Job ID = 9370028 sra ファイルのダウンロード中... Completed: 2213447K bytes transferred in 139 seconds (130265K bits/sec), in 1 file, 2 directories. 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 45399853 spots for /home/okishinya/chipatlas/results/ce10/SRX2710286/SRR5418740.sra Written 45399853 spots total 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: 00:48:08 45399853 reads; of these: 45399853 (100.00%) were unpaired; of these: 16841231 (37.10%) aligned 0 times 14836087 (32.68%) aligned exactly 1 time 13722535 (30.23%) aligned >1 times 62.90% overall alignment rate Time searching: 00:48:08 Overall time: 00:48:09 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 13279829 / 28558622 = 0.4650 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, 04 Aug 2017 13:05:18: # Command line: callpeak -t SRX2710286.bam -f BAM -g ce -n SRX2710286.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2710286.20 # format = BAM # ChIP-seq file = ['SRX2710286.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 04 Aug 2017 13:05:18: #1 read tag files... INFO @ Fri, 04 Aug 2017 13:05:18: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 13:05:18: # Command line: callpeak -t SRX2710286.bam -f BAM -g ce -n SRX2710286.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2710286.10 # format = BAM # ChIP-seq file = ['SRX2710286.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 04 Aug 2017 13:05:18: #1 read tag files... INFO @ Fri, 04 Aug 2017 13:05:18: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 13:05:18: # Command line: callpeak -t SRX2710286.bam -f BAM -g ce -n SRX2710286.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2710286.05 # format = BAM # ChIP-seq file = ['SRX2710286.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 04 Aug 2017 13:05:18: #1 read tag files... INFO @ Fri, 04 Aug 2017 13:05:18: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 13:05:38: 1000000 INFO @ Fri, 04 Aug 2017 13:05:43: 1000000 INFO @ Fri, 04 Aug 2017 13:05:44: 1000000 INFO @ Fri, 04 Aug 2017 13:05:56: 2000000 INFO @ Fri, 04 Aug 2017 13:06:02: 2000000 INFO @ Fri, 04 Aug 2017 13:06:05: 2000000 INFO @ Fri, 04 Aug 2017 13:06:13: 3000000 INFO @ Fri, 04 Aug 2017 13:06:21: 3000000 INFO @ Fri, 04 Aug 2017 13:06:22: 3000000 INFO @ Fri, 04 Aug 2017 13:06:40: 4000000 INFO @ Fri, 04 Aug 2017 13:06:49: 4000000 INFO @ Fri, 04 Aug 2017 13:06:50: 4000000 INFO @ Fri, 04 Aug 2017 13:07:06: 5000000 INFO @ Fri, 04 Aug 2017 13:07:07: 5000000 INFO @ Fri, 04 Aug 2017 13:07:13: 5000000 INFO @ Fri, 04 Aug 2017 13:07:29: 6000000 INFO @ Fri, 04 Aug 2017 13:07:31: 6000000 INFO @ Fri, 04 Aug 2017 13:07:39: 6000000 INFO @ Fri, 04 Aug 2017 13:07:56: 7000000 INFO @ Fri, 04 Aug 2017 13:08:00: 7000000 INFO @ Fri, 04 Aug 2017 13:08:11: 7000000 INFO @ Fri, 04 Aug 2017 13:08:12: 8000000 INFO @ Fri, 04 Aug 2017 13:08:23: 8000000 INFO @ Fri, 04 Aug 2017 13:08:30: 8000000 INFO @ Fri, 04 Aug 2017 13:08:36: 9000000 INFO @ Fri, 04 Aug 2017 13:08:47: 9000000 INFO @ Fri, 04 Aug 2017 13:08:52: 9000000 INFO @ Fri, 04 Aug 2017 13:09:00: 10000000 INFO @ Fri, 04 Aug 2017 13:09:10: 10000000 INFO @ Fri, 04 Aug 2017 13:09:16: 10000000 INFO @ Fri, 04 Aug 2017 13:09:17: 11000000 INFO @ Fri, 04 Aug 2017 13:09:32: 11000000 INFO @ Fri, 04 Aug 2017 13:09:40: 11000000 INFO @ Fri, 04 Aug 2017 13:09:45: 12000000 INFO @ Fri, 04 Aug 2017 13:10:00: 12000000 INFO @ Fri, 04 Aug 2017 13:10:02: 12000000 INFO @ Fri, 04 Aug 2017 13:10:04: 13000000 INFO @ Fri, 04 Aug 2017 13:10:19: 13000000 INFO @ Fri, 04 Aug 2017 13:10:22: 14000000 INFO @ Fri, 04 Aug 2017 13:10:23: 13000000 INFO @ Fri, 04 Aug 2017 13:10:34: 14000000 INFO @ Fri, 04 Aug 2017 13:10:36: 15000000 INFO @ Fri, 04 Aug 2017 13:10:37: 14000000 INFO @ Fri, 04 Aug 2017 13:10:40: #1 tag size is determined as 76 bps INFO @ Fri, 04 Aug 2017 13:10:40: #1 tag size = 76 INFO @ Fri, 04 Aug 2017 13:10:40: #1 total tags in treatment: 15278793 INFO @ Fri, 04 Aug 2017 13:10:40: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 13:10:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 Aug 2017 13:10:40: #1 tags after filtering in treatment: 15278793 INFO @ Fri, 04 Aug 2017 13:10:40: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 Aug 2017 13:10:40: #1 finished! INFO @ Fri, 04 Aug 2017 13:10:40: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 13:10:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 13:10:42: #2 number of paired peaks: 1060 INFO @ Fri, 04 Aug 2017 13:10:42: start model_add_line... INFO @ Fri, 04 Aug 2017 13:10:42: start X-correlation... INFO @ Fri, 04 Aug 2017 13:10:42: end of X-cor INFO @ Fri, 04 Aug 2017 13:10:42: #2 finished! INFO @ Fri, 04 Aug 2017 13:10:42: #2 predicted fragment length is 88 bps INFO @ Fri, 04 Aug 2017 13:10:42: #2 alternative fragment length(s) may be 3,88 bps INFO @ Fri, 04 Aug 2017 13:10:42: #2.2 Generate R script for model : SRX2710286.20_model.r WARNING @ Fri, 04 Aug 2017 13:10:42: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 Aug 2017 13:10:42: #2 You may need to consider one of the other alternative d(s): 3,88 WARNING @ Fri, 04 Aug 2017 13:10:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 04 Aug 2017 13:10:42: #3 Call peaks... INFO @ Fri, 04 Aug 2017 13:10:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 13:10:52: 15000000 INFO @ Fri, 04 Aug 2017 13:10:55: #1 tag size is determined as 76 bps INFO @ Fri, 04 Aug 2017 13:10:55: #1 tag size = 76 INFO @ Fri, 04 Aug 2017 13:10:55: #1 total tags in treatment: 15278793 INFO @ Fri, 04 Aug 2017 13:10:55: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 13:10:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 Aug 2017 13:10:56: #1 tags after filtering in treatment: 15278793 INFO @ Fri, 04 Aug 2017 13:10:56: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 Aug 2017 13:10:56: #1 finished! INFO @ Fri, 04 Aug 2017 13:10:56: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 13:10:56: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 13:10:58: #2 number of paired peaks: 1060 INFO @ Fri, 04 Aug 2017 13:10:58: start model_add_line... INFO @ Fri, 04 Aug 2017 13:10:59: start X-correlation... INFO @ Fri, 04 Aug 2017 13:10:59: end of X-cor INFO @ Fri, 04 Aug 2017 13:10:59: #2 finished! INFO @ Fri, 04 Aug 2017 13:10:59: #2 predicted fragment length is 88 bps INFO @ Fri, 04 Aug 2017 13:10:59: #2 alternative fragment length(s) may be 3,88 bps INFO @ Fri, 04 Aug 2017 13:10:59: #2.2 Generate R script for model : SRX2710286.05_model.r WARNING @ Fri, 04 Aug 2017 13:10:59: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 Aug 2017 13:10:59: #2 You may need to consider one of the other alternative d(s): 3,88 WARNING @ Fri, 04 Aug 2017 13:10:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 04 Aug 2017 13:10:59: #3 Call peaks... INFO @ Fri, 04 Aug 2017 13:10:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 13:10:59: 15000000 INFO @ Fri, 04 Aug 2017 13:11:07: #1 tag size is determined as 76 bps INFO @ Fri, 04 Aug 2017 13:11:07: #1 tag size = 76 INFO @ Fri, 04 Aug 2017 13:11:07: #1 total tags in treatment: 15278793 INFO @ Fri, 04 Aug 2017 13:11:07: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 13:11:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 Aug 2017 13:11:08: #1 tags after filtering in treatment: 15278793 INFO @ Fri, 04 Aug 2017 13:11:08: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 Aug 2017 13:11:08: #1 finished! INFO @ Fri, 04 Aug 2017 13:11:08: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 13:11:08: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 13:11:10: #2 number of paired peaks: 1060 INFO @ Fri, 04 Aug 2017 13:11:10: start model_add_line... INFO @ Fri, 04 Aug 2017 13:11:10: start X-correlation... INFO @ Fri, 04 Aug 2017 13:11:10: end of X-cor INFO @ Fri, 04 Aug 2017 13:11:10: #2 finished! INFO @ Fri, 04 Aug 2017 13:11:10: #2 predicted fragment length is 88 bps INFO @ Fri, 04 Aug 2017 13:11:10: #2 alternative fragment length(s) may be 3,88 bps INFO @ Fri, 04 Aug 2017 13:11:10: #2.2 Generate R script for model : SRX2710286.10_model.r WARNING @ Fri, 04 Aug 2017 13:11:10: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 Aug 2017 13:11:10: #2 You may need to consider one of the other alternative d(s): 3,88 WARNING @ Fri, 04 Aug 2017 13:11:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 04 Aug 2017 13:11:10: #3 Call peaks... INFO @ Fri, 04 Aug 2017 13:11:10: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 13:11:52: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 13:12:05: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 13:12:15: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 13:12:25: #4 Write output xls file... SRX2710286.20_peaks.xls INFO @ Fri, 04 Aug 2017 13:12:25: #4 Write peak in narrowPeak format file... SRX2710286.20_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 13:12:25: #4 Write summits bed file... SRX2710286.20_summits.bed INFO @ Fri, 04 Aug 2017 13:12:25: Done! pass1 - making usageList (6 chroms): 11 millis pass2 - checking and writing primary data (2908 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 04 Aug 2017 13:12:41: #4 Write output xls file... SRX2710286.05_peaks.xls INFO @ Fri, 04 Aug 2017 13:12:41: #4 Write peak in narrowPeak format file... SRX2710286.05_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 13:12:41: #4 Write summits bed file... SRX2710286.05_summits.bed INFO @ Fri, 04 Aug 2017 13:12:41: Done! pass1 - making usageList (7 chroms): 11 millis pass2 - checking and writing primary data (13645 records, 4 fields): 32 millis CompletedMACS2peakCalling INFO @ Fri, 04 Aug 2017 13:12:54: #4 Write output xls file... SRX2710286.10_peaks.xls INFO @ Fri, 04 Aug 2017 13:12:55: #4 Write peak in narrowPeak format file... SRX2710286.10_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 13:12:55: #4 Write summits bed file... SRX2710286.10_summits.bed INFO @ Fri, 04 Aug 2017 13:12:55: Done! pass1 - making usageList (7 chroms): 4 millis pass2 - checking and writing primary data (7817 records, 4 fields): 17 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。