Job ID = 1293333 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 88,243,587 reads read : 176,487,174 reads written : 176,487,174 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: 01:08:42 88243587 reads; of these: 88243587 (100.00%) were paired; of these: 46774840 (53.01%) aligned concordantly 0 times 13080545 (14.82%) aligned concordantly exactly 1 time 28388202 (32.17%) aligned concordantly >1 times ---- 46774840 pairs aligned concordantly 0 times; of these: 365378 (0.78%) aligned discordantly 1 time ---- 46409462 pairs aligned 0 times concordantly or discordantly; of these: 92818924 mates make up the pairs; of these: 90643133 (97.66%) aligned 0 times 710853 (0.77%) aligned exactly 1 time 1464938 (1.58%) aligned >1 times 48.64% overall alignment rate Time searching: 01:08:42 Overall time: 01:08:42 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 36 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] 27006489 / 41807427 = 0.6460 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 01:22:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX1818263/ERX1818263.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX1818263/ERX1818263.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX1818263/ERX1818263.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX1818263/ERX1818263.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 01:22:02: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:22:02: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:22:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX1818263/ERX1818263.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX1818263/ERX1818263.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX1818263/ERX1818263.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX1818263/ERX1818263.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 01:22:02: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:22:02: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:22:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX1818263/ERX1818263.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX1818263/ERX1818263.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX1818263/ERX1818263.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX1818263/ERX1818263.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 01:22:02: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:22:02: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:22:09: 1000000 INFO @ Mon, 03 Jun 2019 01:22:10: 1000000 INFO @ Mon, 03 Jun 2019 01:22:13: 1000000 INFO @ Mon, 03 Jun 2019 01:22:16: 2000000 INFO @ Mon, 03 Jun 2019 01:22:18: 2000000 INFO @ Mon, 03 Jun 2019 01:22:23: 3000000 INFO @ Mon, 03 Jun 2019 01:22:24: 2000000 INFO @ Mon, 03 Jun 2019 01:22:26: 3000000 INFO @ Mon, 03 Jun 2019 01:22:29: 4000000 INFO @ Mon, 03 Jun 2019 01:22:33: 4000000 INFO @ Mon, 03 Jun 2019 01:22:34: 3000000 INFO @ Mon, 03 Jun 2019 01:22:36: 5000000 INFO @ Mon, 03 Jun 2019 01:22:41: 5000000 INFO @ Mon, 03 Jun 2019 01:22:43: 6000000 INFO @ Mon, 03 Jun 2019 01:22:45: 4000000 INFO @ Mon, 03 Jun 2019 01:22:48: 6000000 INFO @ Mon, 03 Jun 2019 01:22:49: 7000000 INFO @ Mon, 03 Jun 2019 01:22:55: 5000000 INFO @ Mon, 03 Jun 2019 01:22:56: 8000000 INFO @ Mon, 03 Jun 2019 01:22:56: 7000000 INFO @ Mon, 03 Jun 2019 01:23:02: 9000000 INFO @ Mon, 03 Jun 2019 01:23:03: 8000000 INFO @ Mon, 03 Jun 2019 01:23:06: 6000000 INFO @ Mon, 03 Jun 2019 01:23:09: 10000000 INFO @ Mon, 03 Jun 2019 01:23:11: 9000000 INFO @ Mon, 03 Jun 2019 01:23:15: 11000000 INFO @ Mon, 03 Jun 2019 01:23:16: 7000000 INFO @ Mon, 03 Jun 2019 01:23:18: 10000000 INFO @ Mon, 03 Jun 2019 01:23:22: 12000000 INFO @ Mon, 03 Jun 2019 01:23:25: 11000000 INFO @ Mon, 03 Jun 2019 01:23:26: 8000000 INFO @ Mon, 03 Jun 2019 01:23:28: 13000000 INFO @ Mon, 03 Jun 2019 01:23:33: 12000000 INFO @ Mon, 03 Jun 2019 01:23:34: 14000000 INFO @ Mon, 03 Jun 2019 01:23:36: 9000000 INFO @ Mon, 03 Jun 2019 01:23:40: 13000000 INFO @ Mon, 03 Jun 2019 01:23:40: 15000000 INFO @ Mon, 03 Jun 2019 01:23:45: 10000000 INFO @ Mon, 03 Jun 2019 01:23:46: 16000000 INFO @ Mon, 03 Jun 2019 01:23:47: 14000000 INFO @ Mon, 03 Jun 2019 01:23:53: 17000000 INFO @ Mon, 03 Jun 2019 01:23:54: 15000000 INFO @ Mon, 03 Jun 2019 01:23:55: 11000000 INFO @ Mon, 03 Jun 2019 01:23:59: 18000000 INFO @ Mon, 03 Jun 2019 01:24:01: 16000000 INFO @ Mon, 03 Jun 2019 01:24:04: 12000000 INFO @ Mon, 03 Jun 2019 01:24:05: 19000000 INFO @ Mon, 03 Jun 2019 01:24:08: 17000000 INFO @ Mon, 03 Jun 2019 01:24:11: 20000000 INFO @ Mon, 03 Jun 2019 01:24:12: 13000000 INFO @ Mon, 03 Jun 2019 01:24:15: 18000000 INFO @ Mon, 03 Jun 2019 01:24:17: 21000000 INFO @ Mon, 03 Jun 2019 01:24:20: 14000000 INFO @ Mon, 03 Jun 2019 01:24:22: 19000000 INFO @ Mon, 03 Jun 2019 01:24:24: 22000000 INFO @ Mon, 03 Jun 2019 01:24:29: 15000000 INFO @ Mon, 03 Jun 2019 01:24:29: 20000000 INFO @ Mon, 03 Jun 2019 01:24:30: 23000000 INFO @ Mon, 03 Jun 2019 01:24:36: 21000000 INFO @ Mon, 03 Jun 2019 01:24:36: 24000000 INFO @ Mon, 03 Jun 2019 01:24:37: 16000000 INFO @ Mon, 03 Jun 2019 01:24:42: 25000000 INFO @ Mon, 03 Jun 2019 01:24:43: 22000000 INFO @ Mon, 03 Jun 2019 01:24:45: 17000000 INFO @ Mon, 03 Jun 2019 01:24:49: 26000000 INFO @ Mon, 03 Jun 2019 01:24:50: 23000000 INFO @ Mon, 03 Jun 2019 01:24:54: 18000000 INFO @ Mon, 03 Jun 2019 01:24:55: 27000000 INFO @ Mon, 03 Jun 2019 01:24:57: 24000000 INFO @ Mon, 03 Jun 2019 01:25:02: 28000000 INFO @ Mon, 03 Jun 2019 01:25:02: 19000000 INFO @ Mon, 03 Jun 2019 01:25:04: 25000000 INFO @ Mon, 03 Jun 2019 01:25:08: 29000000 INFO @ Mon, 03 Jun 2019 01:25:11: 26000000 INFO @ Mon, 03 Jun 2019 01:25:11: 20000000 INFO @ Mon, 03 Jun 2019 01:25:15: 30000000 INFO @ Mon, 03 Jun 2019 01:25:18: 27000000 INFO @ Mon, 03 Jun 2019 01:25:19: 21000000 INFO @ Mon, 03 Jun 2019 01:25:21: 31000000 INFO @ Mon, 03 Jun 2019 01:25:25: 28000000 INFO @ Mon, 03 Jun 2019 01:25:27: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 01:25:27: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 01:25:27: #1 total tags in treatment: 14590321 INFO @ Mon, 03 Jun 2019 01:25:27: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:25:27: #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 01:25:27: #1 tags after filtering in treatment: 9015968 INFO @ Mon, 03 Jun 2019 01:25:27: #1 Redundant rate of treatment: 0.38 INFO @ Mon, 03 Jun 2019 01:25:27: #1 finished! INFO @ Mon, 03 Jun 2019 01:25:27: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:25:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:25:28: 22000000 INFO @ Mon, 03 Jun 2019 01:25:28: #2 number of paired peaks: 159 WARNING @ Mon, 03 Jun 2019 01:25:28: Fewer paired peaks (159) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 159 pairs to build model! INFO @ Mon, 03 Jun 2019 01:25:28: start model_add_line... INFO @ Mon, 03 Jun 2019 01:25:28: start X-correlation... INFO @ Mon, 03 Jun 2019 01:25:28: end of X-cor INFO @ Mon, 03 Jun 2019 01:25:28: #2 finished! INFO @ Mon, 03 Jun 2019 01:25:28: #2 predicted fragment length is 125 bps INFO @ Mon, 03 Jun 2019 01:25:28: #2 alternative fragment length(s) may be 125 bps INFO @ Mon, 03 Jun 2019 01:25:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX1818263/ERX1818263.05_model.r INFO @ Mon, 03 Jun 2019 01:25:28: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:25:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:25:33: 29000000 INFO @ Mon, 03 Jun 2019 01:25:36: 23000000 INFO @ Mon, 03 Jun 2019 01:25:40: 30000000 INFO @ Mon, 03 Jun 2019 01:25:44: 24000000 INFO @ Mon, 03 Jun 2019 01:25:47: 31000000 INFO @ Mon, 03 Jun 2019 01:25:53: 25000000 INFO @ Mon, 03 Jun 2019 01:25:54: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 01:25:54: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 01:25:54: #1 total tags in treatment: 14590321 INFO @ Mon, 03 Jun 2019 01:25:54: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:25:54: #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 01:25:54: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:25:54: #1 tags after filtering in treatment: 9015968 INFO @ Mon, 03 Jun 2019 01:25:54: #1 Redundant rate of treatment: 0.38 INFO @ Mon, 03 Jun 2019 01:25:54: #1 finished! INFO @ Mon, 03 Jun 2019 01:25:54: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:25:54: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:25:55: #2 number of paired peaks: 159 WARNING @ Mon, 03 Jun 2019 01:25:55: Fewer paired peaks (159) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 159 pairs to build model! INFO @ Mon, 03 Jun 2019 01:25:55: start model_add_line... INFO @ Mon, 03 Jun 2019 01:25:55: start X-correlation... INFO @ Mon, 03 Jun 2019 01:25:55: end of X-cor INFO @ Mon, 03 Jun 2019 01:25:55: #2 finished! INFO @ Mon, 03 Jun 2019 01:25:55: #2 predicted fragment length is 125 bps INFO @ Mon, 03 Jun 2019 01:25:55: #2 alternative fragment length(s) may be 125 bps INFO @ Mon, 03 Jun 2019 01:25:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX1818263/ERX1818263.20_model.r INFO @ Mon, 03 Jun 2019 01:25:55: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:25:55: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:26:01: 26000000 INFO @ Mon, 03 Jun 2019 01:26:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX1818263/ERX1818263.05_peaks.xls INFO @ Mon, 03 Jun 2019 01:26:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX1818263/ERX1818263.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:26:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX1818263/ERX1818263.05_summits.bed INFO @ Mon, 03 Jun 2019 01:26:06: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2169 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 01:26:10: 27000000 INFO @ Mon, 03 Jun 2019 01:26:18: 28000000 INFO @ Mon, 03 Jun 2019 01:26:21: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:26:27: 29000000 INFO @ Mon, 03 Jun 2019 01:26:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX1818263/ERX1818263.20_peaks.xls INFO @ Mon, 03 Jun 2019 01:26:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX1818263/ERX1818263.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:26:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX1818263/ERX1818263.20_summits.bed INFO @ Mon, 03 Jun 2019 01:26:33: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (372 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 01:26:36: 30000000 INFO @ Mon, 03 Jun 2019 01:26:44: 31000000 INFO @ Mon, 03 Jun 2019 01:26:51: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 01:26:51: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 01:26:51: #1 total tags in treatment: 14590321 INFO @ Mon, 03 Jun 2019 01:26:51: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:26:51: #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 01:26:51: #1 tags after filtering in treatment: 9015968 INFO @ Mon, 03 Jun 2019 01:26:51: #1 Redundant rate of treatment: 0.38 INFO @ Mon, 03 Jun 2019 01:26:51: #1 finished! INFO @ Mon, 03 Jun 2019 01:26:51: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:26:51: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:26:52: #2 number of paired peaks: 159 WARNING @ Mon, 03 Jun 2019 01:26:52: Fewer paired peaks (159) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 159 pairs to build model! INFO @ Mon, 03 Jun 2019 01:26:52: start model_add_line... INFO @ Mon, 03 Jun 2019 01:26:52: start X-correlation... INFO @ Mon, 03 Jun 2019 01:26:52: end of X-cor INFO @ Mon, 03 Jun 2019 01:26:52: #2 finished! INFO @ Mon, 03 Jun 2019 01:26:52: #2 predicted fragment length is 125 bps INFO @ Mon, 03 Jun 2019 01:26:52: #2 alternative fragment length(s) may be 125 bps INFO @ Mon, 03 Jun 2019 01:26:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX1818263/ERX1818263.10_model.r INFO @ Mon, 03 Jun 2019 01:26:52: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:26:52: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:27:18: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:27:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX1818263/ERX1818263.10_peaks.xls INFO @ Mon, 03 Jun 2019 01:27:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX1818263/ERX1818263.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:27:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX1818263/ERX1818263.10_summits.bed INFO @ Mon, 03 Jun 2019 01:27:30: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (839 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。