Job ID = 1296116 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 46,942,810 reads read : 93,885,620 reads written : 93,885,620 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: 00:36:41 46942810 reads; of these: 46942810 (100.00%) were paired; of these: 28267596 (60.22%) aligned concordantly 0 times 15216236 (32.41%) aligned concordantly exactly 1 time 3458978 (7.37%) aligned concordantly >1 times ---- 28267596 pairs aligned concordantly 0 times; of these: 21960 (0.08%) aligned discordantly 1 time ---- 28245636 pairs aligned 0 times concordantly or discordantly; of these: 56491272 mates make up the pairs; of these: 55652984 (98.52%) aligned 0 times 576424 (1.02%) aligned exactly 1 time 261864 (0.46%) aligned >1 times 40.72% overall alignment rate Time searching: 00:36:41 Overall time: 00:36:41 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 12 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] 1610103 / 18685955 = 0.0862 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 17:03:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650736/SRX4650736.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650736/SRX4650736.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650736/SRX4650736.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650736/SRX4650736.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 17:03:06: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:03:06: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:03:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650736/SRX4650736.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650736/SRX4650736.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650736/SRX4650736.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650736/SRX4650736.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 17:03:06: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:03:06: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:03:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650736/SRX4650736.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650736/SRX4650736.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650736/SRX4650736.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650736/SRX4650736.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 17:03:06: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:03:06: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:03:13: 1000000 INFO @ Mon, 03 Jun 2019 17:03:13: 1000000 INFO @ Mon, 03 Jun 2019 17:03:14: 1000000 INFO @ Mon, 03 Jun 2019 17:03:19: 2000000 INFO @ Mon, 03 Jun 2019 17:03:20: 2000000 INFO @ Mon, 03 Jun 2019 17:03:21: 2000000 INFO @ Mon, 03 Jun 2019 17:03:26: 3000000 INFO @ Mon, 03 Jun 2019 17:03:27: 3000000 INFO @ Mon, 03 Jun 2019 17:03:28: 3000000 INFO @ Mon, 03 Jun 2019 17:03:33: 4000000 INFO @ Mon, 03 Jun 2019 17:03:35: 4000000 INFO @ Mon, 03 Jun 2019 17:03:37: 4000000 INFO @ Mon, 03 Jun 2019 17:03:40: 5000000 INFO @ Mon, 03 Jun 2019 17:03:43: 5000000 INFO @ Mon, 03 Jun 2019 17:03:44: 5000000 INFO @ Mon, 03 Jun 2019 17:03:48: 6000000 INFO @ Mon, 03 Jun 2019 17:03:51: 6000000 INFO @ Mon, 03 Jun 2019 17:03:52: 6000000 INFO @ Mon, 03 Jun 2019 17:03:55: 7000000 INFO @ Mon, 03 Jun 2019 17:03:58: 7000000 INFO @ Mon, 03 Jun 2019 17:04:00: 7000000 INFO @ Mon, 03 Jun 2019 17:04:02: 8000000 INFO @ Mon, 03 Jun 2019 17:04:05: 8000000 INFO @ Mon, 03 Jun 2019 17:04:07: 8000000 INFO @ Mon, 03 Jun 2019 17:04:09: 9000000 INFO @ Mon, 03 Jun 2019 17:04:12: 9000000 INFO @ Mon, 03 Jun 2019 17:04:14: 9000000 INFO @ Mon, 03 Jun 2019 17:04:16: 10000000 INFO @ Mon, 03 Jun 2019 17:04:20: 10000000 INFO @ Mon, 03 Jun 2019 17:04:21: 10000000 INFO @ Mon, 03 Jun 2019 17:04:23: 11000000 INFO @ Mon, 03 Jun 2019 17:04:27: 11000000 INFO @ Mon, 03 Jun 2019 17:04:28: 11000000 INFO @ Mon, 03 Jun 2019 17:04:30: 12000000 INFO @ Mon, 03 Jun 2019 17:04:34: 12000000 INFO @ Mon, 03 Jun 2019 17:04:35: 12000000 INFO @ Mon, 03 Jun 2019 17:04:37: 13000000 INFO @ Mon, 03 Jun 2019 17:04:41: 13000000 INFO @ Mon, 03 Jun 2019 17:04:42: 13000000 INFO @ Mon, 03 Jun 2019 17:04:44: 14000000 INFO @ Mon, 03 Jun 2019 17:04:48: 14000000 INFO @ Mon, 03 Jun 2019 17:04:49: 14000000 INFO @ Mon, 03 Jun 2019 17:04:51: 15000000 INFO @ Mon, 03 Jun 2019 17:04:55: 15000000 INFO @ Mon, 03 Jun 2019 17:04:56: 15000000 INFO @ Mon, 03 Jun 2019 17:04:58: 16000000 INFO @ Mon, 03 Jun 2019 17:05:02: 16000000 INFO @ Mon, 03 Jun 2019 17:05:03: 16000000 INFO @ Mon, 03 Jun 2019 17:05:05: 17000000 INFO @ Mon, 03 Jun 2019 17:05:09: 17000000 INFO @ Mon, 03 Jun 2019 17:05:10: 17000000 INFO @ Mon, 03 Jun 2019 17:05:13: 18000000 INFO @ Mon, 03 Jun 2019 17:05:16: 18000000 INFO @ Mon, 03 Jun 2019 17:05:17: 18000000 INFO @ Mon, 03 Jun 2019 17:05:20: 19000000 INFO @ Mon, 03 Jun 2019 17:05:24: 19000000 INFO @ Mon, 03 Jun 2019 17:05:25: 19000000 INFO @ Mon, 03 Jun 2019 17:05:27: 20000000 INFO @ Mon, 03 Jun 2019 17:05:31: 20000000 INFO @ Mon, 03 Jun 2019 17:05:32: 20000000 INFO @ Mon, 03 Jun 2019 17:05:34: 21000000 INFO @ Mon, 03 Jun 2019 17:05:38: 21000000 INFO @ Mon, 03 Jun 2019 17:05:39: 21000000 INFO @ Mon, 03 Jun 2019 17:05:41: 22000000 INFO @ Mon, 03 Jun 2019 17:05:45: 22000000 INFO @ Mon, 03 Jun 2019 17:05:46: 22000000 INFO @ Mon, 03 Jun 2019 17:05:48: 23000000 INFO @ Mon, 03 Jun 2019 17:05:52: 23000000 INFO @ Mon, 03 Jun 2019 17:05:53: 23000000 INFO @ Mon, 03 Jun 2019 17:05:55: 24000000 INFO @ Mon, 03 Jun 2019 17:05:59: 24000000 INFO @ Mon, 03 Jun 2019 17:06:00: 24000000 INFO @ Mon, 03 Jun 2019 17:06:02: 25000000 INFO @ Mon, 03 Jun 2019 17:06:07: 25000000 INFO @ Mon, 03 Jun 2019 17:06:07: 25000000 INFO @ Mon, 03 Jun 2019 17:06:09: 26000000 INFO @ Mon, 03 Jun 2019 17:06:14: 26000000 INFO @ Mon, 03 Jun 2019 17:06:15: 26000000 INFO @ Mon, 03 Jun 2019 17:06:16: 27000000 INFO @ Mon, 03 Jun 2019 17:06:21: 27000000 INFO @ Mon, 03 Jun 2019 17:06:22: 27000000 INFO @ Mon, 03 Jun 2019 17:06:23: 28000000 INFO @ Mon, 03 Jun 2019 17:06:28: 28000000 INFO @ Mon, 03 Jun 2019 17:06:29: 28000000 INFO @ Mon, 03 Jun 2019 17:06:30: 29000000 INFO @ Mon, 03 Jun 2019 17:06:36: 29000000 INFO @ Mon, 03 Jun 2019 17:06:36: 29000000 INFO @ Mon, 03 Jun 2019 17:06:37: 30000000 INFO @ Mon, 03 Jun 2019 17:06:43: 30000000 INFO @ Mon, 03 Jun 2019 17:06:44: 30000000 INFO @ Mon, 03 Jun 2019 17:06:44: 31000000 INFO @ Mon, 03 Jun 2019 17:06:50: 31000000 INFO @ Mon, 03 Jun 2019 17:06:51: 31000000 INFO @ Mon, 03 Jun 2019 17:06:52: 32000000 INFO @ Mon, 03 Jun 2019 17:06:57: 32000000 INFO @ Mon, 03 Jun 2019 17:06:58: 32000000 INFO @ Mon, 03 Jun 2019 17:06:59: 33000000 INFO @ Mon, 03 Jun 2019 17:07:05: 33000000 INFO @ Mon, 03 Jun 2019 17:07:06: 33000000 INFO @ Mon, 03 Jun 2019 17:07:06: 34000000 INFO @ Mon, 03 Jun 2019 17:07:12: 34000000 INFO @ Mon, 03 Jun 2019 17:07:13: 34000000 INFO @ Mon, 03 Jun 2019 17:07:13: 35000000 INFO @ Mon, 03 Jun 2019 17:07:14: #1 tag size is determined as 39 bps INFO @ Mon, 03 Jun 2019 17:07:14: #1 tag size = 39 INFO @ Mon, 03 Jun 2019 17:07:14: #1 total tags in treatment: 17065589 INFO @ Mon, 03 Jun 2019 17:07:14: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:07:14: #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 17:07:14: #1 tags after filtering in treatment: 14009426 INFO @ Mon, 03 Jun 2019 17:07:14: #1 Redundant rate of treatment: 0.18 INFO @ Mon, 03 Jun 2019 17:07:14: #1 finished! INFO @ Mon, 03 Jun 2019 17:07:14: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:07:14: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:07:15: #2 number of paired peaks: 409 WARNING @ Mon, 03 Jun 2019 17:07:15: Fewer paired peaks (409) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 409 pairs to build model! INFO @ Mon, 03 Jun 2019 17:07:15: start model_add_line... INFO @ Mon, 03 Jun 2019 17:07:16: start X-correlation... INFO @ Mon, 03 Jun 2019 17:07:16: end of X-cor INFO @ Mon, 03 Jun 2019 17:07:16: #2 finished! INFO @ Mon, 03 Jun 2019 17:07:16: #2 predicted fragment length is 118 bps INFO @ Mon, 03 Jun 2019 17:07:16: #2 alternative fragment length(s) may be 2,61,89,118,134,163 bps INFO @ Mon, 03 Jun 2019 17:07:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650736/SRX4650736.05_model.r INFO @ Mon, 03 Jun 2019 17:07:16: #3 Call peaks... INFO @ Mon, 03 Jun 2019 17:07:16: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 17:07:20: 35000000 INFO @ Mon, 03 Jun 2019 17:07:20: #1 tag size is determined as 39 bps INFO @ Mon, 03 Jun 2019 17:07:20: #1 tag size = 39 INFO @ Mon, 03 Jun 2019 17:07:20: #1 total tags in treatment: 17065589 INFO @ Mon, 03 Jun 2019 17:07:20: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:07:20: #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 17:07:20: #1 tags after filtering in treatment: 14009426 INFO @ Mon, 03 Jun 2019 17:07:20: #1 Redundant rate of treatment: 0.18 INFO @ Mon, 03 Jun 2019 17:07:20: #1 finished! INFO @ Mon, 03 Jun 2019 17:07:20: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:07:20: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:07:21: 35000000 INFO @ Mon, 03 Jun 2019 17:07:21: #1 tag size is determined as 39 bps INFO @ Mon, 03 Jun 2019 17:07:21: #1 tag size = 39 INFO @ Mon, 03 Jun 2019 17:07:21: #1 total tags in treatment: 17065589 INFO @ Mon, 03 Jun 2019 17:07:21: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:07:21: #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 17:07:21: #1 tags after filtering in treatment: 14009426 INFO @ Mon, 03 Jun 2019 17:07:21: #1 Redundant rate of treatment: 0.18 INFO @ Mon, 03 Jun 2019 17:07:21: #1 finished! INFO @ Mon, 03 Jun 2019 17:07:21: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:07:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:07:22: #2 number of paired peaks: 409 WARNING @ Mon, 03 Jun 2019 17:07:22: Fewer paired peaks (409) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 409 pairs to build model! INFO @ Mon, 03 Jun 2019 17:07:22: start model_add_line... INFO @ Mon, 03 Jun 2019 17:07:22: start X-correlation... INFO @ Mon, 03 Jun 2019 17:07:22: end of X-cor INFO @ Mon, 03 Jun 2019 17:07:22: #2 finished! INFO @ Mon, 03 Jun 2019 17:07:22: #2 predicted fragment length is 118 bps INFO @ Mon, 03 Jun 2019 17:07:22: #2 alternative fragment length(s) may be 2,61,89,118,134,163 bps INFO @ Mon, 03 Jun 2019 17:07:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650736/SRX4650736.10_model.r INFO @ Mon, 03 Jun 2019 17:07:22: #3 Call peaks... INFO @ Mon, 03 Jun 2019 17:07:22: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 17:07:23: #2 number of paired peaks: 409 WARNING @ Mon, 03 Jun 2019 17:07:23: Fewer paired peaks (409) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 409 pairs to build model! INFO @ Mon, 03 Jun 2019 17:07:23: start model_add_line... INFO @ Mon, 03 Jun 2019 17:07:23: start X-correlation... INFO @ Mon, 03 Jun 2019 17:07:23: end of X-cor INFO @ Mon, 03 Jun 2019 17:07:23: #2 finished! INFO @ Mon, 03 Jun 2019 17:07:23: #2 predicted fragment length is 118 bps INFO @ Mon, 03 Jun 2019 17:07:23: #2 alternative fragment length(s) may be 2,61,89,118,134,163 bps INFO @ Mon, 03 Jun 2019 17:07:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650736/SRX4650736.20_model.r INFO @ Mon, 03 Jun 2019 17:07:23: #3 Call peaks... INFO @ Mon, 03 Jun 2019 17:07:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 17:07:55: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 17:08:01: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 17:08:02: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 17:08:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650736/SRX4650736.05_peaks.xls INFO @ Mon, 03 Jun 2019 17:08:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650736/SRX4650736.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 17:08:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650736/SRX4650736.05_summits.bed INFO @ Mon, 03 Jun 2019 17:08:14: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1311 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 17:08:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650736/SRX4650736.10_peaks.xls INFO @ Mon, 03 Jun 2019 17:08:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650736/SRX4650736.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 17:08:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650736/SRX4650736.10_summits.bed INFO @ Mon, 03 Jun 2019 17:08:20: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (804 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 17:08:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650736/SRX4650736.20_peaks.xls INFO @ Mon, 03 Jun 2019 17:08:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650736/SRX4650736.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 17:08:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650736/SRX4650736.20_summits.bed INFO @ Mon, 03 Jun 2019 17:08:23: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (337 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。