Job ID = 9370022 sra ファイルのダウンロード中... Completed: 2262695K bytes transferred in 138 seconds (133398K 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 65854207 spots for /home/okishinya/chipatlas/results/ce10/SRX2710283/SRR5418737.sra Written 65854207 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 01:01:14 65854207 reads; of these: 65854207 (100.00%) were unpaired; of these: 4547447 (6.91%) aligned 0 times 21618817 (32.83%) aligned exactly 1 time 39687943 (60.27%) aligned >1 times 93.09% overall alignment rate Time searching: 01:01:15 Overall time: 01:01:15 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 28 files... [bam_rmdupse_core] 43063212 / 61306760 = 0.7024 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 13:26:55: # Command line: callpeak -t SRX2710283.bam -f BAM -g ce -n SRX2710283.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2710283.05 # format = BAM # ChIP-seq file = ['SRX2710283.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 13:26:55: #1 read tag files... INFO @ Fri, 04 Aug 2017 13:26:55: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 13:26:55: # Command line: callpeak -t SRX2710283.bam -f BAM -g ce -n SRX2710283.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2710283.20 # format = BAM # ChIP-seq file = ['SRX2710283.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 13:26:55: #1 read tag files... INFO @ Fri, 04 Aug 2017 13:26:55: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 13:26:55: # Command line: callpeak -t SRX2710283.bam -f BAM -g ce -n SRX2710283.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2710283.10 # format = BAM # ChIP-seq file = ['SRX2710283.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 13:26:55: #1 read tag files... INFO @ Fri, 04 Aug 2017 13:26:55: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 13:27:08: 1000000 INFO @ Fri, 04 Aug 2017 13:27:08: 1000000 INFO @ Fri, 04 Aug 2017 13:27:08: 1000000 INFO @ Fri, 04 Aug 2017 13:27:18: 2000000 INFO @ Fri, 04 Aug 2017 13:27:19: 2000000 INFO @ Fri, 04 Aug 2017 13:27:20: 2000000 INFO @ Fri, 04 Aug 2017 13:27:29: 3000000 INFO @ Fri, 04 Aug 2017 13:27:30: 3000000 INFO @ Fri, 04 Aug 2017 13:27:31: 3000000 INFO @ Fri, 04 Aug 2017 13:27:40: 4000000 INFO @ Fri, 04 Aug 2017 13:27:41: 4000000 INFO @ Fri, 04 Aug 2017 13:27:42: 4000000 INFO @ Fri, 04 Aug 2017 13:27:49: 5000000 INFO @ Fri, 04 Aug 2017 13:27:50: 5000000 INFO @ Fri, 04 Aug 2017 13:27:50: 5000000 INFO @ Fri, 04 Aug 2017 13:28:02: 6000000 INFO @ Fri, 04 Aug 2017 13:28:02: 6000000 INFO @ Fri, 04 Aug 2017 13:28:03: 6000000 INFO @ Fri, 04 Aug 2017 13:28:12: 7000000 INFO @ Fri, 04 Aug 2017 13:28:12: 7000000 INFO @ Fri, 04 Aug 2017 13:28:12: 7000000 INFO @ Fri, 04 Aug 2017 13:28:23: 8000000 INFO @ Fri, 04 Aug 2017 13:28:23: 8000000 INFO @ Fri, 04 Aug 2017 13:28:26: 8000000 INFO @ Fri, 04 Aug 2017 13:28:34: 9000000 INFO @ Fri, 04 Aug 2017 13:28:34: 9000000 INFO @ Fri, 04 Aug 2017 13:28:37: 9000000 INFO @ Fri, 04 Aug 2017 13:28:45: 10000000 INFO @ Fri, 04 Aug 2017 13:28:45: 10000000 INFO @ Fri, 04 Aug 2017 13:28:49: 10000000 INFO @ Fri, 04 Aug 2017 13:28:56: 11000000 INFO @ Fri, 04 Aug 2017 13:28:57: 11000000 INFO @ Fri, 04 Aug 2017 13:29:02: 11000000 INFO @ Fri, 04 Aug 2017 13:29:23: 12000000 INFO @ Fri, 04 Aug 2017 13:29:27: 12000000 INFO @ Fri, 04 Aug 2017 13:29:43: 12000000 INFO @ Fri, 04 Aug 2017 13:30:02: 13000000 INFO @ Fri, 04 Aug 2017 13:30:08: 13000000 INFO @ Fri, 04 Aug 2017 13:30:27: 13000000 INFO @ Fri, 04 Aug 2017 13:30:33: 14000000 INFO @ Fri, 04 Aug 2017 13:30:42: 14000000 INFO @ Fri, 04 Aug 2017 13:31:01: 14000000 INFO @ Fri, 04 Aug 2017 13:31:02: 15000000 INFO @ Fri, 04 Aug 2017 13:31:06: 15000000 INFO @ Fri, 04 Aug 2017 13:31:19: 15000000 INFO @ Fri, 04 Aug 2017 13:31:22: 16000000 INFO @ Fri, 04 Aug 2017 13:31:25: 16000000 INFO @ Fri, 04 Aug 2017 13:31:40: 16000000 INFO @ Fri, 04 Aug 2017 13:31:44: 17000000 INFO @ Fri, 04 Aug 2017 13:31:52: 17000000 INFO @ Fri, 04 Aug 2017 13:32:00: 17000000 INFO @ Fri, 04 Aug 2017 13:32:06: 18000000 INFO @ Fri, 04 Aug 2017 13:32:12: 18000000 INFO @ Fri, 04 Aug 2017 13:32:12: #1 tag size is determined as 50 bps INFO @ Fri, 04 Aug 2017 13:32:12: #1 tag size = 50 INFO @ Fri, 04 Aug 2017 13:32:12: #1 total tags in treatment: 18243548 INFO @ Fri, 04 Aug 2017 13:32:12: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 13:32:12: #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 13:32:13: #1 tags after filtering in treatment: 18243548 INFO @ Fri, 04 Aug 2017 13:32:13: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 Aug 2017 13:32:13: #1 finished! INFO @ Fri, 04 Aug 2017 13:32:13: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 13:32:13: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 13:32:16: #2 number of paired peaks: 1872 INFO @ Fri, 04 Aug 2017 13:32:16: start model_add_line... INFO @ Fri, 04 Aug 2017 13:32:17: start X-correlation... INFO @ Fri, 04 Aug 2017 13:32:17: end of X-cor INFO @ Fri, 04 Aug 2017 13:32:17: #2 finished! INFO @ Fri, 04 Aug 2017 13:32:17: #2 predicted fragment length is 102 bps INFO @ Fri, 04 Aug 2017 13:32:17: #2 alternative fragment length(s) may be 4,102 bps INFO @ Fri, 04 Aug 2017 13:32:17: #2.2 Generate R script for model : SRX2710283.20_model.r INFO @ Fri, 04 Aug 2017 13:32:17: #3 Call peaks... INFO @ Fri, 04 Aug 2017 13:32:17: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 13:32:18: #1 tag size is determined as 50 bps INFO @ Fri, 04 Aug 2017 13:32:18: #1 tag size = 50 INFO @ Fri, 04 Aug 2017 13:32:18: #1 total tags in treatment: 18243548 INFO @ Fri, 04 Aug 2017 13:32:18: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 13:32:18: #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 13:32:19: #1 tags after filtering in treatment: 18243548 INFO @ Fri, 04 Aug 2017 13:32:19: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 Aug 2017 13:32:19: #1 finished! INFO @ Fri, 04 Aug 2017 13:32:19: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 13:32:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 13:32:21: #2 number of paired peaks: 1872 INFO @ Fri, 04 Aug 2017 13:32:21: start model_add_line... INFO @ Fri, 04 Aug 2017 13:32:22: 18000000 INFO @ Fri, 04 Aug 2017 13:32:22: start X-correlation... INFO @ Fri, 04 Aug 2017 13:32:22: end of X-cor INFO @ Fri, 04 Aug 2017 13:32:22: #2 finished! INFO @ Fri, 04 Aug 2017 13:32:22: #2 predicted fragment length is 102 bps INFO @ Fri, 04 Aug 2017 13:32:22: #2 alternative fragment length(s) may be 4,102 bps INFO @ Fri, 04 Aug 2017 13:32:22: #2.2 Generate R script for model : SRX2710283.05_model.r INFO @ Fri, 04 Aug 2017 13:32:22: #3 Call peaks... INFO @ Fri, 04 Aug 2017 13:32:22: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 13:32:29: #1 tag size is determined as 50 bps INFO @ Fri, 04 Aug 2017 13:32:29: #1 tag size = 50 INFO @ Fri, 04 Aug 2017 13:32:29: #1 total tags in treatment: 18243548 INFO @ Fri, 04 Aug 2017 13:32:29: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 13:32:29: #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 13:32:29: #1 tags after filtering in treatment: 18243548 INFO @ Fri, 04 Aug 2017 13:32:29: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 Aug 2017 13:32:29: #1 finished! INFO @ Fri, 04 Aug 2017 13:32:29: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 13:32:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 13:32:33: #2 number of paired peaks: 1872 INFO @ Fri, 04 Aug 2017 13:32:33: start model_add_line... INFO @ Fri, 04 Aug 2017 13:32:33: start X-correlation... INFO @ Fri, 04 Aug 2017 13:32:33: end of X-cor INFO @ Fri, 04 Aug 2017 13:32:33: #2 finished! INFO @ Fri, 04 Aug 2017 13:32:33: #2 predicted fragment length is 102 bps INFO @ Fri, 04 Aug 2017 13:32:33: #2 alternative fragment length(s) may be 4,102 bps INFO @ Fri, 04 Aug 2017 13:32:33: #2.2 Generate R script for model : SRX2710283.10_model.r INFO @ Fri, 04 Aug 2017 13:32:33: #3 Call peaks... INFO @ Fri, 04 Aug 2017 13:32:33: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 13:33:52: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 13:33:56: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 13:34:09: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 13:34:41: #4 Write output xls file... SRX2710283.20_peaks.xls INFO @ Fri, 04 Aug 2017 13:34:41: #4 Write peak in narrowPeak format file... SRX2710283.20_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 13:34:41: #4 Write summits bed file... SRX2710283.20_summits.bed INFO @ Fri, 04 Aug 2017 13:34:42: Done! pass1 - making usageList (7 chroms): 10 millis pass2 - checking and writing primary data (10617 records, 4 fields): 52 millis CompletedMACS2peakCalling INFO @ Fri, 04 Aug 2017 13:34:50: #4 Write output xls file... SRX2710283.05_peaks.xls INFO @ Fri, 04 Aug 2017 13:34:51: #4 Write peak in narrowPeak format file... SRX2710283.05_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 13:34:51: #4 Write summits bed file... SRX2710283.05_summits.bed INFO @ Fri, 04 Aug 2017 13:34:51: Done! pass1 - making usageList (7 chroms): 14 millis pass2 - checking and writing primary data (25146 records, 4 fields): 58 millis CompletedMACS2peakCalling INFO @ Fri, 04 Aug 2017 13:34:55: #4 Write output xls file... SRX2710283.10_peaks.xls INFO @ Fri, 04 Aug 2017 13:34:56: #4 Write peak in narrowPeak format file... SRX2710283.10_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 13:34:56: #4 Write summits bed file... SRX2710283.10_summits.bed INFO @ Fri, 04 Aug 2017 13:34:56: Done! pass1 - making usageList (7 chroms): 14 millis pass2 - checking and writing primary data (18421 records, 4 fields): 52 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。