Job ID = 9159844 sra ファイルのダウンロード中... Completed: 453620K bytes transferred in 6 seconds (551969K 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 7715204 spots for /home/okishinya/chipatlas/results/dm3/SRX749029/SRR1636757.sra Written 7715204 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: 00:23:42 7715204 reads; of these: 7715204 (100.00%) were paired; of these: 502928 (6.52%) aligned concordantly 0 times 4768622 (61.81%) aligned concordantly exactly 1 time 2443654 (31.67%) aligned concordantly >1 times ---- 502928 pairs aligned concordantly 0 times; of these: 72261 (14.37%) aligned discordantly 1 time ---- 430667 pairs aligned 0 times concordantly or discordantly; of these: 861334 mates make up the pairs; of these: 514317 (59.71%) aligned 0 times 196487 (22.81%) aligned exactly 1 time 150530 (17.48%) aligned >1 times 96.67% overall alignment rate Time searching: 00:23:42 Overall time: 00:23:42 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_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] 675112 / 7274398 = 0.0928 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 @ Wed, 28 Jun 2017 00:42:57: # Command line: callpeak -t SRX749029.bam -f BAM -g dm -n SRX749029.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX749029.05 # format = BAM # ChIP-seq file = ['SRX749029.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 @ Wed, 28 Jun 2017 00:42:57: # Command line: callpeak -t SRX749029.bam -f BAM -g dm -n SRX749029.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX749029.20 # format = BAM # ChIP-seq file = ['SRX749029.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 @ Wed, 28 Jun 2017 00:42:57: # Command line: callpeak -t SRX749029.bam -f BAM -g dm -n SRX749029.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX749029.10 # format = BAM # ChIP-seq file = ['SRX749029.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 @ Wed, 28 Jun 2017 00:42:57: #1 read tag files... INFO @ Wed, 28 Jun 2017 00:42:57: #1 read tag files... INFO @ Wed, 28 Jun 2017 00:42:57: #1 read tag files... INFO @ Wed, 28 Jun 2017 00:42:57: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 00:42:57: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 00:42:57: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 00:43:03: 1000000 INFO @ Wed, 28 Jun 2017 00:43:03: 1000000 INFO @ Wed, 28 Jun 2017 00:43:03: 1000000 INFO @ Wed, 28 Jun 2017 00:43:09: 2000000 INFO @ Wed, 28 Jun 2017 00:43:09: 2000000 INFO @ Wed, 28 Jun 2017 00:43:09: 2000000 INFO @ Wed, 28 Jun 2017 00:43:15: 3000000 INFO @ Wed, 28 Jun 2017 00:43:15: 3000000 INFO @ Wed, 28 Jun 2017 00:43:15: 3000000 INFO @ Wed, 28 Jun 2017 00:43:21: 4000000 INFO @ Wed, 28 Jun 2017 00:43:22: 4000000 INFO @ Wed, 28 Jun 2017 00:43:22: 4000000 INFO @ Wed, 28 Jun 2017 00:43:28: 5000000 INFO @ Wed, 28 Jun 2017 00:43:28: 5000000 INFO @ Wed, 28 Jun 2017 00:43:28: 5000000 INFO @ Wed, 28 Jun 2017 00:43:35: 6000000 INFO @ Wed, 28 Jun 2017 00:43:35: 6000000 INFO @ Wed, 28 Jun 2017 00:43:35: 6000000 INFO @ Wed, 28 Jun 2017 00:43:41: 7000000 INFO @ Wed, 28 Jun 2017 00:43:41: 7000000 INFO @ Wed, 28 Jun 2017 00:43:42: 7000000 INFO @ Wed, 28 Jun 2017 00:43:48: 8000000 INFO @ Wed, 28 Jun 2017 00:43:48: 8000000 INFO @ Wed, 28 Jun 2017 00:43:48: 8000000 INFO @ Wed, 28 Jun 2017 00:43:54: 9000000 INFO @ Wed, 28 Jun 2017 00:43:54: 9000000 INFO @ Wed, 28 Jun 2017 00:43:54: 9000000 INFO @ Wed, 28 Jun 2017 00:44:00: 10000000 INFO @ Wed, 28 Jun 2017 00:44:00: 10000000 INFO @ Wed, 28 Jun 2017 00:44:01: 10000000 INFO @ Wed, 28 Jun 2017 00:44:06: 11000000 INFO @ Wed, 28 Jun 2017 00:44:06: 11000000 INFO @ Wed, 28 Jun 2017 00:44:08: 11000000 INFO @ Wed, 28 Jun 2017 00:44:12: 12000000 INFO @ Wed, 28 Jun 2017 00:44:12: 12000000 INFO @ Wed, 28 Jun 2017 00:44:15: 12000000 INFO @ Wed, 28 Jun 2017 00:44:18: 13000000 INFO @ Wed, 28 Jun 2017 00:44:19: 13000000 INFO @ Wed, 28 Jun 2017 00:44:22: 13000000 INFO @ Wed, 28 Jun 2017 00:44:22: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 00:44:22: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 00:44:22: #1 total tags in treatment: 6539419 INFO @ Wed, 28 Jun 2017 00:44:22: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 00:44:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 00:44:22: #1 tags after filtering in treatment: 6061927 INFO @ Wed, 28 Jun 2017 00:44:22: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 28 Jun 2017 00:44:22: #1 finished! INFO @ Wed, 28 Jun 2017 00:44:22: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 00:44:22: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 00:44:23: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 00:44:23: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 00:44:23: #1 total tags in treatment: 6539419 INFO @ Wed, 28 Jun 2017 00:44:23: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 00:44:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 00:44:23: #1 tags after filtering in treatment: 6061927 INFO @ Wed, 28 Jun 2017 00:44:23: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 28 Jun 2017 00:44:23: #1 finished! INFO @ Wed, 28 Jun 2017 00:44:23: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 00:44:23: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 00:44:23: #2 number of paired peaks: 1577 INFO @ Wed, 28 Jun 2017 00:44:23: start model_add_line... INFO @ Wed, 28 Jun 2017 00:44:23: start X-correlation... INFO @ Wed, 28 Jun 2017 00:44:23: end of X-cor INFO @ Wed, 28 Jun 2017 00:44:23: #2 finished! INFO @ Wed, 28 Jun 2017 00:44:23: #2 predicted fragment length is 154 bps INFO @ Wed, 28 Jun 2017 00:44:23: #2 alternative fragment length(s) may be 154 bps INFO @ Wed, 28 Jun 2017 00:44:23: #2.2 Generate R script for model : SRX749029.10_model.r INFO @ Wed, 28 Jun 2017 00:44:23: #3 Call peaks... INFO @ Wed, 28 Jun 2017 00:44:23: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 00:44:23: #2 number of paired peaks: 1577 INFO @ Wed, 28 Jun 2017 00:44:23: start model_add_line... INFO @ Wed, 28 Jun 2017 00:44:23: start X-correlation... INFO @ Wed, 28 Jun 2017 00:44:23: end of X-cor INFO @ Wed, 28 Jun 2017 00:44:23: #2 finished! INFO @ Wed, 28 Jun 2017 00:44:23: #2 predicted fragment length is 154 bps INFO @ Wed, 28 Jun 2017 00:44:23: #2 alternative fragment length(s) may be 154 bps INFO @ Wed, 28 Jun 2017 00:44:23: #2.2 Generate R script for model : SRX749029.05_model.r INFO @ Wed, 28 Jun 2017 00:44:23: #3 Call peaks... INFO @ Wed, 28 Jun 2017 00:44:23: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 00:44:25: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 00:44:25: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 00:44:25: #1 total tags in treatment: 6539419 INFO @ Wed, 28 Jun 2017 00:44:25: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 00:44:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 00:44:25: #1 tags after filtering in treatment: 6061927 INFO @ Wed, 28 Jun 2017 00:44:25: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 28 Jun 2017 00:44:25: #1 finished! INFO @ Wed, 28 Jun 2017 00:44:25: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 00:44:25: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 00:44:26: #2 number of paired peaks: 1577 INFO @ Wed, 28 Jun 2017 00:44:26: start model_add_line... INFO @ Wed, 28 Jun 2017 00:44:26: start X-correlation... INFO @ Wed, 28 Jun 2017 00:44:26: end of X-cor INFO @ Wed, 28 Jun 2017 00:44:26: #2 finished! INFO @ Wed, 28 Jun 2017 00:44:26: #2 predicted fragment length is 154 bps INFO @ Wed, 28 Jun 2017 00:44:26: #2 alternative fragment length(s) may be 154 bps INFO @ Wed, 28 Jun 2017 00:44:26: #2.2 Generate R script for model : SRX749029.20_model.r INFO @ Wed, 28 Jun 2017 00:44:26: #3 Call peaks... INFO @ Wed, 28 Jun 2017 00:44:26: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 00:44:38: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 00:44:39: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 00:44:41: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 00:44:47: #4 Write output xls file... SRX749029.10_peaks.xls INFO @ Wed, 28 Jun 2017 00:44:47: #4 Write peak in narrowPeak format file... SRX749029.10_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 00:44:47: #4 Write summits bed file... SRX749029.10_summits.bed INFO @ Wed, 28 Jun 2017 00:44:47: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2791 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 00:44:47: #4 Write output xls file... SRX749029.05_peaks.xls INFO @ Wed, 28 Jun 2017 00:44:47: #4 Write peak in narrowPeak format file... SRX749029.05_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 00:44:47: #4 Write summits bed file... SRX749029.05_summits.bed INFO @ Wed, 28 Jun 2017 00:44:47: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4959 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 00:44:49: #4 Write output xls file... SRX749029.20_peaks.xls INFO @ Wed, 28 Jun 2017 00:44:49: #4 Write peak in narrowPeak format file... SRX749029.20_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 00:44:49: #4 Write summits bed file... SRX749029.20_summits.bed INFO @ Wed, 28 Jun 2017 00:44:49: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1449 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。