Job ID = 9157953 sra ファイルのダウンロード中... Completed: 553412K bytes transferred in 19 seconds (232194K 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 32178612 spots for /home/okishinya/chipatlas/results/dm3/SRX2734364/SRR5445341.sra Written 32178612 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: 00:08:41 32178612 reads; of these: 32178612 (100.00%) were unpaired; of these: 13672339 (42.49%) aligned 0 times 11513354 (35.78%) aligned exactly 1 time 6992919 (21.73%) aligned >1 times 57.51% overall alignment rate Time searching: 00:08:41 Overall time: 00:08:41 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 8 files... [bam_rmdupse_core] 5198072 / 18506273 = 0.2809 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 @ Tue, 27 Jun 2017 14:26:35: # Command line: callpeak -t SRX2734364.bam -f BAM -g dm -n SRX2734364.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2734364.10 # format = BAM # ChIP-seq file = ['SRX2734364.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 @ Tue, 27 Jun 2017 14:26:35: #1 read tag files... INFO @ Tue, 27 Jun 2017 14:26:35: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 14:26:35: # Command line: callpeak -t SRX2734364.bam -f BAM -g dm -n SRX2734364.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2734364.05 # format = BAM # ChIP-seq file = ['SRX2734364.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 @ Tue, 27 Jun 2017 14:26:35: #1 read tag files... INFO @ Tue, 27 Jun 2017 14:26:35: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 14:26:35: # Command line: callpeak -t SRX2734364.bam -f BAM -g dm -n SRX2734364.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2734364.20 # format = BAM # ChIP-seq file = ['SRX2734364.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 @ Tue, 27 Jun 2017 14:26:35: #1 read tag files... INFO @ Tue, 27 Jun 2017 14:26:35: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 14:26:42: 1000000 INFO @ Tue, 27 Jun 2017 14:26:42: 1000000 INFO @ Tue, 27 Jun 2017 14:26:42: 1000000 INFO @ Tue, 27 Jun 2017 14:26:49: 2000000 INFO @ Tue, 27 Jun 2017 14:26:49: 2000000 INFO @ Tue, 27 Jun 2017 14:26:49: 2000000 INFO @ Tue, 27 Jun 2017 14:26:55: 3000000 INFO @ Tue, 27 Jun 2017 14:26:55: 3000000 INFO @ Tue, 27 Jun 2017 14:26:55: 3000000 INFO @ Tue, 27 Jun 2017 14:27:02: 4000000 INFO @ Tue, 27 Jun 2017 14:27:02: 4000000 INFO @ Tue, 27 Jun 2017 14:27:02: 4000000 INFO @ Tue, 27 Jun 2017 14:27:09: 5000000 INFO @ Tue, 27 Jun 2017 14:27:09: 5000000 INFO @ Tue, 27 Jun 2017 14:27:09: 5000000 INFO @ Tue, 27 Jun 2017 14:27:15: 6000000 INFO @ Tue, 27 Jun 2017 14:27:15: 6000000 INFO @ Tue, 27 Jun 2017 14:27:16: 6000000 INFO @ Tue, 27 Jun 2017 14:27:22: 7000000 INFO @ Tue, 27 Jun 2017 14:27:22: 7000000 INFO @ Tue, 27 Jun 2017 14:27:23: 7000000 INFO @ Tue, 27 Jun 2017 14:27:29: 8000000 INFO @ Tue, 27 Jun 2017 14:27:29: 8000000 INFO @ Tue, 27 Jun 2017 14:27:30: 8000000 INFO @ Tue, 27 Jun 2017 14:27:36: 9000000 INFO @ Tue, 27 Jun 2017 14:27:36: 9000000 INFO @ Tue, 27 Jun 2017 14:27:37: 9000000 INFO @ Tue, 27 Jun 2017 14:27:42: 10000000 INFO @ Tue, 27 Jun 2017 14:27:42: 10000000 INFO @ Tue, 27 Jun 2017 14:27:44: 10000000 INFO @ Tue, 27 Jun 2017 14:27:49: 11000000 INFO @ Tue, 27 Jun 2017 14:27:49: 11000000 INFO @ Tue, 27 Jun 2017 14:27:51: 11000000 INFO @ Tue, 27 Jun 2017 14:27:56: 12000000 INFO @ Tue, 27 Jun 2017 14:27:56: 12000000 INFO @ Tue, 27 Jun 2017 14:27:58: 12000000 INFO @ Tue, 27 Jun 2017 14:28:03: 13000000 INFO @ Tue, 27 Jun 2017 14:28:03: 13000000 INFO @ Tue, 27 Jun 2017 14:28:05: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 14:28:05: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 14:28:05: #1 total tags in treatment: 13308201 INFO @ Tue, 27 Jun 2017 14:28:05: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 14:28:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 14:28:05: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 14:28:05: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 14:28:05: #1 total tags in treatment: 13308201 INFO @ Tue, 27 Jun 2017 14:28:05: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 14:28:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 14:28:05: #1 tags after filtering in treatment: 13308201 INFO @ Tue, 27 Jun 2017 14:28:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 14:28:05: #1 finished! INFO @ Tue, 27 Jun 2017 14:28:05: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 14:28:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 14:28:05: #1 tags after filtering in treatment: 13308201 INFO @ Tue, 27 Jun 2017 14:28:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 14:28:05: #1 finished! INFO @ Tue, 27 Jun 2017 14:28:05: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 14:28:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 14:28:05: 13000000 INFO @ Tue, 27 Jun 2017 14:28:06: #2 number of paired peaks: 1499 INFO @ Tue, 27 Jun 2017 14:28:06: start model_add_line... INFO @ Tue, 27 Jun 2017 14:28:06: #2 number of paired peaks: 1499 INFO @ Tue, 27 Jun 2017 14:28:06: start model_add_line... INFO @ Tue, 27 Jun 2017 14:28:06: start X-correlation... INFO @ Tue, 27 Jun 2017 14:28:06: end of X-cor INFO @ Tue, 27 Jun 2017 14:28:06: #2 finished! INFO @ Tue, 27 Jun 2017 14:28:06: #2 predicted fragment length is 112 bps INFO @ Tue, 27 Jun 2017 14:28:06: #2 alternative fragment length(s) may be 4,112 bps INFO @ Tue, 27 Jun 2017 14:28:06: #2.2 Generate R script for model : SRX2734364.20_model.r INFO @ Tue, 27 Jun 2017 14:28:06: #3 Call peaks... INFO @ Tue, 27 Jun 2017 14:28:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 14:28:06: start X-correlation... INFO @ Tue, 27 Jun 2017 14:28:06: end of X-cor INFO @ Tue, 27 Jun 2017 14:28:06: #2 finished! INFO @ Tue, 27 Jun 2017 14:28:06: #2 predicted fragment length is 112 bps INFO @ Tue, 27 Jun 2017 14:28:06: #2 alternative fragment length(s) may be 4,112 bps INFO @ Tue, 27 Jun 2017 14:28:06: #2.2 Generate R script for model : SRX2734364.05_model.r INFO @ Tue, 27 Jun 2017 14:28:06: #3 Call peaks... INFO @ Tue, 27 Jun 2017 14:28:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 14:28:07: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 14:28:07: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 14:28:07: #1 total tags in treatment: 13308201 INFO @ Tue, 27 Jun 2017 14:28:07: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 14:28:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 14:28:07: #1 tags after filtering in treatment: 13308201 INFO @ Tue, 27 Jun 2017 14:28:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 14:28:07: #1 finished! INFO @ Tue, 27 Jun 2017 14:28:07: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 14:28:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 14:28:08: #2 number of paired peaks: 1499 INFO @ Tue, 27 Jun 2017 14:28:08: start model_add_line... INFO @ Tue, 27 Jun 2017 14:28:09: start X-correlation... INFO @ Tue, 27 Jun 2017 14:28:09: end of X-cor INFO @ Tue, 27 Jun 2017 14:28:09: #2 finished! INFO @ Tue, 27 Jun 2017 14:28:09: #2 predicted fragment length is 112 bps INFO @ Tue, 27 Jun 2017 14:28:09: #2 alternative fragment length(s) may be 4,112 bps INFO @ Tue, 27 Jun 2017 14:28:09: #2.2 Generate R script for model : SRX2734364.10_model.r INFO @ Tue, 27 Jun 2017 14:28:09: #3 Call peaks... INFO @ Tue, 27 Jun 2017 14:28:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 14:28:39: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 14:28:40: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 14:28:43: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 14:28:56: #4 Write output xls file... SRX2734364.20_peaks.xls INFO @ Tue, 27 Jun 2017 14:28:56: #4 Write peak in narrowPeak format file... SRX2734364.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 14:28:56: #4 Write summits bed file... SRX2734364.20_summits.bed INFO @ Tue, 27 Jun 2017 14:28:56: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1353 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 14:28:57: #4 Write output xls file... SRX2734364.05_peaks.xls INFO @ Tue, 27 Jun 2017 14:28:57: #4 Write peak in narrowPeak format file... SRX2734364.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 14:28:57: #4 Write summits bed file... SRX2734364.05_summits.bed INFO @ Tue, 27 Jun 2017 14:28:57: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6434 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 14:29:01: #4 Write output xls file... SRX2734364.10_peaks.xls INFO @ Tue, 27 Jun 2017 14:29:01: #4 Write peak in narrowPeak format file... SRX2734364.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 14:29:01: #4 Write summits bed file... SRX2734364.10_summits.bed INFO @ Tue, 27 Jun 2017 14:29:01: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2934 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。