Job ID = 9730444 sra ファイルのダウンロード中... Completed: 1776878K bytes transferred in 28 seconds (515619K 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 25864112 spots for /home/okishinya/chipatlas/results/dm3/SRX2559031/SRR5253495.sra Written 25864112 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: 01:05:16 25864112 reads; of these: 25864112 (100.00%) were paired; of these: 1408212 (5.44%) aligned concordantly 0 times 18922334 (73.16%) aligned concordantly exactly 1 time 5533566 (21.39%) aligned concordantly >1 times ---- 1408212 pairs aligned concordantly 0 times; of these: 13486 (0.96%) aligned discordantly 1 time ---- 1394726 pairs aligned 0 times concordantly or discordantly; of these: 2789452 mates make up the pairs; of these: 1868256 (66.98%) aligned 0 times 677654 (24.29%) aligned exactly 1 time 243542 (8.73%) aligned >1 times 96.39% overall alignment rate Time searching: 01:05:16 Overall time: 01:05:16 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 24 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] 7060307 / 24456384 = 0.2887 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 @ Sun, 03 Sep 2017 02:15:25: # Command line: callpeak -t SRX2559031.bam -f BAM -g dm -n SRX2559031.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2559031.10 # format = BAM # ChIP-seq file = ['SRX2559031.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 @ Sun, 03 Sep 2017 02:15:25: # Command line: callpeak -t SRX2559031.bam -f BAM -g dm -n SRX2559031.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2559031.20 # format = BAM # ChIP-seq file = ['SRX2559031.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 @ Sun, 03 Sep 2017 02:15:25: # Command line: callpeak -t SRX2559031.bam -f BAM -g dm -n SRX2559031.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2559031.05 # format = BAM # ChIP-seq file = ['SRX2559031.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 @ Sun, 03 Sep 2017 02:15:25: #1 read tag files... INFO @ Sun, 03 Sep 2017 02:15:25: #1 read tag files... INFO @ Sun, 03 Sep 2017 02:15:25: #1 read tag files... INFO @ Sun, 03 Sep 2017 02:15:25: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 02:15:25: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 02:15:25: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 02:15:31: 1000000 INFO @ Sun, 03 Sep 2017 02:15:31: 1000000 INFO @ Sun, 03 Sep 2017 02:15:31: 1000000 INFO @ Sun, 03 Sep 2017 02:15:37: 2000000 INFO @ Sun, 03 Sep 2017 02:15:37: 2000000 INFO @ Sun, 03 Sep 2017 02:15:37: 2000000 INFO @ Sun, 03 Sep 2017 02:15:43: 3000000 INFO @ Sun, 03 Sep 2017 02:15:43: 3000000 INFO @ Sun, 03 Sep 2017 02:15:43: 3000000 INFO @ Sun, 03 Sep 2017 02:15:48: 4000000 INFO @ Sun, 03 Sep 2017 02:15:48: 4000000 INFO @ Sun, 03 Sep 2017 02:15:48: 4000000 INFO @ Sun, 03 Sep 2017 02:15:54: 5000000 INFO @ Sun, 03 Sep 2017 02:15:54: 5000000 INFO @ Sun, 03 Sep 2017 02:15:54: 5000000 INFO @ Sun, 03 Sep 2017 02:16:00: 6000000 INFO @ Sun, 03 Sep 2017 02:16:00: 6000000 INFO @ Sun, 03 Sep 2017 02:16:00: 6000000 INFO @ Sun, 03 Sep 2017 02:16:06: 7000000 INFO @ Sun, 03 Sep 2017 02:16:06: 7000000 INFO @ Sun, 03 Sep 2017 02:16:06: 7000000 INFO @ Sun, 03 Sep 2017 02:16:12: 8000000 INFO @ Sun, 03 Sep 2017 02:16:12: 8000000 INFO @ Sun, 03 Sep 2017 02:16:12: 8000000 INFO @ Sun, 03 Sep 2017 02:16:17: 9000000 INFO @ Sun, 03 Sep 2017 02:16:17: 9000000 INFO @ Sun, 03 Sep 2017 02:16:17: 9000000 INFO @ Sun, 03 Sep 2017 02:16:23: 10000000 INFO @ Sun, 03 Sep 2017 02:16:23: 10000000 INFO @ Sun, 03 Sep 2017 02:16:23: 10000000 INFO @ Sun, 03 Sep 2017 02:16:29: 11000000 INFO @ Sun, 03 Sep 2017 02:16:29: 11000000 INFO @ Sun, 03 Sep 2017 02:16:29: 11000000 INFO @ Sun, 03 Sep 2017 02:16:35: 12000000 INFO @ Sun, 03 Sep 2017 02:16:35: 12000000 INFO @ Sun, 03 Sep 2017 02:16:35: 12000000 INFO @ Sun, 03 Sep 2017 02:16:41: 13000000 INFO @ Sun, 03 Sep 2017 02:16:41: 13000000 INFO @ Sun, 03 Sep 2017 02:16:42: 13000000 INFO @ Sun, 03 Sep 2017 02:16:47: 14000000 INFO @ Sun, 03 Sep 2017 02:16:47: 14000000 INFO @ Sun, 03 Sep 2017 02:16:48: 14000000 INFO @ Sun, 03 Sep 2017 02:16:53: 15000000 INFO @ Sun, 03 Sep 2017 02:16:53: 15000000 INFO @ Sun, 03 Sep 2017 02:16:54: 15000000 INFO @ Sun, 03 Sep 2017 02:16:59: 16000000 INFO @ Sun, 03 Sep 2017 02:16:59: 16000000 INFO @ Sun, 03 Sep 2017 02:17:01: 16000000 INFO @ Sun, 03 Sep 2017 02:17:05: 17000000 INFO @ Sun, 03 Sep 2017 02:17:05: 17000000 INFO @ Sun, 03 Sep 2017 02:17:07: 17000000 INFO @ Sun, 03 Sep 2017 02:17:12: 18000000 INFO @ Sun, 03 Sep 2017 02:17:12: 18000000 INFO @ Sun, 03 Sep 2017 02:17:14: 18000000 INFO @ Sun, 03 Sep 2017 02:17:18: 19000000 INFO @ Sun, 03 Sep 2017 02:17:18: 19000000 INFO @ Sun, 03 Sep 2017 02:17:20: 19000000 INFO @ Sun, 03 Sep 2017 02:17:24: 20000000 INFO @ Sun, 03 Sep 2017 02:17:24: 20000000 INFO @ Sun, 03 Sep 2017 02:17:26: 20000000 INFO @ Sun, 03 Sep 2017 02:17:30: 21000000 INFO @ Sun, 03 Sep 2017 02:17:30: 21000000 INFO @ Sun, 03 Sep 2017 02:17:33: 21000000 INFO @ Sun, 03 Sep 2017 02:17:36: 22000000 INFO @ Sun, 03 Sep 2017 02:17:36: 22000000 INFO @ Sun, 03 Sep 2017 02:17:39: 22000000 INFO @ Sun, 03 Sep 2017 02:17:42: 23000000 INFO @ Sun, 03 Sep 2017 02:17:42: 23000000 INFO @ Sun, 03 Sep 2017 02:17:45: 23000000 INFO @ Sun, 03 Sep 2017 02:17:48: 24000000 INFO @ Sun, 03 Sep 2017 02:17:48: 24000000 INFO @ Sun, 03 Sep 2017 02:17:52: 24000000 INFO @ Sun, 03 Sep 2017 02:17:54: 25000000 INFO @ Sun, 03 Sep 2017 02:17:54: 25000000 INFO @ Sun, 03 Sep 2017 02:17:58: 25000000 INFO @ Sun, 03 Sep 2017 02:18:00: 26000000 INFO @ Sun, 03 Sep 2017 02:18:00: 26000000 INFO @ Sun, 03 Sep 2017 02:18:05: 26000000 INFO @ Sun, 03 Sep 2017 02:18:06: 27000000 INFO @ Sun, 03 Sep 2017 02:18:06: 27000000 INFO @ Sun, 03 Sep 2017 02:18:11: 27000000 INFO @ Sun, 03 Sep 2017 02:18:12: 28000000 INFO @ Sun, 03 Sep 2017 02:18:12: 28000000 INFO @ Sun, 03 Sep 2017 02:18:17: 28000000 INFO @ Sun, 03 Sep 2017 02:18:18: 29000000 INFO @ Sun, 03 Sep 2017 02:18:18: 29000000 INFO @ Sun, 03 Sep 2017 02:18:24: 29000000 INFO @ Sun, 03 Sep 2017 02:18:24: 30000000 INFO @ Sun, 03 Sep 2017 02:18:25: 30000000 INFO @ Sun, 03 Sep 2017 02:18:30: 30000000 INFO @ Sun, 03 Sep 2017 02:18:31: 31000000 INFO @ Sun, 03 Sep 2017 02:18:31: 31000000 INFO @ Sun, 03 Sep 2017 02:18:36: 31000000 INFO @ Sun, 03 Sep 2017 02:18:37: 32000000 INFO @ Sun, 03 Sep 2017 02:18:37: 32000000 INFO @ Sun, 03 Sep 2017 02:18:43: 33000000 INFO @ Sun, 03 Sep 2017 02:18:43: 33000000 INFO @ Sun, 03 Sep 2017 02:18:43: 32000000 INFO @ Sun, 03 Sep 2017 02:18:49: 34000000 INFO @ Sun, 03 Sep 2017 02:18:49: 34000000 INFO @ Sun, 03 Sep 2017 02:18:49: 33000000 INFO @ Sun, 03 Sep 2017 02:18:55: 35000000 INFO @ Sun, 03 Sep 2017 02:18:55: 35000000 INFO @ Sun, 03 Sep 2017 02:18:55: 34000000 INFO @ Sun, 03 Sep 2017 02:18:59: #1 tag size is determined as 50 bps INFO @ Sun, 03 Sep 2017 02:18:59: #1 tag size = 50 INFO @ Sun, 03 Sep 2017 02:18:59: #1 total tags in treatment: 17397600 INFO @ Sun, 03 Sep 2017 02:18:59: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 02:18:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 02:18:59: #1 tag size is determined as 50 bps INFO @ Sun, 03 Sep 2017 02:18:59: #1 tag size = 50 INFO @ Sun, 03 Sep 2017 02:18:59: #1 total tags in treatment: 17397600 INFO @ Sun, 03 Sep 2017 02:18:59: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 02:18:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 02:19:00: #1 tags after filtering in treatment: 15242238 INFO @ Sun, 03 Sep 2017 02:19:00: #1 Redundant rate of treatment: 0.12 INFO @ Sun, 03 Sep 2017 02:19:00: #1 finished! INFO @ Sun, 03 Sep 2017 02:19:00: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 02:19:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 02:19:00: #1 tags after filtering in treatment: 15242238 INFO @ Sun, 03 Sep 2017 02:19:00: #1 Redundant rate of treatment: 0.12 INFO @ Sun, 03 Sep 2017 02:19:00: #1 finished! INFO @ Sun, 03 Sep 2017 02:19:00: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 02:19:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 02:19:01: #2 number of paired peaks: 1533 INFO @ Sun, 03 Sep 2017 02:19:01: start model_add_line... INFO @ Sun, 03 Sep 2017 02:19:01: #2 number of paired peaks: 1533 INFO @ Sun, 03 Sep 2017 02:19:01: start model_add_line... INFO @ Sun, 03 Sep 2017 02:19:01: start X-correlation... INFO @ Sun, 03 Sep 2017 02:19:01: start X-correlation... INFO @ Sun, 03 Sep 2017 02:19:01: end of X-cor INFO @ Sun, 03 Sep 2017 02:19:01: #2 finished! INFO @ Sun, 03 Sep 2017 02:19:01: #2 predicted fragment length is 128 bps INFO @ Sun, 03 Sep 2017 02:19:01: #2 alternative fragment length(s) may be 128 bps INFO @ Sun, 03 Sep 2017 02:19:01: #2.2 Generate R script for model : SRX2559031.10_model.r INFO @ Sun, 03 Sep 2017 02:19:01: end of X-cor INFO @ Sun, 03 Sep 2017 02:19:01: #2 finished! INFO @ Sun, 03 Sep 2017 02:19:01: #2 predicted fragment length is 128 bps INFO @ Sun, 03 Sep 2017 02:19:01: #2 alternative fragment length(s) may be 128 bps INFO @ Sun, 03 Sep 2017 02:19:01: #2.2 Generate R script for model : SRX2559031.05_model.r INFO @ Sun, 03 Sep 2017 02:19:01: #3 Call peaks... INFO @ Sun, 03 Sep 2017 02:19:01: #3 Call peaks... INFO @ Sun, 03 Sep 2017 02:19:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Sep 2017 02:19:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Sep 2017 02:19:01: 35000000 INFO @ Sun, 03 Sep 2017 02:19:05: #1 tag size is determined as 50 bps INFO @ Sun, 03 Sep 2017 02:19:05: #1 tag size = 50 INFO @ Sun, 03 Sep 2017 02:19:05: #1 total tags in treatment: 17397600 INFO @ Sun, 03 Sep 2017 02:19:05: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 02:19:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 02:19:06: #1 tags after filtering in treatment: 15242238 INFO @ Sun, 03 Sep 2017 02:19:06: #1 Redundant rate of treatment: 0.12 INFO @ Sun, 03 Sep 2017 02:19:06: #1 finished! INFO @ Sun, 03 Sep 2017 02:19:06: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 02:19:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 02:19:07: #2 number of paired peaks: 1533 INFO @ Sun, 03 Sep 2017 02:19:07: start model_add_line... INFO @ Sun, 03 Sep 2017 02:19:07: start X-correlation... INFO @ Sun, 03 Sep 2017 02:19:07: end of X-cor INFO @ Sun, 03 Sep 2017 02:19:07: #2 finished! INFO @ Sun, 03 Sep 2017 02:19:07: #2 predicted fragment length is 128 bps INFO @ Sun, 03 Sep 2017 02:19:07: #2 alternative fragment length(s) may be 128 bps INFO @ Sun, 03 Sep 2017 02:19:07: #2.2 Generate R script for model : SRX2559031.20_model.r INFO @ Sun, 03 Sep 2017 02:19:07: #3 Call peaks... INFO @ Sun, 03 Sep 2017 02:19:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Sep 2017 02:19:37: #3 Call peaks for each chromosome... INFO @ Sun, 03 Sep 2017 02:19:39: #3 Call peaks for each chromosome... INFO @ Sun, 03 Sep 2017 02:19:46: #3 Call peaks for each chromosome... INFO @ Sun, 03 Sep 2017 02:19:56: #4 Write output xls file... SRX2559031.05_peaks.xls INFO @ Sun, 03 Sep 2017 02:19:56: #4 Write peak in narrowPeak format file... SRX2559031.05_peaks.narrowPeak INFO @ Sun, 03 Sep 2017 02:19:56: #4 Write summits bed file... SRX2559031.05_summits.bed INFO @ Sun, 03 Sep 2017 02:19:56: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7783 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 03 Sep 2017 02:19:59: #4 Write output xls file... SRX2559031.10_peaks.xls INFO @ Sun, 03 Sep 2017 02:19:59: #4 Write peak in narrowPeak format file... SRX2559031.10_peaks.narrowPeak INFO @ Sun, 03 Sep 2017 02:19:59: #4 Write summits bed file... SRX2559031.10_summits.bed INFO @ Sun, 03 Sep 2017 02:19:59: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3618 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 03 Sep 2017 02:20:05: #4 Write output xls file... SRX2559031.20_peaks.xls INFO @ Sun, 03 Sep 2017 02:20:05: #4 Write peak in narrowPeak format file... SRX2559031.20_peaks.narrowPeak INFO @ Sun, 03 Sep 2017 02:20:05: #4 Write summits bed file... SRX2559031.20_summits.bed INFO @ Sun, 03 Sep 2017 02:20:05: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1603 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。