Job ID = 9158159 sra ファイルのダウンロード中... Completed: 363844K bytes transferred in 5 seconds (503514K 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 8758136 spots for /home/okishinya/chipatlas/results/dm3/SRX1056716/SRR2060650.sra Written 8758136 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: 00:20:26 8758136 reads; of these: 8758136 (100.00%) were paired; of these: 1388362 (15.85%) aligned concordantly 0 times 5729454 (65.42%) aligned concordantly exactly 1 time 1640320 (18.73%) aligned concordantly >1 times ---- 1388362 pairs aligned concordantly 0 times; of these: 180532 (13.00%) aligned discordantly 1 time ---- 1207830 pairs aligned 0 times concordantly or discordantly; of these: 2415660 mates make up the pairs; of these: 1707976 (70.70%) aligned 0 times 376351 (15.58%) aligned exactly 1 time 331333 (13.72%) aligned >1 times 90.25% overall alignment rate Time searching: 00:20:26 Overall time: 00:20:26 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] 617266 / 7546636 = 0.0818 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 15:54:25: # Command line: callpeak -t SRX1056716.bam -f BAM -g dm -n SRX1056716.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1056716.20 # format = BAM # ChIP-seq file = ['SRX1056716.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 15:54:25: #1 read tag files... INFO @ Tue, 27 Jun 2017 15:54:25: # Command line: callpeak -t SRX1056716.bam -f BAM -g dm -n SRX1056716.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1056716.05 # format = BAM # ChIP-seq file = ['SRX1056716.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 15:54:25: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 15:54:25: #1 read tag files... INFO @ Tue, 27 Jun 2017 15:54:25: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 15:54:25: # Command line: callpeak -t SRX1056716.bam -f BAM -g dm -n SRX1056716.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1056716.10 # format = BAM # ChIP-seq file = ['SRX1056716.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 15:54:25: #1 read tag files... INFO @ Tue, 27 Jun 2017 15:54:25: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 15:54:32: 1000000 INFO @ Tue, 27 Jun 2017 15:54:32: 1000000 INFO @ Tue, 27 Jun 2017 15:54:32: 1000000 INFO @ Tue, 27 Jun 2017 15:54:39: 2000000 INFO @ Tue, 27 Jun 2017 15:54:39: 2000000 INFO @ Tue, 27 Jun 2017 15:54:39: 2000000 INFO @ Tue, 27 Jun 2017 15:54:46: 3000000 INFO @ Tue, 27 Jun 2017 15:54:46: 3000000 INFO @ Tue, 27 Jun 2017 15:54:46: 3000000 INFO @ Tue, 27 Jun 2017 15:54:53: 4000000 INFO @ Tue, 27 Jun 2017 15:54:53: 4000000 INFO @ Tue, 27 Jun 2017 15:54:53: 4000000 INFO @ Tue, 27 Jun 2017 15:55:00: 5000000 INFO @ Tue, 27 Jun 2017 15:55:00: 5000000 INFO @ Tue, 27 Jun 2017 15:55:00: 5000000 INFO @ Tue, 27 Jun 2017 15:55:07: 6000000 INFO @ Tue, 27 Jun 2017 15:55:07: 6000000 INFO @ Tue, 27 Jun 2017 15:55:07: 6000000 INFO @ Tue, 27 Jun 2017 15:55:14: 7000000 INFO @ Tue, 27 Jun 2017 15:55:14: 7000000 INFO @ Tue, 27 Jun 2017 15:55:15: 7000000 INFO @ Tue, 27 Jun 2017 15:55:21: 8000000 INFO @ Tue, 27 Jun 2017 15:55:21: 8000000 INFO @ Tue, 27 Jun 2017 15:55:22: 8000000 INFO @ Tue, 27 Jun 2017 15:55:28: 9000000 INFO @ Tue, 27 Jun 2017 15:55:28: 9000000 INFO @ Tue, 27 Jun 2017 15:55:29: 9000000 INFO @ Tue, 27 Jun 2017 15:55:35: 10000000 INFO @ Tue, 27 Jun 2017 15:55:35: 10000000 INFO @ Tue, 27 Jun 2017 15:55:36: 10000000 INFO @ Tue, 27 Jun 2017 15:55:42: 11000000 INFO @ Tue, 27 Jun 2017 15:55:42: 11000000 INFO @ Tue, 27 Jun 2017 15:55:43: 11000000 INFO @ Tue, 27 Jun 2017 15:55:49: 12000000 INFO @ Tue, 27 Jun 2017 15:55:50: 12000000 INFO @ Tue, 27 Jun 2017 15:55:51: 12000000 INFO @ Tue, 27 Jun 2017 15:55:56: 13000000 INFO @ Tue, 27 Jun 2017 15:55:56: 13000000 INFO @ Tue, 27 Jun 2017 15:55:59: 13000000 INFO @ Tue, 27 Jun 2017 15:56:03: 14000000 INFO @ Tue, 27 Jun 2017 15:56:04: 14000000 INFO @ Tue, 27 Jun 2017 15:56:07: #1 tag size is determined as 36 bps INFO @ Tue, 27 Jun 2017 15:56:07: #1 tag size = 36 INFO @ Tue, 27 Jun 2017 15:56:07: #1 total tags in treatment: 6758353 INFO @ Tue, 27 Jun 2017 15:56:07: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 15:56:07: #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 15:56:07: #1 tags after filtering in treatment: 6163325 INFO @ Tue, 27 Jun 2017 15:56:07: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 27 Jun 2017 15:56:07: #1 finished! INFO @ Tue, 27 Jun 2017 15:56:07: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 15:56:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 15:56:07: 14000000 INFO @ Tue, 27 Jun 2017 15:56:08: #2 number of paired peaks: 5773 INFO @ Tue, 27 Jun 2017 15:56:08: start model_add_line... INFO @ Tue, 27 Jun 2017 15:56:08: start X-correlation... INFO @ Tue, 27 Jun 2017 15:56:08: end of X-cor INFO @ Tue, 27 Jun 2017 15:56:08: #2 finished! INFO @ Tue, 27 Jun 2017 15:56:08: #2 predicted fragment length is 223 bps INFO @ Tue, 27 Jun 2017 15:56:08: #2 alternative fragment length(s) may be 223 bps INFO @ Tue, 27 Jun 2017 15:56:08: #2.2 Generate R script for model : SRX1056716.05_model.r INFO @ Tue, 27 Jun 2017 15:56:08: #3 Call peaks... INFO @ Tue, 27 Jun 2017 15:56:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 15:56:08: #1 tag size is determined as 36 bps INFO @ Tue, 27 Jun 2017 15:56:08: #1 tag size = 36 INFO @ Tue, 27 Jun 2017 15:56:08: #1 total tags in treatment: 6758353 INFO @ Tue, 27 Jun 2017 15:56:08: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 15:56:08: #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 15:56:08: #1 tags after filtering in treatment: 6163325 INFO @ Tue, 27 Jun 2017 15:56:08: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 27 Jun 2017 15:56:08: #1 finished! INFO @ Tue, 27 Jun 2017 15:56:08: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 15:56:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 15:56:09: #2 number of paired peaks: 5773 INFO @ Tue, 27 Jun 2017 15:56:09: start model_add_line... INFO @ Tue, 27 Jun 2017 15:56:09: start X-correlation... INFO @ Tue, 27 Jun 2017 15:56:09: end of X-cor INFO @ Tue, 27 Jun 2017 15:56:09: #2 finished! INFO @ Tue, 27 Jun 2017 15:56:09: #2 predicted fragment length is 223 bps INFO @ Tue, 27 Jun 2017 15:56:09: #2 alternative fragment length(s) may be 223 bps INFO @ Tue, 27 Jun 2017 15:56:09: #2.2 Generate R script for model : SRX1056716.20_model.r INFO @ Tue, 27 Jun 2017 15:56:09: #3 Call peaks... INFO @ Tue, 27 Jun 2017 15:56:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 15:56:11: #1 tag size is determined as 36 bps INFO @ Tue, 27 Jun 2017 15:56:11: #1 tag size = 36 INFO @ Tue, 27 Jun 2017 15:56:11: #1 total tags in treatment: 6758353 INFO @ Tue, 27 Jun 2017 15:56:11: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 15:56:11: #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 15:56:11: #1 tags after filtering in treatment: 6163325 INFO @ Tue, 27 Jun 2017 15:56:11: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 27 Jun 2017 15:56:11: #1 finished! INFO @ Tue, 27 Jun 2017 15:56:11: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 15:56:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 15:56:12: #2 number of paired peaks: 5773 INFO @ Tue, 27 Jun 2017 15:56:12: start model_add_line... INFO @ Tue, 27 Jun 2017 15:56:12: start X-correlation... INFO @ Tue, 27 Jun 2017 15:56:12: end of X-cor INFO @ Tue, 27 Jun 2017 15:56:12: #2 finished! INFO @ Tue, 27 Jun 2017 15:56:12: #2 predicted fragment length is 223 bps INFO @ Tue, 27 Jun 2017 15:56:12: #2 alternative fragment length(s) may be 223 bps INFO @ Tue, 27 Jun 2017 15:56:12: #2.2 Generate R script for model : SRX1056716.10_model.r INFO @ Tue, 27 Jun 2017 15:56:12: #3 Call peaks... INFO @ Tue, 27 Jun 2017 15:56:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 15:56:26: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 15:56:29: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 15:56:32: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 15:56:36: #4 Write output xls file... SRX1056716.05_peaks.xls INFO @ Tue, 27 Jun 2017 15:56:36: #4 Write peak in narrowPeak format file... SRX1056716.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 15:56:36: #4 Write summits bed file... SRX1056716.05_summits.bed INFO @ Tue, 27 Jun 2017 15:56:36: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (11703 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 15:56:38: #4 Write output xls file... SRX1056716.20_peaks.xls INFO @ Tue, 27 Jun 2017 15:56:38: #4 Write peak in narrowPeak format file... SRX1056716.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 15:56:38: #4 Write summits bed file... SRX1056716.20_summits.bed INFO @ Tue, 27 Jun 2017 15:56:38: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4069 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 15:56:42: #4 Write output xls file... SRX1056716.10_peaks.xls INFO @ Tue, 27 Jun 2017 15:56:42: #4 Write peak in narrowPeak format file... SRX1056716.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 15:56:42: #4 Write summits bed file... SRX1056716.10_summits.bed INFO @ Tue, 27 Jun 2017 15:56:42: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8022 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。