Job ID = 9158158 sra ファイルのダウンロード中... Completed: 336393K bytes transferred in 5 seconds (465110K 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: PAIRED fastq に変換中... Written 7985711 spots for /home/okishinya/chipatlas/results/dm3/SRX1056715/SRR2060649.sra Written 7985711 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: 00:19:39 7985711 reads; of these: 7985711 (100.00%) were paired; of these: 1324695 (16.59%) aligned concordantly 0 times 4841615 (60.63%) aligned concordantly exactly 1 time 1819401 (22.78%) aligned concordantly >1 times ---- 1324695 pairs aligned concordantly 0 times; of these: 207882 (15.69%) aligned discordantly 1 time ---- 1116813 pairs aligned 0 times concordantly or discordantly; of these: 2233626 mates make up the pairs; of these: 1542324 (69.05%) aligned 0 times 369028 (16.52%) aligned exactly 1 time 322274 (14.43%) aligned >1 times 90.34% overall alignment rate Time searching: 00:19:39 Overall time: 00:19:39 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_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 1949714 / 6864922 = 0.2840 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 15:52:23: # Command line: callpeak -t SRX1056715.bam -f BAM -g dm -n SRX1056715.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1056715.05 # format = BAM # ChIP-seq file = ['SRX1056715.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 15:52:23: #1 read tag files... INFO @ Tue, 27 Jun 2017 15:52:23: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 15:52:23: # Command line: callpeak -t SRX1056715.bam -f BAM -g dm -n SRX1056715.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1056715.20 # format = BAM # ChIP-seq file = ['SRX1056715.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 15:52:23: #1 read tag files... INFO @ Tue, 27 Jun 2017 15:52:23: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 15:52:23: # Command line: callpeak -t SRX1056715.bam -f BAM -g dm -n SRX1056715.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1056715.10 # format = BAM # ChIP-seq file = ['SRX1056715.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 15:52:23: #1 read tag files... INFO @ Tue, 27 Jun 2017 15:52:23: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 15:52:29: 1000000 INFO @ Tue, 27 Jun 2017 15:52:29: 1000000 INFO @ Tue, 27 Jun 2017 15:52:29: 1000000 INFO @ Tue, 27 Jun 2017 15:52:35: 2000000 INFO @ Tue, 27 Jun 2017 15:52:36: 2000000 INFO @ Tue, 27 Jun 2017 15:52:36: 2000000 INFO @ Tue, 27 Jun 2017 15:52:41: 3000000 INFO @ Tue, 27 Jun 2017 15:52:43: 3000000 INFO @ Tue, 27 Jun 2017 15:52:43: 3000000 INFO @ Tue, 27 Jun 2017 15:52:47: 4000000 INFO @ Tue, 27 Jun 2017 15:52:49: 4000000 INFO @ Tue, 27 Jun 2017 15:52:49: 4000000 INFO @ Tue, 27 Jun 2017 15:52:53: 5000000 INFO @ Tue, 27 Jun 2017 15:52:56: 5000000 INFO @ Tue, 27 Jun 2017 15:52:56: 5000000 INFO @ Tue, 27 Jun 2017 15:52:58: 6000000 INFO @ Tue, 27 Jun 2017 15:53:02: 6000000 INFO @ Tue, 27 Jun 2017 15:53:02: 6000000 INFO @ Tue, 27 Jun 2017 15:53:04: 7000000 INFO @ Tue, 27 Jun 2017 15:53:09: 7000000 INFO @ Tue, 27 Jun 2017 15:53:09: 7000000 INFO @ Tue, 27 Jun 2017 15:53:10: 8000000 INFO @ Tue, 27 Jun 2017 15:53:15: 8000000 INFO @ Tue, 27 Jun 2017 15:53:15: 8000000 INFO @ Tue, 27 Jun 2017 15:53:16: 9000000 INFO @ Tue, 27 Jun 2017 15:53:22: 10000000 INFO @ Tue, 27 Jun 2017 15:53:22: 9000000 INFO @ Tue, 27 Jun 2017 15:53:22: 9000000 INFO @ Tue, 27 Jun 2017 15:53:25: #1 tag size is determined as 36 bps INFO @ Tue, 27 Jun 2017 15:53:25: #1 tag size = 36 INFO @ Tue, 27 Jun 2017 15:53:25: #1 total tags in treatment: 4744099 INFO @ Tue, 27 Jun 2017 15:53:25: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 15:53:25: #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 15:53:25: #1 tags after filtering in treatment: 4434885 INFO @ Tue, 27 Jun 2017 15:53:25: #1 Redundant rate of treatment: 0.07 INFO @ Tue, 27 Jun 2017 15:53:25: #1 finished! INFO @ Tue, 27 Jun 2017 15:53:25: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 15:53:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 15:53:25: #2 number of paired peaks: 2492 INFO @ Tue, 27 Jun 2017 15:53:25: start model_add_line... INFO @ Tue, 27 Jun 2017 15:53:26: start X-correlation... INFO @ Tue, 27 Jun 2017 15:53:26: end of X-cor INFO @ Tue, 27 Jun 2017 15:53:26: #2 finished! INFO @ Tue, 27 Jun 2017 15:53:26: #2 predicted fragment length is 196 bps INFO @ Tue, 27 Jun 2017 15:53:26: #2 alternative fragment length(s) may be 196 bps INFO @ Tue, 27 Jun 2017 15:53:26: #2.2 Generate R script for model : SRX1056715.10_model.r INFO @ Tue, 27 Jun 2017 15:53:26: #3 Call peaks... INFO @ Tue, 27 Jun 2017 15:53:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 15:53:29: 10000000 INFO @ Tue, 27 Jun 2017 15:53:29: 10000000 INFO @ Tue, 27 Jun 2017 15:53:32: #1 tag size is determined as 36 bps INFO @ Tue, 27 Jun 2017 15:53:32: #1 tag size = 36 INFO @ Tue, 27 Jun 2017 15:53:32: #1 total tags in treatment: 4744099 INFO @ Tue, 27 Jun 2017 15:53:32: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 15:53:32: #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 15:53:32: #1 tag size is determined as 36 bps INFO @ Tue, 27 Jun 2017 15:53:32: #1 tag size = 36 INFO @ Tue, 27 Jun 2017 15:53:32: #1 total tags in treatment: 4744099 INFO @ Tue, 27 Jun 2017 15:53:32: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 15:53:32: #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 15:53:32: #1 tags after filtering in treatment: 4434885 INFO @ Tue, 27 Jun 2017 15:53:32: #1 Redundant rate of treatment: 0.07 INFO @ Tue, 27 Jun 2017 15:53:32: #1 finished! INFO @ Tue, 27 Jun 2017 15:53:32: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 15:53:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 15:53:32: #1 tags after filtering in treatment: 4434885 INFO @ Tue, 27 Jun 2017 15:53:32: #1 Redundant rate of treatment: 0.07 INFO @ Tue, 27 Jun 2017 15:53:32: #1 finished! INFO @ Tue, 27 Jun 2017 15:53:32: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 15:53:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 15:53:32: #2 number of paired peaks: 2492 INFO @ Tue, 27 Jun 2017 15:53:32: start model_add_line... INFO @ Tue, 27 Jun 2017 15:53:33: #2 number of paired peaks: 2492 INFO @ Tue, 27 Jun 2017 15:53:33: start model_add_line... INFO @ Tue, 27 Jun 2017 15:53:33: start X-correlation... INFO @ Tue, 27 Jun 2017 15:53:33: end of X-cor INFO @ Tue, 27 Jun 2017 15:53:33: #2 finished! INFO @ Tue, 27 Jun 2017 15:53:33: #2 predicted fragment length is 196 bps INFO @ Tue, 27 Jun 2017 15:53:33: #2 alternative fragment length(s) may be 196 bps INFO @ Tue, 27 Jun 2017 15:53:33: #2.2 Generate R script for model : SRX1056715.20_model.r INFO @ Tue, 27 Jun 2017 15:53:33: #3 Call peaks... INFO @ Tue, 27 Jun 2017 15:53:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 15:53:33: start X-correlation... INFO @ Tue, 27 Jun 2017 15:53:33: end of X-cor INFO @ Tue, 27 Jun 2017 15:53:33: #2 finished! INFO @ Tue, 27 Jun 2017 15:53:33: #2 predicted fragment length is 196 bps INFO @ Tue, 27 Jun 2017 15:53:33: #2 alternative fragment length(s) may be 196 bps INFO @ Tue, 27 Jun 2017 15:53:33: #2.2 Generate R script for model : SRX1056715.05_model.r INFO @ Tue, 27 Jun 2017 15:53:33: #3 Call peaks... INFO @ Tue, 27 Jun 2017 15:53:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 15:53:37: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 15:53:44: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 15:53:44: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 15:53:45: #4 Write output xls file... SRX1056715.10_peaks.xls INFO @ Tue, 27 Jun 2017 15:53:45: #4 Write peak in narrowPeak format file... SRX1056715.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 15:53:45: #4 Write summits bed file... SRX1056715.10_summits.bed INFO @ Tue, 27 Jun 2017 15:53:45: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3048 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 15:53:50: #4 Write output xls file... SRX1056715.05_peaks.xls INFO @ Tue, 27 Jun 2017 15:53:50: #4 Write peak in narrowPeak format file... SRX1056715.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 15:53:50: #4 Write summits bed file... SRX1056715.05_summits.bed INFO @ Tue, 27 Jun 2017 15:53:50: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6149 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 15:53:50: #4 Write output xls file... SRX1056715.20_peaks.xls INFO @ Tue, 27 Jun 2017 15:53:50: #4 Write peak in narrowPeak format file... SRX1056715.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 15:53:50: #4 Write summits bed file... SRX1056715.20_summits.bed INFO @ Tue, 27 Jun 2017 15:53:50: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1142 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。