Job ID = 2590292 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 24,209,971 reads read : 48,419,942 reads written : 48,419,942 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: 00:33:38 24209971 reads; of these: 24209971 (100.00%) were paired; of these: 9540850 (39.41%) aligned concordantly 0 times 13217012 (54.59%) aligned concordantly exactly 1 time 1452109 (6.00%) aligned concordantly >1 times ---- 9540850 pairs aligned concordantly 0 times; of these: 1784759 (18.71%) aligned discordantly 1 time ---- 7756091 pairs aligned 0 times concordantly or discordantly; of these: 15512182 mates make up the pairs; of these: 14405884 (92.87%) aligned 0 times 719903 (4.64%) aligned exactly 1 time 386395 (2.49%) aligned >1 times 70.25% overall alignment rate Time searching: 00:33:38 Overall time: 00:33:38 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] 596237 / 16378873 = 0.0364 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, 12 Aug 2019 22:01:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2950506/SRX2950506.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2950506/SRX2950506.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2950506/SRX2950506.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2950506/SRX2950506.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, 12 Aug 2019 22:01:23: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:01:23: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:01:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2950506/SRX2950506.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2950506/SRX2950506.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2950506/SRX2950506.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2950506/SRX2950506.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, 12 Aug 2019 22:01:24: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:01:24: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:01:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2950506/SRX2950506.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2950506/SRX2950506.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2950506/SRX2950506.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2950506/SRX2950506.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, 12 Aug 2019 22:01:25: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:01:25: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:01:34: 1000000 INFO @ Mon, 12 Aug 2019 22:01:35: 1000000 INFO @ Mon, 12 Aug 2019 22:01:39: 1000000 INFO @ Mon, 12 Aug 2019 22:01:44: 2000000 INFO @ Mon, 12 Aug 2019 22:01:44: 2000000 INFO @ Mon, 12 Aug 2019 22:01:53: 3000000 INFO @ Mon, 12 Aug 2019 22:01:54: 2000000 INFO @ Mon, 12 Aug 2019 22:01:54: 3000000 INFO @ Mon, 12 Aug 2019 22:02:03: 4000000 INFO @ Mon, 12 Aug 2019 22:02:04: 4000000 INFO @ Mon, 12 Aug 2019 22:02:08: 3000000 INFO @ Mon, 12 Aug 2019 22:02:13: 5000000 INFO @ Mon, 12 Aug 2019 22:02:14: 5000000 INFO @ Mon, 12 Aug 2019 22:02:22: 4000000 INFO @ Mon, 12 Aug 2019 22:02:23: 6000000 INFO @ Mon, 12 Aug 2019 22:02:23: 6000000 INFO @ Mon, 12 Aug 2019 22:02:32: 7000000 INFO @ Mon, 12 Aug 2019 22:02:33: 7000000 INFO @ Mon, 12 Aug 2019 22:02:36: 5000000 INFO @ Mon, 12 Aug 2019 22:02:42: 8000000 INFO @ Mon, 12 Aug 2019 22:02:43: 8000000 INFO @ Mon, 12 Aug 2019 22:02:50: 6000000 INFO @ Mon, 12 Aug 2019 22:02:52: 9000000 INFO @ Mon, 12 Aug 2019 22:02:53: 9000000 INFO @ Mon, 12 Aug 2019 22:03:02: 10000000 INFO @ Mon, 12 Aug 2019 22:03:03: 10000000 INFO @ Mon, 12 Aug 2019 22:03:04: 7000000 INFO @ Mon, 12 Aug 2019 22:03:12: 11000000 INFO @ Mon, 12 Aug 2019 22:03:12: 11000000 INFO @ Mon, 12 Aug 2019 22:03:18: 8000000 INFO @ Mon, 12 Aug 2019 22:03:21: 12000000 INFO @ Mon, 12 Aug 2019 22:03:22: 12000000 INFO @ Mon, 12 Aug 2019 22:03:31: 13000000 INFO @ Mon, 12 Aug 2019 22:03:32: 13000000 INFO @ Mon, 12 Aug 2019 22:03:34: 9000000 INFO @ Mon, 12 Aug 2019 22:03:41: 14000000 INFO @ Mon, 12 Aug 2019 22:03:41: 14000000 INFO @ Mon, 12 Aug 2019 22:03:50: 15000000 INFO @ Mon, 12 Aug 2019 22:03:50: 10000000 INFO @ Mon, 12 Aug 2019 22:03:51: 15000000 INFO @ Mon, 12 Aug 2019 22:04:00: 16000000 INFO @ Mon, 12 Aug 2019 22:04:00: 16000000 INFO @ Mon, 12 Aug 2019 22:04:07: 11000000 INFO @ Mon, 12 Aug 2019 22:04:09: 17000000 INFO @ Mon, 12 Aug 2019 22:04:10: 17000000 INFO @ Mon, 12 Aug 2019 22:04:19: 18000000 INFO @ Mon, 12 Aug 2019 22:04:19: 18000000 INFO @ Mon, 12 Aug 2019 22:04:24: 12000000 INFO @ Mon, 12 Aug 2019 22:04:28: 19000000 INFO @ Mon, 12 Aug 2019 22:04:29: 19000000 INFO @ Mon, 12 Aug 2019 22:04:37: 20000000 INFO @ Mon, 12 Aug 2019 22:04:38: 20000000 INFO @ Mon, 12 Aug 2019 22:04:41: 13000000 INFO @ Mon, 12 Aug 2019 22:04:47: 21000000 INFO @ Mon, 12 Aug 2019 22:04:48: 21000000 INFO @ Mon, 12 Aug 2019 22:04:56: 22000000 INFO @ Mon, 12 Aug 2019 22:04:57: 22000000 INFO @ Mon, 12 Aug 2019 22:04:58: 14000000 INFO @ Mon, 12 Aug 2019 22:05:06: 23000000 INFO @ Mon, 12 Aug 2019 22:05:07: 23000000 INFO @ Mon, 12 Aug 2019 22:05:15: 15000000 INFO @ Mon, 12 Aug 2019 22:05:15: 24000000 INFO @ Mon, 12 Aug 2019 22:05:16: 24000000 INFO @ Mon, 12 Aug 2019 22:05:25: 25000000 INFO @ Mon, 12 Aug 2019 22:05:26: 25000000 INFO @ Mon, 12 Aug 2019 22:05:32: 16000000 INFO @ Mon, 12 Aug 2019 22:05:34: 26000000 INFO @ Mon, 12 Aug 2019 22:05:35: 26000000 INFO @ Mon, 12 Aug 2019 22:05:44: 27000000 INFO @ Mon, 12 Aug 2019 22:05:45: 27000000 INFO @ Mon, 12 Aug 2019 22:05:49: 17000000 INFO @ Mon, 12 Aug 2019 22:05:54: 28000000 INFO @ Mon, 12 Aug 2019 22:05:54: 28000000 INFO @ Mon, 12 Aug 2019 22:06:03: 29000000 INFO @ Mon, 12 Aug 2019 22:06:04: 29000000 INFO @ Mon, 12 Aug 2019 22:06:05: 18000000 INFO @ Mon, 12 Aug 2019 22:06:13: 30000000 INFO @ Mon, 12 Aug 2019 22:06:13: 30000000 INFO @ Mon, 12 Aug 2019 22:06:21: 19000000 INFO @ Mon, 12 Aug 2019 22:06:22: 31000000 INFO @ Mon, 12 Aug 2019 22:06:23: 31000000 INFO @ Mon, 12 Aug 2019 22:06:32: 32000000 INFO @ Mon, 12 Aug 2019 22:06:32: 32000000 INFO @ Mon, 12 Aug 2019 22:06:39: 20000000 INFO @ Mon, 12 Aug 2019 22:06:40: #1 tag size is determined as 101 bps INFO @ Mon, 12 Aug 2019 22:06:40: #1 tag size = 101 INFO @ Mon, 12 Aug 2019 22:06:40: #1 total tags in treatment: 14120537 INFO @ Mon, 12 Aug 2019 22:06:40: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:06:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 22:06:40: #1 tags after filtering in treatment: 13465383 INFO @ Mon, 12 Aug 2019 22:06:40: #1 Redundant rate of treatment: 0.05 INFO @ Mon, 12 Aug 2019 22:06:40: #1 finished! INFO @ Mon, 12 Aug 2019 22:06:40: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:06:40: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:06:40: #1 tag size is determined as 101 bps INFO @ Mon, 12 Aug 2019 22:06:40: #1 tag size = 101 INFO @ Mon, 12 Aug 2019 22:06:40: #1 total tags in treatment: 14120537 INFO @ Mon, 12 Aug 2019 22:06:40: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:06:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 22:06:41: #1 tags after filtering in treatment: 13465383 INFO @ Mon, 12 Aug 2019 22:06:41: #1 Redundant rate of treatment: 0.05 INFO @ Mon, 12 Aug 2019 22:06:41: #1 finished! INFO @ Mon, 12 Aug 2019 22:06:41: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:06:41: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:06:41: #2 number of paired peaks: 170 WARNING @ Mon, 12 Aug 2019 22:06:41: Fewer paired peaks (170) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 170 pairs to build model! INFO @ Mon, 12 Aug 2019 22:06:41: start model_add_line... INFO @ Mon, 12 Aug 2019 22:06:41: start X-correlation... INFO @ Mon, 12 Aug 2019 22:06:41: end of X-cor INFO @ Mon, 12 Aug 2019 22:06:41: #2 finished! INFO @ Mon, 12 Aug 2019 22:06:41: #2 predicted fragment length is 232 bps INFO @ Mon, 12 Aug 2019 22:06:41: #2 alternative fragment length(s) may be 232 bps INFO @ Mon, 12 Aug 2019 22:06:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2950506/SRX2950506.05_model.r INFO @ Mon, 12 Aug 2019 22:06:41: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:06:41: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:06:42: #2 number of paired peaks: 170 WARNING @ Mon, 12 Aug 2019 22:06:42: Fewer paired peaks (170) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 170 pairs to build model! INFO @ Mon, 12 Aug 2019 22:06:42: start model_add_line... INFO @ Mon, 12 Aug 2019 22:06:42: start X-correlation... INFO @ Mon, 12 Aug 2019 22:06:42: end of X-cor INFO @ Mon, 12 Aug 2019 22:06:42: #2 finished! INFO @ Mon, 12 Aug 2019 22:06:42: #2 predicted fragment length is 232 bps INFO @ Mon, 12 Aug 2019 22:06:42: #2 alternative fragment length(s) may be 232 bps INFO @ Mon, 12 Aug 2019 22:06:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2950506/SRX2950506.20_model.r INFO @ Mon, 12 Aug 2019 22:06:42: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:06:42: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:06:55: 21000000 INFO @ Mon, 12 Aug 2019 22:07:11: 22000000 INFO @ Mon, 12 Aug 2019 22:07:20: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:07:20: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:07:27: 23000000 INFO @ Mon, 12 Aug 2019 22:07:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2950506/SRX2950506.05_peaks.xls INFO @ Mon, 12 Aug 2019 22:07:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2950506/SRX2950506.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:07:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2950506/SRX2950506.05_summits.bed INFO @ Mon, 12 Aug 2019 22:07:39: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (4537 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 22:07:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2950506/SRX2950506.20_peaks.xls INFO @ Mon, 12 Aug 2019 22:07:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2950506/SRX2950506.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:07:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2950506/SRX2950506.20_summits.bed INFO @ Mon, 12 Aug 2019 22:07:39: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (614 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 22:07:43: 24000000 INFO @ Mon, 12 Aug 2019 22:07:59: 25000000 INFO @ Mon, 12 Aug 2019 22:08:16: 26000000 INFO @ Mon, 12 Aug 2019 22:08:32: 27000000 INFO @ Mon, 12 Aug 2019 22:08:48: 28000000 INFO @ Mon, 12 Aug 2019 22:09:05: 29000000 INFO @ Mon, 12 Aug 2019 22:09:20: 30000000 INFO @ Mon, 12 Aug 2019 22:09:33: 31000000 INFO @ Mon, 12 Aug 2019 22:09:46: 32000000 INFO @ Mon, 12 Aug 2019 22:09:57: #1 tag size is determined as 101 bps INFO @ Mon, 12 Aug 2019 22:09:57: #1 tag size = 101 INFO @ Mon, 12 Aug 2019 22:09:57: #1 total tags in treatment: 14120537 INFO @ Mon, 12 Aug 2019 22:09:57: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:09:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 22:09:57: #1 tags after filtering in treatment: 13465383 INFO @ Mon, 12 Aug 2019 22:09:57: #1 Redundant rate of treatment: 0.05 INFO @ Mon, 12 Aug 2019 22:09:57: #1 finished! INFO @ Mon, 12 Aug 2019 22:09:57: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:09:57: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:09:58: #2 number of paired peaks: 170 WARNING @ Mon, 12 Aug 2019 22:09:58: Fewer paired peaks (170) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 170 pairs to build model! INFO @ Mon, 12 Aug 2019 22:09:58: start model_add_line... INFO @ Mon, 12 Aug 2019 22:09:58: start X-correlation... INFO @ Mon, 12 Aug 2019 22:09:58: end of X-cor INFO @ Mon, 12 Aug 2019 22:09:58: #2 finished! INFO @ Mon, 12 Aug 2019 22:09:58: #2 predicted fragment length is 232 bps INFO @ Mon, 12 Aug 2019 22:09:58: #2 alternative fragment length(s) may be 232 bps INFO @ Mon, 12 Aug 2019 22:09:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2950506/SRX2950506.10_model.r INFO @ Mon, 12 Aug 2019 22:09:58: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:09:58: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:10:36: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:10:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2950506/SRX2950506.10_peaks.xls INFO @ Mon, 12 Aug 2019 22:10:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2950506/SRX2950506.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:10:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2950506/SRX2950506.10_summits.bed INFO @ Mon, 12 Aug 2019 22:10:55: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1988 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。