Job ID = 9371431 sra ファイルのダウンロード中... Completed: 694154K bytes transferred in 11 seconds (512031K 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 31310321 spots for /home/okishinya/chipatlas/results/dm3/SRX2520632/SRR5206751.sra Written 31310321 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: 00:26:34 31310321 reads; of these: 31310321 (100.00%) were unpaired; of these: 1299930 (4.15%) aligned 0 times 22869378 (73.04%) aligned exactly 1 time 7141013 (22.81%) aligned >1 times 95.85% overall alignment rate Time searching: 00:26:34 Overall time: 00:26:34 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] 9691023 / 30010391 = 0.3229 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 14:38:49: # Command line: callpeak -t SRX2520632.bam -f BAM -g dm -n SRX2520632.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2520632.20 # format = BAM # ChIP-seq file = ['SRX2520632.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 @ Fri, 04 Aug 2017 14:38:49: #1 read tag files... INFO @ Fri, 04 Aug 2017 14:38:49: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 14:38:49: # Command line: callpeak -t SRX2520632.bam -f BAM -g dm -n SRX2520632.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2520632.10 # format = BAM # ChIP-seq file = ['SRX2520632.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 @ Fri, 04 Aug 2017 14:38:49: #1 read tag files... INFO @ Fri, 04 Aug 2017 14:38:49: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 14:38:50: # Command line: callpeak -t SRX2520632.bam -f BAM -g dm -n SRX2520632.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2520632.05 # format = BAM # ChIP-seq file = ['SRX2520632.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 @ Fri, 04 Aug 2017 14:38:50: #1 read tag files... INFO @ Fri, 04 Aug 2017 14:38:50: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 14:39:06: 1000000 INFO @ Fri, 04 Aug 2017 14:39:07: 1000000 INFO @ Fri, 04 Aug 2017 14:39:08: 1000000 INFO @ Fri, 04 Aug 2017 14:39:22: 2000000 INFO @ Fri, 04 Aug 2017 14:39:28: 2000000 INFO @ Fri, 04 Aug 2017 14:39:28: 2000000 INFO @ Fri, 04 Aug 2017 14:39:41: 3000000 INFO @ Fri, 04 Aug 2017 14:39:46: 3000000 INFO @ Fri, 04 Aug 2017 14:39:46: 3000000 INFO @ Fri, 04 Aug 2017 14:39:56: 4000000 INFO @ Fri, 04 Aug 2017 14:40:03: 4000000 INFO @ Fri, 04 Aug 2017 14:40:04: 4000000 INFO @ Fri, 04 Aug 2017 14:40:08: 5000000 INFO @ Fri, 04 Aug 2017 14:40:19: 5000000 INFO @ Fri, 04 Aug 2017 14:40:21: 6000000 INFO @ Fri, 04 Aug 2017 14:40:22: 5000000 INFO @ Fri, 04 Aug 2017 14:40:33: 7000000 INFO @ Fri, 04 Aug 2017 14:40:36: 6000000 INFO @ Fri, 04 Aug 2017 14:40:41: 6000000 INFO @ Fri, 04 Aug 2017 14:40:48: 8000000 INFO @ Fri, 04 Aug 2017 14:40:54: 7000000 INFO @ Fri, 04 Aug 2017 14:41:00: 7000000 INFO @ Fri, 04 Aug 2017 14:41:01: 9000000 INFO @ Fri, 04 Aug 2017 14:41:12: 8000000 INFO @ Fri, 04 Aug 2017 14:41:17: 10000000 INFO @ Fri, 04 Aug 2017 14:41:19: 8000000 INFO @ Fri, 04 Aug 2017 14:41:29: 9000000 INFO @ Fri, 04 Aug 2017 14:41:34: 11000000 INFO @ Fri, 04 Aug 2017 14:41:36: 9000000 INFO @ Fri, 04 Aug 2017 14:41:47: 12000000 INFO @ Fri, 04 Aug 2017 14:41:47: 10000000 INFO @ Fri, 04 Aug 2017 14:41:53: 10000000 INFO @ Fri, 04 Aug 2017 14:42:02: 13000000 INFO @ Fri, 04 Aug 2017 14:42:04: 11000000 INFO @ Fri, 04 Aug 2017 14:42:10: 11000000 INFO @ Fri, 04 Aug 2017 14:42:15: 14000000 INFO @ Fri, 04 Aug 2017 14:42:23: 12000000 INFO @ Fri, 04 Aug 2017 14:42:28: 12000000 INFO @ Fri, 04 Aug 2017 14:42:29: 15000000 INFO @ Fri, 04 Aug 2017 14:42:41: 13000000 INFO @ Fri, 04 Aug 2017 14:42:42: 16000000 INFO @ Fri, 04 Aug 2017 14:42:45: 13000000 INFO @ Fri, 04 Aug 2017 14:42:57: 17000000 INFO @ Fri, 04 Aug 2017 14:43:00: 14000000 INFO @ Fri, 04 Aug 2017 14:43:00: 14000000 INFO @ Fri, 04 Aug 2017 14:43:13: 18000000 INFO @ Fri, 04 Aug 2017 14:43:18: 15000000 INFO @ Fri, 04 Aug 2017 14:43:20: 15000000 INFO @ Fri, 04 Aug 2017 14:43:26: 19000000 INFO @ Fri, 04 Aug 2017 14:43:38: 16000000 INFO @ Fri, 04 Aug 2017 14:43:42: 16000000 INFO @ Fri, 04 Aug 2017 14:43:42: 20000000 INFO @ Fri, 04 Aug 2017 14:43:46: #1 tag size is determined as 50 bps INFO @ Fri, 04 Aug 2017 14:43:46: #1 tag size = 50 INFO @ Fri, 04 Aug 2017 14:43:46: #1 total tags in treatment: 20319368 INFO @ Fri, 04 Aug 2017 14:43:46: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 14:43:46: #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 14:43:47: #1 tags after filtering in treatment: 20319368 INFO @ Fri, 04 Aug 2017 14:43:47: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 Aug 2017 14:43:47: #1 finished! INFO @ Fri, 04 Aug 2017 14:43:47: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 14:43:47: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 14:43:49: #2 number of paired peaks: 840 WARNING @ Fri, 04 Aug 2017 14:43:49: Fewer paired peaks (840) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 840 pairs to build model! INFO @ Fri, 04 Aug 2017 14:43:49: start model_add_line... INFO @ Fri, 04 Aug 2017 14:43:49: start X-correlation... INFO @ Fri, 04 Aug 2017 14:43:49: end of X-cor INFO @ Fri, 04 Aug 2017 14:43:49: #2 finished! INFO @ Fri, 04 Aug 2017 14:43:49: #2 predicted fragment length is 210 bps INFO @ Fri, 04 Aug 2017 14:43:49: #2 alternative fragment length(s) may be 210 bps INFO @ Fri, 04 Aug 2017 14:43:49: #2.2 Generate R script for model : SRX2520632.10_model.r INFO @ Fri, 04 Aug 2017 14:43:49: #3 Call peaks... INFO @ Fri, 04 Aug 2017 14:43:49: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 14:44:00: 17000000 INFO @ Fri, 04 Aug 2017 14:44:04: 17000000 INFO @ Fri, 04 Aug 2017 14:44:21: 18000000 INFO @ Fri, 04 Aug 2017 14:44:22: 18000000 INFO @ Fri, 04 Aug 2017 14:44:38: 19000000 INFO @ Fri, 04 Aug 2017 14:44:40: 19000000 INFO @ Fri, 04 Aug 2017 14:44:57: 20000000 INFO @ Fri, 04 Aug 2017 14:44:58: 20000000 INFO @ Fri, 04 Aug 2017 14:45:02: #1 tag size is determined as 50 bps INFO @ Fri, 04 Aug 2017 14:45:02: #1 tag size = 50 INFO @ Fri, 04 Aug 2017 14:45:02: #1 total tags in treatment: 20319368 INFO @ Fri, 04 Aug 2017 14:45:02: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 14:45:02: #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 14:45:03: #1 tags after filtering in treatment: 20319368 INFO @ Fri, 04 Aug 2017 14:45:03: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 Aug 2017 14:45:03: #1 finished! INFO @ Fri, 04 Aug 2017 14:45:03: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 14:45:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 14:45:03: #1 tag size is determined as 50 bps INFO @ Fri, 04 Aug 2017 14:45:03: #1 tag size = 50 INFO @ Fri, 04 Aug 2017 14:45:03: #1 total tags in treatment: 20319368 INFO @ Fri, 04 Aug 2017 14:45:03: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 14:45:03: #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 14:45:04: #1 tags after filtering in treatment: 20319368 INFO @ Fri, 04 Aug 2017 14:45:04: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 Aug 2017 14:45:04: #1 finished! INFO @ Fri, 04 Aug 2017 14:45:04: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 14:45:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 14:45:04: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 14:45:05: #2 number of paired peaks: 840 WARNING @ Fri, 04 Aug 2017 14:45:05: Fewer paired peaks (840) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 840 pairs to build model! INFO @ Fri, 04 Aug 2017 14:45:05: start model_add_line... INFO @ Fri, 04 Aug 2017 14:45:05: start X-correlation... INFO @ Fri, 04 Aug 2017 14:45:05: end of X-cor INFO @ Fri, 04 Aug 2017 14:45:05: #2 finished! INFO @ Fri, 04 Aug 2017 14:45:05: #2 predicted fragment length is 210 bps INFO @ Fri, 04 Aug 2017 14:45:05: #2 alternative fragment length(s) may be 210 bps INFO @ Fri, 04 Aug 2017 14:45:05: #2.2 Generate R script for model : SRX2520632.05_model.r INFO @ Fri, 04 Aug 2017 14:45:05: #3 Call peaks... INFO @ Fri, 04 Aug 2017 14:45:05: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 14:45:06: #2 number of paired peaks: 840 WARNING @ Fri, 04 Aug 2017 14:45:06: Fewer paired peaks (840) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 840 pairs to build model! INFO @ Fri, 04 Aug 2017 14:45:06: start model_add_line... INFO @ Fri, 04 Aug 2017 14:45:06: start X-correlation... INFO @ Fri, 04 Aug 2017 14:45:06: end of X-cor INFO @ Fri, 04 Aug 2017 14:45:06: #2 finished! INFO @ Fri, 04 Aug 2017 14:45:06: #2 predicted fragment length is 210 bps INFO @ Fri, 04 Aug 2017 14:45:06: #2 alternative fragment length(s) may be 210 bps INFO @ Fri, 04 Aug 2017 14:45:06: #2.2 Generate R script for model : SRX2520632.20_model.r INFO @ Fri, 04 Aug 2017 14:45:06: #3 Call peaks... INFO @ Fri, 04 Aug 2017 14:45:06: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 14:45:45: #4 Write output xls file... SRX2520632.10_peaks.xls INFO @ Fri, 04 Aug 2017 14:45:45: #4 Write peak in narrowPeak format file... SRX2520632.10_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 14:45:45: #4 Write summits bed file... SRX2520632.10_summits.bed INFO @ Fri, 04 Aug 2017 14:45:45: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (5585 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Fri, 04 Aug 2017 14:46:13: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 14:46:15: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 14:46:52: #4 Write output xls file... SRX2520632.05_peaks.xls INFO @ Fri, 04 Aug 2017 14:46:52: #4 Write peak in narrowPeak format file... SRX2520632.05_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 14:46:52: #4 Write summits bed file... SRX2520632.05_summits.bed INFO @ Fri, 04 Aug 2017 14:46:52: #4 Write output xls file... SRX2520632.20_peaks.xls INFO @ Fri, 04 Aug 2017 14:46:52: Done! INFO @ Fri, 04 Aug 2017 14:46:52: #4 Write peak in narrowPeak format file... SRX2520632.20_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 14:46:52: #4 Write summits bed file... SRX2520632.20_summits.bed INFO @ Fri, 04 Aug 2017 14:46:52: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (7832 records, 4 fields): 16 millis pass1 - making usageList (15 chroms): 2 millis CompletedMACS2peakCalling pass2 - checking and writing primary data (3455 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。