Job ID = 1295477 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 23,362,686 reads read : 46,725,372 reads written : 46,725,372 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:51:34 23362686 reads; of these: 23362686 (100.00%) were paired; of these: 5690786 (24.36%) aligned concordantly 0 times 12943615 (55.40%) aligned concordantly exactly 1 time 4728285 (20.24%) aligned concordantly >1 times ---- 5690786 pairs aligned concordantly 0 times; of these: 116059 (2.04%) aligned discordantly 1 time ---- 5574727 pairs aligned 0 times concordantly or discordantly; of these: 11149454 mates make up the pairs; of these: 9732647 (87.29%) aligned 0 times 616377 (5.53%) aligned exactly 1 time 800430 (7.18%) aligned >1 times 79.17% overall alignment rate Time searching: 00:51:34 Overall time: 00:51:34 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] 1590356 / 17775212 = 0.0895 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 @ Mon, 03 Jun 2019 15:09:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3393679/SRX3393679.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3393679/SRX3393679.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3393679/SRX3393679.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3393679/SRX3393679.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 @ Mon, 03 Jun 2019 15:09:31: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:09:31: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:09:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3393679/SRX3393679.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3393679/SRX3393679.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3393679/SRX3393679.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3393679/SRX3393679.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 @ Mon, 03 Jun 2019 15:09:31: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:09:31: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:09:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3393679/SRX3393679.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3393679/SRX3393679.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3393679/SRX3393679.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3393679/SRX3393679.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 @ Mon, 03 Jun 2019 15:09:31: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:09:31: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:09:38: 1000000 INFO @ Mon, 03 Jun 2019 15:09:40: 1000000 INFO @ Mon, 03 Jun 2019 15:09:42: 1000000 INFO @ Mon, 03 Jun 2019 15:09:45: 2000000 INFO @ Mon, 03 Jun 2019 15:09:47: 2000000 INFO @ Mon, 03 Jun 2019 15:09:52: 3000000 INFO @ Mon, 03 Jun 2019 15:09:53: 2000000 INFO @ Mon, 03 Jun 2019 15:09:54: 3000000 INFO @ Mon, 03 Jun 2019 15:09:58: 4000000 INFO @ Mon, 03 Jun 2019 15:10:00: 4000000 INFO @ Mon, 03 Jun 2019 15:10:04: 3000000 INFO @ Mon, 03 Jun 2019 15:10:05: 5000000 INFO @ Mon, 03 Jun 2019 15:10:07: 5000000 INFO @ Mon, 03 Jun 2019 15:10:12: 6000000 INFO @ Mon, 03 Jun 2019 15:10:14: 4000000 INFO @ Mon, 03 Jun 2019 15:10:14: 6000000 INFO @ Mon, 03 Jun 2019 15:10:19: 7000000 INFO @ Mon, 03 Jun 2019 15:10:21: 7000000 INFO @ Mon, 03 Jun 2019 15:10:25: 5000000 INFO @ Mon, 03 Jun 2019 15:10:26: 8000000 INFO @ Mon, 03 Jun 2019 15:10:28: 8000000 INFO @ Mon, 03 Jun 2019 15:10:33: 9000000 INFO @ Mon, 03 Jun 2019 15:10:35: 9000000 INFO @ Mon, 03 Jun 2019 15:10:35: 6000000 INFO @ Mon, 03 Jun 2019 15:10:40: 10000000 INFO @ Mon, 03 Jun 2019 15:10:42: 10000000 INFO @ Mon, 03 Jun 2019 15:10:46: 7000000 INFO @ Mon, 03 Jun 2019 15:10:46: 11000000 INFO @ Mon, 03 Jun 2019 15:10:49: 11000000 INFO @ Mon, 03 Jun 2019 15:10:53: 12000000 INFO @ Mon, 03 Jun 2019 15:10:55: 12000000 INFO @ Mon, 03 Jun 2019 15:10:56: 8000000 INFO @ Mon, 03 Jun 2019 15:11:00: 13000000 INFO @ Mon, 03 Jun 2019 15:11:02: 13000000 INFO @ Mon, 03 Jun 2019 15:11:07: 9000000 INFO @ Mon, 03 Jun 2019 15:11:07: 14000000 INFO @ Mon, 03 Jun 2019 15:11:09: 14000000 INFO @ Mon, 03 Jun 2019 15:11:14: 15000000 INFO @ Mon, 03 Jun 2019 15:11:16: 15000000 INFO @ Mon, 03 Jun 2019 15:11:17: 10000000 INFO @ Mon, 03 Jun 2019 15:11:21: 16000000 INFO @ Mon, 03 Jun 2019 15:11:23: 16000000 INFO @ Mon, 03 Jun 2019 15:11:27: 17000000 INFO @ Mon, 03 Jun 2019 15:11:28: 11000000 INFO @ Mon, 03 Jun 2019 15:11:30: 17000000 INFO @ Mon, 03 Jun 2019 15:11:34: 18000000 INFO @ Mon, 03 Jun 2019 15:11:36: 18000000 INFO @ Mon, 03 Jun 2019 15:11:38: 12000000 INFO @ Mon, 03 Jun 2019 15:11:41: 19000000 INFO @ Mon, 03 Jun 2019 15:11:43: 19000000 INFO @ Mon, 03 Jun 2019 15:11:48: 20000000 INFO @ Mon, 03 Jun 2019 15:11:48: 13000000 INFO @ Mon, 03 Jun 2019 15:11:50: 20000000 INFO @ Mon, 03 Jun 2019 15:11:55: 21000000 INFO @ Mon, 03 Jun 2019 15:11:57: 21000000 INFO @ Mon, 03 Jun 2019 15:11:59: 14000000 INFO @ Mon, 03 Jun 2019 15:12:02: 22000000 INFO @ Mon, 03 Jun 2019 15:12:04: 22000000 INFO @ Mon, 03 Jun 2019 15:12:08: 23000000 INFO @ Mon, 03 Jun 2019 15:12:09: 15000000 INFO @ Mon, 03 Jun 2019 15:12:11: 23000000 INFO @ Mon, 03 Jun 2019 15:12:15: 24000000 INFO @ Mon, 03 Jun 2019 15:12:17: 24000000 INFO @ Mon, 03 Jun 2019 15:12:19: 16000000 INFO @ Mon, 03 Jun 2019 15:12:22: 25000000 INFO @ Mon, 03 Jun 2019 15:12:24: 25000000 INFO @ Mon, 03 Jun 2019 15:12:29: 26000000 INFO @ Mon, 03 Jun 2019 15:12:29: 17000000 INFO @ Mon, 03 Jun 2019 15:12:31: 26000000 INFO @ Mon, 03 Jun 2019 15:12:36: 27000000 INFO @ Mon, 03 Jun 2019 15:12:38: 27000000 INFO @ Mon, 03 Jun 2019 15:12:40: 18000000 INFO @ Mon, 03 Jun 2019 15:12:42: 28000000 INFO @ Mon, 03 Jun 2019 15:12:45: 28000000 INFO @ Mon, 03 Jun 2019 15:12:49: 29000000 INFO @ Mon, 03 Jun 2019 15:12:50: 19000000 INFO @ Mon, 03 Jun 2019 15:12:52: 29000000 INFO @ Mon, 03 Jun 2019 15:12:59: 30000000 INFO @ Mon, 03 Jun 2019 15:12:59: 20000000 INFO @ Mon, 03 Jun 2019 15:13:00: 30000000 INFO @ Mon, 03 Jun 2019 15:13:06: 31000000 INFO @ Mon, 03 Jun 2019 15:13:07: 31000000 INFO @ Mon, 03 Jun 2019 15:13:09: 21000000 INFO @ Mon, 03 Jun 2019 15:13:13: 32000000 INFO @ Mon, 03 Jun 2019 15:13:14: 32000000 INFO @ Mon, 03 Jun 2019 15:13:19: 22000000 INFO @ Mon, 03 Jun 2019 15:13:20: 33000000 INFO @ Mon, 03 Jun 2019 15:13:21: 33000000 INFO @ Mon, 03 Jun 2019 15:13:26: #1 tag size is determined as 42 bps INFO @ Mon, 03 Jun 2019 15:13:26: #1 tag size = 42 INFO @ Mon, 03 Jun 2019 15:13:26: #1 total tags in treatment: 16084925 INFO @ Mon, 03 Jun 2019 15:13:26: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:13:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 15:13:26: #1 tags after filtering in treatment: 8514334 INFO @ Mon, 03 Jun 2019 15:13:26: #1 Redundant rate of treatment: 0.47 INFO @ Mon, 03 Jun 2019 15:13:26: #1 finished! INFO @ Mon, 03 Jun 2019 15:13:26: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:13:26: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:13:27: #1 tag size is determined as 42 bps INFO @ Mon, 03 Jun 2019 15:13:27: #1 tag size = 42 INFO @ Mon, 03 Jun 2019 15:13:27: #1 total tags in treatment: 16084925 INFO @ Mon, 03 Jun 2019 15:13:27: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:13:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 15:13:27: #1 tags after filtering in treatment: 8514334 INFO @ Mon, 03 Jun 2019 15:13:27: #1 Redundant rate of treatment: 0.47 INFO @ Mon, 03 Jun 2019 15:13:27: #1 finished! INFO @ Mon, 03 Jun 2019 15:13:27: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:13:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:13:28: #2 number of paired peaks: 9975 INFO @ Mon, 03 Jun 2019 15:13:28: start model_add_line... INFO @ Mon, 03 Jun 2019 15:13:28: start X-correlation... INFO @ Mon, 03 Jun 2019 15:13:28: end of X-cor INFO @ Mon, 03 Jun 2019 15:13:28: #2 finished! INFO @ Mon, 03 Jun 2019 15:13:28: #2 predicted fragment length is 199 bps INFO @ Mon, 03 Jun 2019 15:13:28: #2 alternative fragment length(s) may be 199 bps INFO @ Mon, 03 Jun 2019 15:13:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3393679/SRX3393679.05_model.r INFO @ Mon, 03 Jun 2019 15:13:28: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:13:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:13:28: 23000000 INFO @ Mon, 03 Jun 2019 15:13:29: #2 number of paired peaks: 9975 INFO @ Mon, 03 Jun 2019 15:13:29: start model_add_line... INFO @ Mon, 03 Jun 2019 15:13:29: start X-correlation... INFO @ Mon, 03 Jun 2019 15:13:29: end of X-cor INFO @ Mon, 03 Jun 2019 15:13:29: #2 finished! INFO @ Mon, 03 Jun 2019 15:13:29: #2 predicted fragment length is 199 bps INFO @ Mon, 03 Jun 2019 15:13:29: #2 alternative fragment length(s) may be 199 bps INFO @ Mon, 03 Jun 2019 15:13:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3393679/SRX3393679.20_model.r INFO @ Mon, 03 Jun 2019 15:13:29: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:13:29: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:13:37: 24000000 INFO @ Mon, 03 Jun 2019 15:13:46: 25000000 INFO @ Mon, 03 Jun 2019 15:13:56: 26000000 INFO @ Mon, 03 Jun 2019 15:14:03: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:14:04: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:14:05: 27000000 INFO @ Mon, 03 Jun 2019 15:14:14: 28000000 INFO @ Mon, 03 Jun 2019 15:14:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3393679/SRX3393679.05_peaks.xls INFO @ Mon, 03 Jun 2019 15:14:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3393679/SRX3393679.20_peaks.xls INFO @ Mon, 03 Jun 2019 15:14:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3393679/SRX3393679.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:14:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3393679/SRX3393679.20_summits.bed INFO @ Mon, 03 Jun 2019 15:14:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3393679/SRX3393679.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:14:16: Done! INFO @ Mon, 03 Jun 2019 15:14:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3393679/SRX3393679.05_summits.bed INFO @ Mon, 03 Jun 2019 15:14:17: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (8156 records, 4 fields): 17 millis CompletedMACS2peakCalling pass1 - making usageList (15 chroms): 5 millis pass2 - checking and writing primary data (10359 records, 4 fields): 16 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 03 Jun 2019 15:14:23: 29000000 INFO @ Mon, 03 Jun 2019 15:14:32: 30000000 INFO @ Mon, 03 Jun 2019 15:14:41: 31000000 INFO @ Mon, 03 Jun 2019 15:14:50: 32000000 BigWig に変換しました。 INFO @ Mon, 03 Jun 2019 15:15:00: 33000000 INFO @ Mon, 03 Jun 2019 15:15:08: #1 tag size is determined as 42 bps INFO @ Mon, 03 Jun 2019 15:15:08: #1 tag size = 42 INFO @ Mon, 03 Jun 2019 15:15:08: #1 total tags in treatment: 16084925 INFO @ Mon, 03 Jun 2019 15:15:08: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:15:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 15:15:08: #1 tags after filtering in treatment: 8514334 INFO @ Mon, 03 Jun 2019 15:15:08: #1 Redundant rate of treatment: 0.47 INFO @ Mon, 03 Jun 2019 15:15:08: #1 finished! INFO @ Mon, 03 Jun 2019 15:15:08: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:15:08: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:15:10: #2 number of paired peaks: 9975 INFO @ Mon, 03 Jun 2019 15:15:10: start model_add_line... INFO @ Mon, 03 Jun 2019 15:15:10: start X-correlation... INFO @ Mon, 03 Jun 2019 15:15:10: end of X-cor INFO @ Mon, 03 Jun 2019 15:15:10: #2 finished! INFO @ Mon, 03 Jun 2019 15:15:10: #2 predicted fragment length is 199 bps INFO @ Mon, 03 Jun 2019 15:15:10: #2 alternative fragment length(s) may be 199 bps INFO @ Mon, 03 Jun 2019 15:15:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3393679/SRX3393679.10_model.r INFO @ Mon, 03 Jun 2019 15:15:10: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:15:10: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:15:45: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:15:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3393679/SRX3393679.10_peaks.xls INFO @ Mon, 03 Jun 2019 15:15:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3393679/SRX3393679.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:15:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3393679/SRX3393679.10_summits.bed INFO @ Mon, 03 Jun 2019 15:15:58: Done! pass1 - making usageList (15 chroms): 5 millis pass2 - checking and writing primary data (9288 records, 4 fields): 15 millis CompletedMACS2peakCalling