Job ID = 10320361 sra ファイルのダウンロード中... Completed: 468719K bytes transferred in 59 seconds (64240K bits/sec), in 1 file. 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 21038377 spots for /home/okishinya/chipatlas/results/dm3/SRX3293414/SRR6183239.sra Written 21038377 spots total rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません 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: 00:39:25 21038377 reads; of these: 21038377 (100.00%) were paired; of these: 9913308 (47.12%) aligned concordantly 0 times 5387875 (25.61%) aligned concordantly exactly 1 time 5737194 (27.27%) aligned concordantly >1 times ---- 9913308 pairs aligned concordantly 0 times; of these: 399196 (4.03%) aligned discordantly 1 time ---- 9514112 pairs aligned 0 times concordantly or discordantly; of these: 19028224 mates make up the pairs; of these: 15530173 (81.62%) aligned 0 times 1565634 (8.23%) aligned exactly 1 time 1932417 (10.16%) aligned >1 times 63.09% overall alignment rate Time searching: 00:39:25 Overall time: 00:39:25 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] 2985670 / 11259637 = 0.2652 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 @ Thu, 11 Jan 2018 02:53:36: # Command line: callpeak -t SRX3293414.bam -f BAM -g dm -n SRX3293414.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3293414.05 # format = BAM # ChIP-seq file = ['SRX3293414.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 @ Thu, 11 Jan 2018 02:53:36: #1 read tag files... INFO @ Thu, 11 Jan 2018 02:53:36: #1 read treatment tags... INFO @ Thu, 11 Jan 2018 02:53:36: # Command line: callpeak -t SRX3293414.bam -f BAM -g dm -n SRX3293414.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3293414.20 # format = BAM # ChIP-seq file = ['SRX3293414.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 @ Thu, 11 Jan 2018 02:53:36: #1 read tag files... INFO @ Thu, 11 Jan 2018 02:53:36: #1 read treatment tags... INFO @ Thu, 11 Jan 2018 02:53:36: # Command line: callpeak -t SRX3293414.bam -f BAM -g dm -n SRX3293414.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3293414.10 # format = BAM # ChIP-seq file = ['SRX3293414.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 @ Thu, 11 Jan 2018 02:53:36: #1 read tag files... INFO @ Thu, 11 Jan 2018 02:53:36: #1 read treatment tags... INFO @ Thu, 11 Jan 2018 02:53:41: 1000000 INFO @ Thu, 11 Jan 2018 02:53:41: 1000000 INFO @ Thu, 11 Jan 2018 02:53:41: 1000000 INFO @ Thu, 11 Jan 2018 02:53:46: 2000000 INFO @ Thu, 11 Jan 2018 02:53:47: 2000000 INFO @ Thu, 11 Jan 2018 02:53:47: 2000000 INFO @ Thu, 11 Jan 2018 02:53:51: 3000000 INFO @ Thu, 11 Jan 2018 02:53:52: 3000000 INFO @ Thu, 11 Jan 2018 02:53:52: 3000000 INFO @ Thu, 11 Jan 2018 02:53:56: 4000000 INFO @ Thu, 11 Jan 2018 02:53:57: 4000000 INFO @ Thu, 11 Jan 2018 02:53:57: 4000000 INFO @ Thu, 11 Jan 2018 02:54:01: 5000000 INFO @ Thu, 11 Jan 2018 02:54:03: 5000000 INFO @ Thu, 11 Jan 2018 02:54:03: 5000000 INFO @ Thu, 11 Jan 2018 02:54:06: 6000000 INFO @ Thu, 11 Jan 2018 02:54:08: 6000000 INFO @ Thu, 11 Jan 2018 02:54:08: 6000000 INFO @ Thu, 11 Jan 2018 02:54:11: 7000000 INFO @ Thu, 11 Jan 2018 02:54:14: 7000000 INFO @ Thu, 11 Jan 2018 02:54:14: 7000000 INFO @ Thu, 11 Jan 2018 02:54:16: 8000000 INFO @ Thu, 11 Jan 2018 02:54:19: 8000000 INFO @ Thu, 11 Jan 2018 02:54:19: 8000000 INFO @ Thu, 11 Jan 2018 02:54:22: 9000000 INFO @ Thu, 11 Jan 2018 02:54:24: 9000000 INFO @ Thu, 11 Jan 2018 02:54:24: 9000000 INFO @ Thu, 11 Jan 2018 02:54:27: 10000000 INFO @ Thu, 11 Jan 2018 02:54:30: 10000000 INFO @ Thu, 11 Jan 2018 02:54:30: 10000000 INFO @ Thu, 11 Jan 2018 02:54:32: 11000000 INFO @ Thu, 11 Jan 2018 02:54:35: 11000000 INFO @ Thu, 11 Jan 2018 02:54:35: 11000000 INFO @ Thu, 11 Jan 2018 02:54:37: 12000000 INFO @ Thu, 11 Jan 2018 02:54:41: 12000000 INFO @ Thu, 11 Jan 2018 02:54:41: 12000000 INFO @ Thu, 11 Jan 2018 02:54:42: 13000000 INFO @ Thu, 11 Jan 2018 02:54:46: 13000000 INFO @ Thu, 11 Jan 2018 02:54:46: 13000000 INFO @ Thu, 11 Jan 2018 02:54:47: 14000000 INFO @ Thu, 11 Jan 2018 02:54:51: 14000000 INFO @ Thu, 11 Jan 2018 02:54:51: 14000000 INFO @ Thu, 11 Jan 2018 02:54:52: 15000000 INFO @ Thu, 11 Jan 2018 02:54:56: 15000000 INFO @ Thu, 11 Jan 2018 02:54:56: 15000000 INFO @ Thu, 11 Jan 2018 02:54:57: 16000000 INFO @ Thu, 11 Jan 2018 02:55:02: 17000000 INFO @ Thu, 11 Jan 2018 02:55:02: 16000000 INFO @ Thu, 11 Jan 2018 02:55:02: 16000000 INFO @ Thu, 11 Jan 2018 02:55:07: 18000000 INFO @ Thu, 11 Jan 2018 02:55:07: 17000000 INFO @ Thu, 11 Jan 2018 02:55:07: 17000000 INFO @ Thu, 11 Jan 2018 02:55:12: 19000000 INFO @ Thu, 11 Jan 2018 02:55:12: 18000000 INFO @ Thu, 11 Jan 2018 02:55:12: 18000000 INFO @ Thu, 11 Jan 2018 02:55:17: 20000000 INFO @ Thu, 11 Jan 2018 02:55:17: 19000000 INFO @ Thu, 11 Jan 2018 02:55:17: 19000000 INFO @ Thu, 11 Jan 2018 02:55:19: #1 tag size is determined as 25 bps INFO @ Thu, 11 Jan 2018 02:55:19: #1 tag size = 25 INFO @ Thu, 11 Jan 2018 02:55:19: #1 total tags in treatment: 8146672 INFO @ Thu, 11 Jan 2018 02:55:19: #1 user defined the maximum tags... INFO @ Thu, 11 Jan 2018 02:55:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 11 Jan 2018 02:55:20: #1 tags after filtering in treatment: 6913469 INFO @ Thu, 11 Jan 2018 02:55:20: #1 Redundant rate of treatment: 0.15 INFO @ Thu, 11 Jan 2018 02:55:20: #1 finished! INFO @ Thu, 11 Jan 2018 02:55:20: #2 Build Peak Model... INFO @ Thu, 11 Jan 2018 02:55:20: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 11 Jan 2018 02:55:20: #2 number of paired peaks: 1030 INFO @ Thu, 11 Jan 2018 02:55:20: start model_add_line... INFO @ Thu, 11 Jan 2018 02:55:20: start X-correlation... INFO @ Thu, 11 Jan 2018 02:55:20: end of X-cor INFO @ Thu, 11 Jan 2018 02:55:20: #2 finished! INFO @ Thu, 11 Jan 2018 02:55:20: #2 predicted fragment length is 105 bps INFO @ Thu, 11 Jan 2018 02:55:20: #2 alternative fragment length(s) may be 105 bps INFO @ Thu, 11 Jan 2018 02:55:20: #2.2 Generate R script for model : SRX3293414.10_model.r INFO @ Thu, 11 Jan 2018 02:55:20: #3 Call peaks... INFO @ Thu, 11 Jan 2018 02:55:20: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 11 Jan 2018 02:55:23: 20000000 INFO @ Thu, 11 Jan 2018 02:55:23: 20000000 INFO @ Thu, 11 Jan 2018 02:55:26: #1 tag size is determined as 25 bps INFO @ Thu, 11 Jan 2018 02:55:26: #1 tag size = 25 INFO @ Thu, 11 Jan 2018 02:55:26: #1 total tags in treatment: 8146672 INFO @ Thu, 11 Jan 2018 02:55:26: #1 user defined the maximum tags... INFO @ Thu, 11 Jan 2018 02:55:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 11 Jan 2018 02:55:26: #1 tag size is determined as 25 bps INFO @ Thu, 11 Jan 2018 02:55:26: #1 tag size = 25 INFO @ Thu, 11 Jan 2018 02:55:26: #1 total tags in treatment: 8146672 INFO @ Thu, 11 Jan 2018 02:55:26: #1 user defined the maximum tags... INFO @ Thu, 11 Jan 2018 02:55:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 11 Jan 2018 02:55:26: #1 tags after filtering in treatment: 6913469 INFO @ Thu, 11 Jan 2018 02:55:26: #1 Redundant rate of treatment: 0.15 INFO @ Thu, 11 Jan 2018 02:55:26: #1 finished! INFO @ Thu, 11 Jan 2018 02:55:26: #2 Build Peak Model... INFO @ Thu, 11 Jan 2018 02:55:26: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 11 Jan 2018 02:55:26: #1 tags after filtering in treatment: 6913469 INFO @ Thu, 11 Jan 2018 02:55:26: #1 Redundant rate of treatment: 0.15 INFO @ Thu, 11 Jan 2018 02:55:26: #1 finished! INFO @ Thu, 11 Jan 2018 02:55:26: #2 Build Peak Model... INFO @ Thu, 11 Jan 2018 02:55:26: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 11 Jan 2018 02:55:27: #2 number of paired peaks: 1030 INFO @ Thu, 11 Jan 2018 02:55:27: start model_add_line... INFO @ Thu, 11 Jan 2018 02:55:27: #2 number of paired peaks: 1030 INFO @ Thu, 11 Jan 2018 02:55:27: start model_add_line... INFO @ Thu, 11 Jan 2018 02:55:27: start X-correlation... INFO @ Thu, 11 Jan 2018 02:55:27: end of X-cor INFO @ Thu, 11 Jan 2018 02:55:27: #2 finished! INFO @ Thu, 11 Jan 2018 02:55:27: #2 predicted fragment length is 105 bps INFO @ Thu, 11 Jan 2018 02:55:27: #2 alternative fragment length(s) may be 105 bps INFO @ Thu, 11 Jan 2018 02:55:27: #2.2 Generate R script for model : SRX3293414.20_model.r INFO @ Thu, 11 Jan 2018 02:55:27: #3 Call peaks... INFO @ Thu, 11 Jan 2018 02:55:27: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 11 Jan 2018 02:55:27: start X-correlation... INFO @ Thu, 11 Jan 2018 02:55:27: end of X-cor INFO @ Thu, 11 Jan 2018 02:55:27: #2 finished! INFO @ Thu, 11 Jan 2018 02:55:27: #2 predicted fragment length is 105 bps INFO @ Thu, 11 Jan 2018 02:55:27: #2 alternative fragment length(s) may be 105 bps INFO @ Thu, 11 Jan 2018 02:55:27: #2.2 Generate R script for model : SRX3293414.05_model.r INFO @ Thu, 11 Jan 2018 02:55:27: #3 Call peaks... INFO @ Thu, 11 Jan 2018 02:55:27: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 11 Jan 2018 02:55:36: #3 Call peaks for each chromosome... INFO @ Thu, 11 Jan 2018 02:55:42: #3 Call peaks for each chromosome... INFO @ Thu, 11 Jan 2018 02:55:43: #3 Call peaks for each chromosome... INFO @ Thu, 11 Jan 2018 02:55:44: #4 Write output xls file... SRX3293414.10_peaks.xls INFO @ Thu, 11 Jan 2018 02:55:44: #4 Write peak in narrowPeak format file... SRX3293414.10_peaks.narrowPeak INFO @ Thu, 11 Jan 2018 02:55:44: #4 Write summits bed file... SRX3293414.10_summits.bed INFO @ Thu, 11 Jan 2018 02:55:44: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1422 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 11 Jan 2018 02:55:51: #4 Write output xls file... SRX3293414.20_peaks.xls INFO @ Thu, 11 Jan 2018 02:55:51: #4 Write peak in narrowPeak format file... SRX3293414.20_peaks.narrowPeak INFO @ Thu, 11 Jan 2018 02:55:51: #4 Write summits bed file... SRX3293414.20_summits.bed INFO @ Thu, 11 Jan 2018 02:55:51: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (642 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 11 Jan 2018 02:55:52: #4 Write output xls file... SRX3293414.05_peaks.xls INFO @ Thu, 11 Jan 2018 02:55:52: #4 Write peak in narrowPeak format file... SRX3293414.05_peaks.narrowPeak INFO @ Thu, 11 Jan 2018 02:55:52: #4 Write summits bed file... SRX3293414.05_summits.bed INFO @ Thu, 11 Jan 2018 02:55:52: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2190 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。