:33:36: #1 user defined the maximum tags... INFO @ Thu, 11 Jan 2018 02:33:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 11 Jan 2018 02:33:36: #1 tags after filtering in treatment: 19682941 INFO @ Thu, 11 Jan 2018 02:33:36: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 11 Jan 2018 02:33:36: #1 finished! INFO @ Thu, 11 Jan 2018 02:33:36: #2 Build Peak Model... INFO @ Thu, 11 Jan 2018 02:33:36: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 11 Jan 2018 02:33:38: #2 number of paired peaks: 1604 INFO @ Thu, 11 Jan 2018 02:33:38: start model_add_line... INFO @ Thu, 11 Jan 2018 02:33:38: start X-correlation... INFO @ Thu, 11 Jan 2018 02:33:38: end of X-cor INFO @ Thu, 11 Jan 2018 02:33:38: #2 finished! INFO @ Thu, 11 Jan 2018 02:33:38: #2 predicted fragment length is 50 bps INFO @ Thu, 11 Jan 2018 02:33:38: #2 alternative fragment length(s) may be 3,50 bps INFO @ Thu, 11 Jan 2018 02:33:38: #2.2 Generate R script for model : SRX3166317.10_model.r WARNING @ Thu, 11 Jan 2018 02:33:38: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 11 Jan 2018 02:33:38: #2 You may need to consider one of the other alternative d(s): 3,50 WARNING @ Thu, 11 Jan 2018 02:33:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 11 Jan 2018 02:33:38: #3 Call peaks... INFO @ Thu, 11 Jan 2018 02:33:38: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 11 Jan 2018 02:33:39: #1 tag size is determined as 51 bps INFO @ Thu, 11 Jan 2018 02:33:39: #1 tag size = 51 INFO @ Thu, 11 Jan 2018 02:33:39: #1 total tags in treatment: 19682941 INFO @ Thu, 11 Jan 2018 02:33:39: #1 user defined the maximum tags... INFO @ Thu, 11 Jan 2018 02:33:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 11 Jan 2018 02:33:39: #1 tags after filtering in treatment: 19682941 INFO @ Thu, 11 Jan 2018 02:33:39: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 11 Jan 2018 02:33:39: #1 finished! INFO @ Thu, 11 Jan 2018 02:33:39: #2 Build Peak Model... INFO @ Thu, 11 Jan 2018 02:33:39: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 11 Jan 2018 02:33:40: #1 tag size is determined as 51 bps INFO @ Thu, 11 Jan 2018 02:33:40: #1 tag size = 51 INFO @ Thu, 11 Jan 2018 02:33:40: #1 total tags in treatment: 19682941 INFO @ Thu, 11 Jan 2018 02:33:40: #1 user defined the maximum tags... INFO @ Thu, 11 Jan 2018 02:33:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 11 Jan 2018 02:33:40: #1 tags after filtering in treatment: 19682941 INFO @ Thu, 11 Jan 2018 02:33:40: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 11 Jan 2018 02:33:40: #1 finished! INFO @ Thu, 11 Jan 2018 02:33:40: #2 Build Peak Model... INFO @ Thu, 11 Jan 2018 02:33:40: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 11 Jan 2018 02:33:41: #2 number of paired peaks: 1604 INFO @ Thu, 11 Jan 2018 02:33:41: start model_add_line... INFO @ Thu, 11 Jan 2018 02:33:41: start X-correlation... INFO @ Thu, 11 Jan 2018 02:33:41: end of X-cor INFO @ Thu, 11 Jan 2018 02:33:41: #2 finished! INFO @ Thu, 11 Jan 2018 02:33:41: #2 predicted fragment length is 50 bps INFO @ Thu, 11 Jan 2018 02:33:41: #2 alternative fragment length(s) may be 3,50 bps INFO @ Thu, 11 Jan 2018 02:33:41: #2.2 Generate R script for model : SRX3166317.05_model.r WARNING @ Thu, 11 Jan 2018 02:33:41: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 11 Jan 2018 02:33:41: #2 You may need to consider one of the other alternative d(s): 3,50 WARNING @ Thu, 11 Jan 2018 02:33:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 11 Jan 2018 02:33:41: #3 Call peaks... INFO @ Thu, 11 Jan 2018 02:33:41: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 11 Jan 2018 02:33:42: #2 number of paired peaks: 1604 INFO @ Thu, 11 Jan 2018 02:33:42: start model_add_line... INFO @ Thu, 11 Jan 2018 02:33:42: start X-correlation... INFO @ Thu, 11 Jan 2018 02:33:42: end of X-cor INFO @ Thu, 11 Jan 2018 02:33:42: #2 finished! INFO @ Thu, 11 Jan 2018 02:33:42: #2 predicted fragment length is 50 bps INFO @ Thu, 11 Jan 2018 02:33:42: #2 alternative fragment length(s) may be 3,50 bps INFO @ Thu, 11 Jan 2018 02:33:42: #2.2 Generate R script for model : SRX3166317.20_model.r WARNING @ Thu, 11 Jan 2018 02:33:42: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 11 Jan 2018 02:33:42: #2 You may need to consider one of the other alternative d(s): 3,50 WARNING @ Thu, 11 Jan 2018 02:33:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 11 Jan 2018 02:33:42: #3 Call peaks... INFO @ Thu, 11 Jan 2018 02:33:42: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 11 Jan 2018 02:34:16: #3 Call peaks for each chromosome... INFO @ Thu, 11 Jan 2018 02:34:23: #3 Call peaks for each chromosome... INFO @ Thu, 11 Jan 2018 02:34:24: #3 Call peaks for each chromosome... INFO @ Thu, 11 Jan 2018 02:34:39: #4 Write output xls file... SRX3166317.10_peaks.xls INFO @ Thu, 11 Jan 2018 02:34:39: #4 Write peak in narrowPeak format file... SRX3166317.10_peaks.narrowPeak INFO @ Thu, 11 Jan 2018 02:34:39: #4 Write summits bed file... SRX3166317.10_summits.bed INFO @ Thu, 11 Jan 2018 02:34:39: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6817 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Thu, 11 Jan 2018 02:34:48: #4 Write output xls file... SRX3166317.20_peaks.xls INFO @ Thu, 11 Jan 2018 02:34:48: #4 Write peak in narrowPeak format file... SRX3166317.20_peaks.narrowPeak INFO @ Thu, 11 Jan 2018 02:34:48: #4 Write summits bed file... SRX3166317.20_summits.bed INFO @ Thu, 11 Jan 2018 02:34:48: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1584 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 11 Jan 2018 02:34:48: #4 Write output xls file... SRX3166317.05_peaks.xls INFO @ Thu, 11 Jan 2018 02:34:48: #4 Write peak in narrowPeak format file... SRX3166317.05_peaks.narrowPeak INFO @ Thu, 11 Jan 2018 02:34:48: #4 Write summits bed file... SRX3166317.05_summits.bed INFO @ Thu, 11 Jan 2018 02:34:48: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (16395 records, 4 fields): 29 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。