Job ID = 2590956 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 19,638,434 reads read : 39,276,868 reads written : 39,276,868 rm: cannot remove ‘[DSE]RR*’: No such file or directory 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: 00:41:14 19638434 reads; of these: 19638434 (100.00%) were paired; of these: 4880911 (24.85%) aligned concordantly 0 times 10360949 (52.76%) aligned concordantly exactly 1 time 4396574 (22.39%) aligned concordantly >1 times ---- 4880911 pairs aligned concordantly 0 times; of these: 644256 (13.20%) aligned discordantly 1 time ---- 4236655 pairs aligned 0 times concordantly or discordantly; of these: 8473310 mates make up the pairs; of these: 7161000 (84.51%) aligned 0 times 511080 (6.03%) aligned exactly 1 time 801230 (9.46%) aligned >1 times 81.77% overall alignment rate Time searching: 00:41:14 Overall time: 00:41:14 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 16 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] 2192957 / 15278288 = 0.1435 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, 13 Aug 2019 01:12:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5865772/SRX5865772.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5865772/SRX5865772.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5865772/SRX5865772.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5865772/SRX5865772.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, 13 Aug 2019 01:12:59: #1 read tag files... INFO @ Tue, 13 Aug 2019 01:12:59: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 01:13:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5865772/SRX5865772.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5865772/SRX5865772.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5865772/SRX5865772.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5865772/SRX5865772.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, 13 Aug 2019 01:13:00: #1 read tag files... INFO @ Tue, 13 Aug 2019 01:13:00: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 01:13:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5865772/SRX5865772.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5865772/SRX5865772.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5865772/SRX5865772.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5865772/SRX5865772.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, 13 Aug 2019 01:13:01: #1 read tag files... INFO @ Tue, 13 Aug 2019 01:13:01: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 01:13:08: 1000000 INFO @ Tue, 13 Aug 2019 01:13:10: 1000000 INFO @ Tue, 13 Aug 2019 01:13:11: 1000000 INFO @ Tue, 13 Aug 2019 01:13:17: 2000000 INFO @ Tue, 13 Aug 2019 01:13:19: 2000000 INFO @ Tue, 13 Aug 2019 01:13:19: 2000000 INFO @ Tue, 13 Aug 2019 01:13:24: 3000000 INFO @ Tue, 13 Aug 2019 01:13:27: 3000000 INFO @ Tue, 13 Aug 2019 01:13:28: 3000000 INFO @ Tue, 13 Aug 2019 01:13:31: 4000000 INFO @ Tue, 13 Aug 2019 01:13:35: 4000000 INFO @ Tue, 13 Aug 2019 01:13:35: 4000000 INFO @ Tue, 13 Aug 2019 01:13:38: 5000000 INFO @ Tue, 13 Aug 2019 01:13:42: 5000000 INFO @ Tue, 13 Aug 2019 01:13:43: 5000000 INFO @ Tue, 13 Aug 2019 01:13:45: 6000000 INFO @ Tue, 13 Aug 2019 01:13:50: 6000000 INFO @ Tue, 13 Aug 2019 01:13:51: 6000000 INFO @ Tue, 13 Aug 2019 01:13:52: 7000000 INFO @ Tue, 13 Aug 2019 01:13:58: 7000000 INFO @ Tue, 13 Aug 2019 01:13:59: 7000000 INFO @ Tue, 13 Aug 2019 01:14:00: 8000000 INFO @ Tue, 13 Aug 2019 01:14:07: 8000000 INFO @ Tue, 13 Aug 2019 01:14:08: 8000000 INFO @ Tue, 13 Aug 2019 01:14:09: 9000000 INFO @ Tue, 13 Aug 2019 01:14:17: 9000000 INFO @ Tue, 13 Aug 2019 01:14:18: 9000000 INFO @ Tue, 13 Aug 2019 01:14:19: 10000000 INFO @ Tue, 13 Aug 2019 01:14:26: 10000000 INFO @ Tue, 13 Aug 2019 01:14:27: 10000000 INFO @ Tue, 13 Aug 2019 01:14:28: 11000000 INFO @ Tue, 13 Aug 2019 01:14:35: 11000000 INFO @ Tue, 13 Aug 2019 01:14:36: 11000000 INFO @ Tue, 13 Aug 2019 01:14:37: 12000000 INFO @ Tue, 13 Aug 2019 01:14:44: 12000000 INFO @ Tue, 13 Aug 2019 01:14:45: 12000000 INFO @ Tue, 13 Aug 2019 01:14:46: 13000000 INFO @ Tue, 13 Aug 2019 01:14:51: 13000000 INFO @ Tue, 13 Aug 2019 01:14:53: 13000000 INFO @ Tue, 13 Aug 2019 01:14:54: 14000000 INFO @ Tue, 13 Aug 2019 01:14:58: 14000000 INFO @ Tue, 13 Aug 2019 01:15:01: 14000000 INFO @ Tue, 13 Aug 2019 01:15:02: 15000000 INFO @ Tue, 13 Aug 2019 01:15:05: 15000000 INFO @ Tue, 13 Aug 2019 01:15:09: 15000000 INFO @ Tue, 13 Aug 2019 01:15:10: 16000000 INFO @ Tue, 13 Aug 2019 01:15:12: 16000000 INFO @ Tue, 13 Aug 2019 01:15:17: 16000000 INFO @ Tue, 13 Aug 2019 01:15:17: 17000000 INFO @ Tue, 13 Aug 2019 01:15:19: 17000000 INFO @ Tue, 13 Aug 2019 01:15:24: 17000000 INFO @ Tue, 13 Aug 2019 01:15:25: 18000000 INFO @ Tue, 13 Aug 2019 01:15:26: 18000000 INFO @ Tue, 13 Aug 2019 01:15:32: 18000000 INFO @ Tue, 13 Aug 2019 01:15:32: 19000000 INFO @ Tue, 13 Aug 2019 01:15:33: 19000000 INFO @ Tue, 13 Aug 2019 01:15:39: 20000000 INFO @ Tue, 13 Aug 2019 01:15:40: 19000000 INFO @ Tue, 13 Aug 2019 01:15:41: 20000000 INFO @ Tue, 13 Aug 2019 01:15:46: 21000000 INFO @ Tue, 13 Aug 2019 01:15:47: 20000000 INFO @ Tue, 13 Aug 2019 01:15:48: 21000000 INFO @ Tue, 13 Aug 2019 01:15:53: 22000000 INFO @ Tue, 13 Aug 2019 01:15:55: 21000000 INFO @ Tue, 13 Aug 2019 01:15:56: 22000000 INFO @ Tue, 13 Aug 2019 01:16:01: 23000000 INFO @ Tue, 13 Aug 2019 01:16:03: 22000000 INFO @ Tue, 13 Aug 2019 01:16:04: 23000000 INFO @ Tue, 13 Aug 2019 01:16:10: 24000000 INFO @ Tue, 13 Aug 2019 01:16:12: 23000000 INFO @ Tue, 13 Aug 2019 01:16:14: 24000000 INFO @ Tue, 13 Aug 2019 01:16:20: 25000000 INFO @ Tue, 13 Aug 2019 01:16:21: 24000000 INFO @ Tue, 13 Aug 2019 01:16:23: 25000000 INFO @ Tue, 13 Aug 2019 01:16:29: 26000000 INFO @ Tue, 13 Aug 2019 01:16:31: 25000000 INFO @ Tue, 13 Aug 2019 01:16:32: 26000000 INFO @ Tue, 13 Aug 2019 01:16:38: 27000000 INFO @ Tue, 13 Aug 2019 01:16:40: 26000000 INFO @ Tue, 13 Aug 2019 01:16:41: 27000000 INFO @ Tue, 13 Aug 2019 01:16:45: #1 tag size is determined as 50 bps INFO @ Tue, 13 Aug 2019 01:16:45: #1 tag size = 50 INFO @ Tue, 13 Aug 2019 01:16:45: #1 total tags in treatment: 12619666 INFO @ Tue, 13 Aug 2019 01:16:45: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 01:16:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 13 Aug 2019 01:16:45: #1 tags after filtering in treatment: 10463900 INFO @ Tue, 13 Aug 2019 01:16:45: #1 Redundant rate of treatment: 0.17 INFO @ Tue, 13 Aug 2019 01:16:45: #1 finished! INFO @ Tue, 13 Aug 2019 01:16:45: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 01:16:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 01:16:46: #2 number of paired peaks: 468 WARNING @ Tue, 13 Aug 2019 01:16:46: Fewer paired peaks (468) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 468 pairs to build model! INFO @ Tue, 13 Aug 2019 01:16:46: start model_add_line... INFO @ Tue, 13 Aug 2019 01:16:46: start X-correlation... INFO @ Tue, 13 Aug 2019 01:16:46: end of X-cor INFO @ Tue, 13 Aug 2019 01:16:46: #2 finished! INFO @ Tue, 13 Aug 2019 01:16:46: #2 predicted fragment length is 116 bps INFO @ Tue, 13 Aug 2019 01:16:46: #2 alternative fragment length(s) may be 3,116 bps INFO @ Tue, 13 Aug 2019 01:16:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5865772/SRX5865772.10_model.r INFO @ Tue, 13 Aug 2019 01:16:46: #3 Call peaks... INFO @ Tue, 13 Aug 2019 01:16:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 01:16:48: #1 tag size is determined as 50 bps INFO @ Tue, 13 Aug 2019 01:16:48: #1 tag size = 50 INFO @ Tue, 13 Aug 2019 01:16:48: #1 total tags in treatment: 12619666 INFO @ Tue, 13 Aug 2019 01:16:48: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 01:16:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 13 Aug 2019 01:16:48: #1 tags after filtering in treatment: 10463900 INFO @ Tue, 13 Aug 2019 01:16:48: #1 Redundant rate of treatment: 0.17 INFO @ Tue, 13 Aug 2019 01:16:48: #1 finished! INFO @ Tue, 13 Aug 2019 01:16:48: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 01:16:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 01:16:48: 27000000 INFO @ Tue, 13 Aug 2019 01:16:49: #2 number of paired peaks: 468 WARNING @ Tue, 13 Aug 2019 01:16:49: Fewer paired peaks (468) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 468 pairs to build model! INFO @ Tue, 13 Aug 2019 01:16:49: start model_add_line... INFO @ Tue, 13 Aug 2019 01:16:49: start X-correlation... INFO @ Tue, 13 Aug 2019 01:16:49: end of X-cor INFO @ Tue, 13 Aug 2019 01:16:49: #2 finished! INFO @ Tue, 13 Aug 2019 01:16:49: #2 predicted fragment length is 116 bps INFO @ Tue, 13 Aug 2019 01:16:49: #2 alternative fragment length(s) may be 3,116 bps INFO @ Tue, 13 Aug 2019 01:16:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5865772/SRX5865772.05_model.r INFO @ Tue, 13 Aug 2019 01:16:49: #3 Call peaks... INFO @ Tue, 13 Aug 2019 01:16:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 01:16:53: #1 tag size is determined as 50 bps INFO @ Tue, 13 Aug 2019 01:16:53: #1 tag size = 50 INFO @ Tue, 13 Aug 2019 01:16:53: #1 total tags in treatment: 12619666 INFO @ Tue, 13 Aug 2019 01:16:53: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 01:16:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 13 Aug 2019 01:16:54: #1 tags after filtering in treatment: 10463900 INFO @ Tue, 13 Aug 2019 01:16:54: #1 Redundant rate of treatment: 0.17 INFO @ Tue, 13 Aug 2019 01:16:54: #1 finished! INFO @ Tue, 13 Aug 2019 01:16:54: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 01:16:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 01:16:55: #2 number of paired peaks: 468 WARNING @ Tue, 13 Aug 2019 01:16:55: Fewer paired peaks (468) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 468 pairs to build model! INFO @ Tue, 13 Aug 2019 01:16:55: start model_add_line... INFO @ Tue, 13 Aug 2019 01:16:55: start X-correlation... INFO @ Tue, 13 Aug 2019 01:16:55: end of X-cor INFO @ Tue, 13 Aug 2019 01:16:55: #2 finished! INFO @ Tue, 13 Aug 2019 01:16:55: #2 predicted fragment length is 116 bps INFO @ Tue, 13 Aug 2019 01:16:55: #2 alternative fragment length(s) may be 3,116 bps INFO @ Tue, 13 Aug 2019 01:16:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5865772/SRX5865772.20_model.r INFO @ Tue, 13 Aug 2019 01:16:55: #3 Call peaks... INFO @ Tue, 13 Aug 2019 01:16:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 01:17:16: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 01:17:19: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 01:17:24: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 01:17:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5865772/SRX5865772.10_peaks.xls INFO @ Tue, 13 Aug 2019 01:17:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5865772/SRX5865772.10_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 01:17:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5865772/SRX5865772.10_summits.bed INFO @ Tue, 13 Aug 2019 01:17:31: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (578 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 01:17:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5865772/SRX5865772.05_peaks.xls INFO @ Tue, 13 Aug 2019 01:17:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5865772/SRX5865772.05_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 01:17:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5865772/SRX5865772.05_summits.bed INFO @ Tue, 13 Aug 2019 01:17:34: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2431 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 01:17:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5865772/SRX5865772.20_peaks.xls INFO @ Tue, 13 Aug 2019 01:17:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5865772/SRX5865772.20_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 01:17:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5865772/SRX5865772.20_summits.bed INFO @ Tue, 13 Aug 2019 01:17:40: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (228 records, 4 fields): 21 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。