Job ID = 1293403 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 25,450,096 reads read : 50,900,192 reads written : 50,900,192 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: 01:13:57 25450096 reads; of these: 25450096 (100.00%) were paired; of these: 3263489 (12.82%) aligned concordantly 0 times 16012567 (62.92%) aligned concordantly exactly 1 time 6174040 (24.26%) aligned concordantly >1 times ---- 3263489 pairs aligned concordantly 0 times; of these: 239124 (7.33%) aligned discordantly 1 time ---- 3024365 pairs aligned 0 times concordantly or discordantly; of these: 6048730 mates make up the pairs; of these: 5179452 (85.63%) aligned 0 times 516746 (8.54%) aligned exactly 1 time 352532 (5.83%) aligned >1 times 89.82% overall alignment rate Time searching: 01:13:57 Overall time: 01:13:57 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] 8460276 / 22399214 = 0.3777 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 01:19:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX2075299/ERX2075299.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX2075299/ERX2075299.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX2075299/ERX2075299.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX2075299/ERX2075299.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 01:19:45: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:19:45: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:19:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX2075299/ERX2075299.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX2075299/ERX2075299.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX2075299/ERX2075299.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX2075299/ERX2075299.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 01:19:45: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:19:45: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:19:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX2075299/ERX2075299.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX2075299/ERX2075299.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX2075299/ERX2075299.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX2075299/ERX2075299.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 01:19:45: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:19:45: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:19:54: 1000000 INFO @ Mon, 03 Jun 2019 01:19:54: 1000000 INFO @ Mon, 03 Jun 2019 01:19:54: 1000000 INFO @ Mon, 03 Jun 2019 01:20:02: 2000000 INFO @ Mon, 03 Jun 2019 01:20:02: 2000000 INFO @ Mon, 03 Jun 2019 01:20:02: 2000000 INFO @ Mon, 03 Jun 2019 01:20:11: 3000000 INFO @ Mon, 03 Jun 2019 01:20:11: 3000000 INFO @ Mon, 03 Jun 2019 01:20:11: 3000000 INFO @ Mon, 03 Jun 2019 01:20:20: 4000000 INFO @ Mon, 03 Jun 2019 01:20:20: 4000000 INFO @ Mon, 03 Jun 2019 01:20:20: 4000000 INFO @ Mon, 03 Jun 2019 01:20:28: 5000000 INFO @ Mon, 03 Jun 2019 01:20:29: 5000000 INFO @ Mon, 03 Jun 2019 01:20:29: 5000000 INFO @ Mon, 03 Jun 2019 01:20:36: 6000000 INFO @ Mon, 03 Jun 2019 01:20:38: 6000000 INFO @ Mon, 03 Jun 2019 01:20:38: 6000000 INFO @ Mon, 03 Jun 2019 01:20:44: 7000000 INFO @ Mon, 03 Jun 2019 01:20:46: 7000000 INFO @ Mon, 03 Jun 2019 01:20:47: 7000000 INFO @ Mon, 03 Jun 2019 01:20:53: 8000000 INFO @ Mon, 03 Jun 2019 01:20:55: 8000000 INFO @ Mon, 03 Jun 2019 01:20:55: 8000000 INFO @ Mon, 03 Jun 2019 01:21:01: 9000000 INFO @ Mon, 03 Jun 2019 01:21:04: 9000000 INFO @ Mon, 03 Jun 2019 01:21:04: 9000000 INFO @ Mon, 03 Jun 2019 01:21:09: 10000000 INFO @ Mon, 03 Jun 2019 01:21:13: 10000000 INFO @ Mon, 03 Jun 2019 01:21:13: 10000000 INFO @ Mon, 03 Jun 2019 01:21:18: 11000000 INFO @ Mon, 03 Jun 2019 01:21:21: 11000000 INFO @ Mon, 03 Jun 2019 01:21:22: 11000000 INFO @ Mon, 03 Jun 2019 01:21:26: 12000000 INFO @ Mon, 03 Jun 2019 01:21:30: 12000000 INFO @ Mon, 03 Jun 2019 01:21:30: 12000000 INFO @ Mon, 03 Jun 2019 01:21:34: 13000000 INFO @ Mon, 03 Jun 2019 01:21:39: 13000000 INFO @ Mon, 03 Jun 2019 01:21:39: 13000000 INFO @ Mon, 03 Jun 2019 01:21:42: 14000000 INFO @ Mon, 03 Jun 2019 01:21:47: 14000000 INFO @ Mon, 03 Jun 2019 01:21:48: 14000000 INFO @ Mon, 03 Jun 2019 01:21:50: 15000000 INFO @ Mon, 03 Jun 2019 01:21:56: 15000000 INFO @ Mon, 03 Jun 2019 01:21:56: 15000000 INFO @ Mon, 03 Jun 2019 01:21:59: 16000000 INFO @ Mon, 03 Jun 2019 01:22:05: 16000000 INFO @ Mon, 03 Jun 2019 01:22:05: 16000000 INFO @ Mon, 03 Jun 2019 01:22:07: 17000000 INFO @ Mon, 03 Jun 2019 01:22:13: 17000000 INFO @ Mon, 03 Jun 2019 01:22:14: 17000000 INFO @ Mon, 03 Jun 2019 01:22:15: 18000000 INFO @ Mon, 03 Jun 2019 01:22:22: 18000000 INFO @ Mon, 03 Jun 2019 01:22:22: 18000000 INFO @ Mon, 03 Jun 2019 01:22:23: 19000000 INFO @ Mon, 03 Jun 2019 01:22:31: 19000000 INFO @ Mon, 03 Jun 2019 01:22:31: 19000000 INFO @ Mon, 03 Jun 2019 01:22:31: 20000000 INFO @ Mon, 03 Jun 2019 01:22:39: 20000000 INFO @ Mon, 03 Jun 2019 01:22:39: 21000000 INFO @ Mon, 03 Jun 2019 01:22:39: 20000000 INFO @ Mon, 03 Jun 2019 01:22:47: 21000000 INFO @ Mon, 03 Jun 2019 01:22:47: 22000000 INFO @ Mon, 03 Jun 2019 01:22:47: 21000000 INFO @ Mon, 03 Jun 2019 01:22:55: 23000000 INFO @ Mon, 03 Jun 2019 01:22:55: 22000000 INFO @ Mon, 03 Jun 2019 01:22:56: 22000000 INFO @ Mon, 03 Jun 2019 01:23:03: 24000000 INFO @ Mon, 03 Jun 2019 01:23:04: 23000000 INFO @ Mon, 03 Jun 2019 01:23:04: 23000000 INFO @ Mon, 03 Jun 2019 01:23:11: 25000000 INFO @ Mon, 03 Jun 2019 01:23:12: 24000000 INFO @ Mon, 03 Jun 2019 01:23:12: 24000000 INFO @ Mon, 03 Jun 2019 01:23:19: 26000000 INFO @ Mon, 03 Jun 2019 01:23:20: 25000000 INFO @ Mon, 03 Jun 2019 01:23:20: 25000000 INFO @ Mon, 03 Jun 2019 01:23:27: 27000000 INFO @ Mon, 03 Jun 2019 01:23:28: 26000000 INFO @ Mon, 03 Jun 2019 01:23:29: 26000000 INFO @ Mon, 03 Jun 2019 01:23:35: 28000000 INFO @ Mon, 03 Jun 2019 01:23:36: 27000000 INFO @ Mon, 03 Jun 2019 01:23:37: 27000000 INFO @ Mon, 03 Jun 2019 01:23:41: #1 tag size is determined as 75 bps INFO @ Mon, 03 Jun 2019 01:23:41: #1 tag size = 75 INFO @ Mon, 03 Jun 2019 01:23:41: #1 total tags in treatment: 13795982 INFO @ Mon, 03 Jun 2019 01:23:41: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:23:41: #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 01:23:42: #1 tags after filtering in treatment: 12825280 INFO @ Mon, 03 Jun 2019 01:23:42: #1 Redundant rate of treatment: 0.07 INFO @ Mon, 03 Jun 2019 01:23:42: #1 finished! INFO @ Mon, 03 Jun 2019 01:23:42: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:23:42: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:23:43: #2 number of paired peaks: 338 WARNING @ Mon, 03 Jun 2019 01:23:43: Fewer paired peaks (338) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 338 pairs to build model! INFO @ Mon, 03 Jun 2019 01:23:43: start model_add_line... INFO @ Mon, 03 Jun 2019 01:23:43: start X-correlation... INFO @ Mon, 03 Jun 2019 01:23:43: end of X-cor INFO @ Mon, 03 Jun 2019 01:23:43: #2 finished! INFO @ Mon, 03 Jun 2019 01:23:43: #2 predicted fragment length is 135 bps INFO @ Mon, 03 Jun 2019 01:23:43: #2 alternative fragment length(s) may be 135,577 bps INFO @ Mon, 03 Jun 2019 01:23:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX2075299/ERX2075299.05_model.r WARNING @ Mon, 03 Jun 2019 01:23:43: #2 Since the d (135) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 01:23:43: #2 You may need to consider one of the other alternative d(s): 135,577 WARNING @ Mon, 03 Jun 2019 01:23:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 01:23:43: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:23:43: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:23:44: 28000000 INFO @ Mon, 03 Jun 2019 01:23:45: 28000000 INFO @ Mon, 03 Jun 2019 01:23:51: #1 tag size is determined as 75 bps INFO @ Mon, 03 Jun 2019 01:23:51: #1 tag size = 75 INFO @ Mon, 03 Jun 2019 01:23:51: #1 total tags in treatment: 13795982 INFO @ Mon, 03 Jun 2019 01:23:51: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:23:51: #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 01:23:51: #1 tags after filtering in treatment: 12825280 INFO @ Mon, 03 Jun 2019 01:23:51: #1 Redundant rate of treatment: 0.07 INFO @ Mon, 03 Jun 2019 01:23:51: #1 finished! INFO @ Mon, 03 Jun 2019 01:23:51: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:23:51: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:23:51: #1 tag size is determined as 75 bps INFO @ Mon, 03 Jun 2019 01:23:51: #1 tag size = 75 INFO @ Mon, 03 Jun 2019 01:23:51: #1 total tags in treatment: 13795982 INFO @ Mon, 03 Jun 2019 01:23:51: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:23:51: #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 01:23:52: #1 tags after filtering in treatment: 12825280 INFO @ Mon, 03 Jun 2019 01:23:52: #1 Redundant rate of treatment: 0.07 INFO @ Mon, 03 Jun 2019 01:23:52: #1 finished! INFO @ Mon, 03 Jun 2019 01:23:52: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:23:52: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:23:52: #2 number of paired peaks: 338 WARNING @ Mon, 03 Jun 2019 01:23:52: Fewer paired peaks (338) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 338 pairs to build model! INFO @ Mon, 03 Jun 2019 01:23:52: start model_add_line... INFO @ Mon, 03 Jun 2019 01:23:52: start X-correlation... INFO @ Mon, 03 Jun 2019 01:23:52: end of X-cor INFO @ Mon, 03 Jun 2019 01:23:52: #2 finished! INFO @ Mon, 03 Jun 2019 01:23:52: #2 predicted fragment length is 135 bps INFO @ Mon, 03 Jun 2019 01:23:52: #2 alternative fragment length(s) may be 135,577 bps INFO @ Mon, 03 Jun 2019 01:23:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX2075299/ERX2075299.10_model.r WARNING @ Mon, 03 Jun 2019 01:23:52: #2 Since the d (135) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 01:23:52: #2 You may need to consider one of the other alternative d(s): 135,577 WARNING @ Mon, 03 Jun 2019 01:23:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 01:23:52: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:23:52: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:23:53: #2 number of paired peaks: 338 WARNING @ Mon, 03 Jun 2019 01:23:53: Fewer paired peaks (338) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 338 pairs to build model! INFO @ Mon, 03 Jun 2019 01:23:53: start model_add_line... INFO @ Mon, 03 Jun 2019 01:23:53: start X-correlation... INFO @ Mon, 03 Jun 2019 01:23:53: end of X-cor INFO @ Mon, 03 Jun 2019 01:23:53: #2 finished! INFO @ Mon, 03 Jun 2019 01:23:53: #2 predicted fragment length is 135 bps INFO @ Mon, 03 Jun 2019 01:23:53: #2 alternative fragment length(s) may be 135,577 bps INFO @ Mon, 03 Jun 2019 01:23:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX2075299/ERX2075299.20_model.r WARNING @ Mon, 03 Jun 2019 01:23:53: #2 Since the d (135) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 01:23:53: #2 You may need to consider one of the other alternative d(s): 135,577 WARNING @ Mon, 03 Jun 2019 01:23:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 01:23:53: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:23:53: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:24:19: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:24:28: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:24:29: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:24:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX2075299/ERX2075299.05_peaks.xls INFO @ Mon, 03 Jun 2019 01:24:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX2075299/ERX2075299.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:24:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX2075299/ERX2075299.05_summits.bed INFO @ Mon, 03 Jun 2019 01:24:36: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4149 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 01:24:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX2075299/ERX2075299.10_peaks.xls INFO @ Mon, 03 Jun 2019 01:24:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX2075299/ERX2075299.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:24:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX2075299/ERX2075299.10_summits.bed INFO @ Mon, 03 Jun 2019 01:24:45: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (1888 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 01:24:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX2075299/ERX2075299.20_peaks.xls INFO @ Mon, 03 Jun 2019 01:24:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX2075299/ERX2075299.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:24:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX2075299/ERX2075299.20_summits.bed INFO @ Mon, 03 Jun 2019 01:24:45: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (871 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。