Job ID = 1299214 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 21,490,501 reads read : 42,981,002 reads written : 42,981,002 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: 00:34:13 21490501 reads; of these: 21490501 (100.00%) were paired; of these: 1985793 (9.24%) aligned concordantly 0 times 16559159 (77.05%) aligned concordantly exactly 1 time 2945549 (13.71%) aligned concordantly >1 times ---- 1985793 pairs aligned concordantly 0 times; of these: 225278 (11.34%) aligned discordantly 1 time ---- 1760515 pairs aligned 0 times concordantly or discordantly; of these: 3521030 mates make up the pairs; of these: 2880366 (81.80%) aligned 0 times 521654 (14.82%) aligned exactly 1 time 119010 (3.38%) aligned >1 times 93.30% overall alignment rate Time searching: 00:34:13 Overall time: 00:34:13 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 20 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] 4154502 / 19717753 = 0.2107 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 19:07:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474567/SRX474567.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474567/SRX474567.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474567/SRX474567.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474567/SRX474567.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 19:07:10: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:07:10: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:07:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474567/SRX474567.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474567/SRX474567.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474567/SRX474567.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474567/SRX474567.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 19:07:10: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:07:10: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:07:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474567/SRX474567.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474567/SRX474567.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474567/SRX474567.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474567/SRX474567.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 19:07:10: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:07:10: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:07:19: 1000000 INFO @ Mon, 03 Jun 2019 19:07:19: 1000000 INFO @ Mon, 03 Jun 2019 19:07:20: 1000000 INFO @ Mon, 03 Jun 2019 19:07:28: 2000000 INFO @ Mon, 03 Jun 2019 19:07:29: 2000000 INFO @ Mon, 03 Jun 2019 19:07:30: 2000000 INFO @ Mon, 03 Jun 2019 19:07:37: 3000000 INFO @ Mon, 03 Jun 2019 19:07:38: 3000000 INFO @ Mon, 03 Jun 2019 19:07:40: 3000000 INFO @ Mon, 03 Jun 2019 19:07:46: 4000000 INFO @ Mon, 03 Jun 2019 19:07:47: 4000000 INFO @ Mon, 03 Jun 2019 19:07:50: 4000000 INFO @ Mon, 03 Jun 2019 19:07:55: 5000000 INFO @ Mon, 03 Jun 2019 19:07:56: 5000000 INFO @ Mon, 03 Jun 2019 19:08:00: 5000000 INFO @ Mon, 03 Jun 2019 19:08:04: 6000000 INFO @ Mon, 03 Jun 2019 19:08:05: 6000000 INFO @ Mon, 03 Jun 2019 19:08:11: 6000000 INFO @ Mon, 03 Jun 2019 19:08:13: 7000000 INFO @ Mon, 03 Jun 2019 19:08:14: 7000000 INFO @ Mon, 03 Jun 2019 19:08:21: 7000000 INFO @ Mon, 03 Jun 2019 19:08:22: 8000000 INFO @ Mon, 03 Jun 2019 19:08:24: 8000000 INFO @ Mon, 03 Jun 2019 19:08:31: 8000000 INFO @ Mon, 03 Jun 2019 19:08:31: 9000000 INFO @ Mon, 03 Jun 2019 19:08:33: 9000000 INFO @ Mon, 03 Jun 2019 19:08:40: 10000000 INFO @ Mon, 03 Jun 2019 19:08:41: 9000000 INFO @ Mon, 03 Jun 2019 19:08:42: 10000000 INFO @ Mon, 03 Jun 2019 19:08:48: 11000000 INFO @ Mon, 03 Jun 2019 19:08:51: 10000000 INFO @ Mon, 03 Jun 2019 19:08:51: 11000000 INFO @ Mon, 03 Jun 2019 19:08:57: 12000000 INFO @ Mon, 03 Jun 2019 19:09:00: 12000000 INFO @ Mon, 03 Jun 2019 19:09:01: 11000000 INFO @ Mon, 03 Jun 2019 19:09:06: 13000000 INFO @ Mon, 03 Jun 2019 19:09:09: 13000000 INFO @ Mon, 03 Jun 2019 19:09:11: 12000000 INFO @ Mon, 03 Jun 2019 19:09:15: 14000000 INFO @ Mon, 03 Jun 2019 19:09:18: 14000000 INFO @ Mon, 03 Jun 2019 19:09:21: 13000000 INFO @ Mon, 03 Jun 2019 19:09:23: 15000000 INFO @ Mon, 03 Jun 2019 19:09:27: 15000000 INFO @ Mon, 03 Jun 2019 19:09:30: 14000000 INFO @ Mon, 03 Jun 2019 19:09:32: 16000000 INFO @ Mon, 03 Jun 2019 19:09:36: 16000000 INFO @ Mon, 03 Jun 2019 19:09:40: 15000000 INFO @ Mon, 03 Jun 2019 19:09:41: 17000000 INFO @ Mon, 03 Jun 2019 19:09:45: 17000000 INFO @ Mon, 03 Jun 2019 19:09:49: 18000000 INFO @ Mon, 03 Jun 2019 19:09:50: 16000000 INFO @ Mon, 03 Jun 2019 19:09:53: 18000000 INFO @ Mon, 03 Jun 2019 19:09:58: 19000000 INFO @ Mon, 03 Jun 2019 19:10:00: 17000000 INFO @ Mon, 03 Jun 2019 19:10:02: 19000000 INFO @ Mon, 03 Jun 2019 19:10:06: 20000000 INFO @ Mon, 03 Jun 2019 19:10:10: 18000000 INFO @ Mon, 03 Jun 2019 19:10:11: 20000000 INFO @ Mon, 03 Jun 2019 19:10:15: 21000000 INFO @ Mon, 03 Jun 2019 19:10:20: 21000000 INFO @ Mon, 03 Jun 2019 19:10:20: 19000000 INFO @ Mon, 03 Jun 2019 19:10:23: 22000000 INFO @ Mon, 03 Jun 2019 19:10:28: 22000000 INFO @ Mon, 03 Jun 2019 19:10:29: 20000000 INFO @ Mon, 03 Jun 2019 19:10:32: 23000000 INFO @ Mon, 03 Jun 2019 19:10:37: 23000000 INFO @ Mon, 03 Jun 2019 19:10:39: 21000000 INFO @ Mon, 03 Jun 2019 19:10:40: 24000000 INFO @ Mon, 03 Jun 2019 19:10:46: 24000000 INFO @ Mon, 03 Jun 2019 19:10:48: 22000000 INFO @ Mon, 03 Jun 2019 19:10:49: 25000000 INFO @ Mon, 03 Jun 2019 19:10:55: 25000000 INFO @ Mon, 03 Jun 2019 19:10:57: 26000000 INFO @ Mon, 03 Jun 2019 19:10:58: 23000000 INFO @ Mon, 03 Jun 2019 19:11:03: 26000000 INFO @ Mon, 03 Jun 2019 19:11:06: 27000000 INFO @ Mon, 03 Jun 2019 19:11:08: 24000000 INFO @ Mon, 03 Jun 2019 19:11:12: 27000000 INFO @ Mon, 03 Jun 2019 19:11:14: 28000000 INFO @ Mon, 03 Jun 2019 19:11:17: 25000000 INFO @ Mon, 03 Jun 2019 19:11:21: 28000000 INFO @ Mon, 03 Jun 2019 19:11:23: 29000000 INFO @ Mon, 03 Jun 2019 19:11:27: 26000000 INFO @ Mon, 03 Jun 2019 19:11:29: 29000000 INFO @ Mon, 03 Jun 2019 19:11:31: 30000000 INFO @ Mon, 03 Jun 2019 19:11:37: 27000000 INFO @ Mon, 03 Jun 2019 19:11:38: 30000000 INFO @ Mon, 03 Jun 2019 19:11:39: 31000000 INFO @ Mon, 03 Jun 2019 19:11:46: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 19:11:46: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 19:11:46: #1 total tags in treatment: 15367070 INFO @ Mon, 03 Jun 2019 19:11:46: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:11:46: #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 19:11:46: 28000000 INFO @ Mon, 03 Jun 2019 19:11:46: #1 tags after filtering in treatment: 12148047 INFO @ Mon, 03 Jun 2019 19:11:46: #1 Redundant rate of treatment: 0.21 INFO @ Mon, 03 Jun 2019 19:11:46: #1 finished! INFO @ Mon, 03 Jun 2019 19:11:46: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:11:46: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:11:46: 31000000 INFO @ Mon, 03 Jun 2019 19:11:48: #2 number of paired peaks: 1403 INFO @ Mon, 03 Jun 2019 19:11:48: start model_add_line... INFO @ Mon, 03 Jun 2019 19:11:48: start X-correlation... INFO @ Mon, 03 Jun 2019 19:11:48: end of X-cor INFO @ Mon, 03 Jun 2019 19:11:48: #2 finished! INFO @ Mon, 03 Jun 2019 19:11:48: #2 predicted fragment length is 156 bps INFO @ Mon, 03 Jun 2019 19:11:48: #2 alternative fragment length(s) may be 18,156,176,197,247,265,290,308,312,502 bps INFO @ Mon, 03 Jun 2019 19:11:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX474567/SRX474567.05_model.r INFO @ Mon, 03 Jun 2019 19:11:48: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:11:48: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:11:53: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 19:11:53: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 19:11:53: #1 total tags in treatment: 15367070 INFO @ Mon, 03 Jun 2019 19:11:53: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:11:53: #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 19:11:53: #1 tags after filtering in treatment: 12148047 INFO @ Mon, 03 Jun 2019 19:11:53: #1 Redundant rate of treatment: 0.21 INFO @ Mon, 03 Jun 2019 19:11:53: #1 finished! INFO @ Mon, 03 Jun 2019 19:11:53: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:11:53: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:11:55: #2 number of paired peaks: 1403 INFO @ Mon, 03 Jun 2019 19:11:55: start model_add_line... INFO @ Mon, 03 Jun 2019 19:11:55: start X-correlation... INFO @ Mon, 03 Jun 2019 19:11:55: end of X-cor INFO @ Mon, 03 Jun 2019 19:11:55: #2 finished! INFO @ Mon, 03 Jun 2019 19:11:55: #2 predicted fragment length is 156 bps INFO @ Mon, 03 Jun 2019 19:11:55: #2 alternative fragment length(s) may be 18,156,176,197,247,265,290,308,312,502 bps INFO @ Mon, 03 Jun 2019 19:11:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX474567/SRX474567.20_model.r INFO @ Mon, 03 Jun 2019 19:11:55: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:11:55: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:11:55: 29000000 INFO @ Mon, 03 Jun 2019 19:12:04: 30000000 INFO @ Mon, 03 Jun 2019 19:12:13: 31000000 INFO @ Mon, 03 Jun 2019 19:12:21: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 19:12:21: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 19:12:21: #1 total tags in treatment: 15367070 INFO @ Mon, 03 Jun 2019 19:12:21: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:12:21: #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 19:12:21: #1 tags after filtering in treatment: 12148047 INFO @ Mon, 03 Jun 2019 19:12:21: #1 Redundant rate of treatment: 0.21 INFO @ Mon, 03 Jun 2019 19:12:21: #1 finished! INFO @ Mon, 03 Jun 2019 19:12:21: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:12:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:12:22: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:12:22: #2 number of paired peaks: 1403 INFO @ Mon, 03 Jun 2019 19:12:22: start model_add_line... INFO @ Mon, 03 Jun 2019 19:12:22: start X-correlation... INFO @ Mon, 03 Jun 2019 19:12:22: end of X-cor INFO @ Mon, 03 Jun 2019 19:12:22: #2 finished! INFO @ Mon, 03 Jun 2019 19:12:22: #2 predicted fragment length is 156 bps INFO @ Mon, 03 Jun 2019 19:12:22: #2 alternative fragment length(s) may be 18,156,176,197,247,265,290,308,312,502 bps INFO @ Mon, 03 Jun 2019 19:12:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX474567/SRX474567.10_model.r INFO @ Mon, 03 Jun 2019 19:12:22: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:12:22: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:12:29: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:12:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX474567/SRX474567.05_peaks.xls INFO @ Mon, 03 Jun 2019 19:12:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX474567/SRX474567.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:12:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX474567/SRX474567.05_summits.bed INFO @ Mon, 03 Jun 2019 19:12:39: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (795 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 19:12:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX474567/SRX474567.20_peaks.xls INFO @ Mon, 03 Jun 2019 19:12:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX474567/SRX474567.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:12:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX474567/SRX474567.20_summits.bed INFO @ Mon, 03 Jun 2019 19:12:46: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (219 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 19:12:56: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:13:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX474567/SRX474567.10_peaks.xls INFO @ Mon, 03 Jun 2019 19:13:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX474567/SRX474567.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:13:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX474567/SRX474567.10_summits.bed INFO @ Mon, 03 Jun 2019 19:13:12: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (434 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。