Job ID = 1293897 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 59,200,042 reads read : 59,200,042 reads written : 59,200,042 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: 00:12:54 59200042 reads; of these: 59200042 (100.00%) were unpaired; of these: 16795288 (28.37%) aligned 0 times 32522296 (54.94%) aligned exactly 1 time 9882458 (16.69%) aligned >1 times 71.63% overall alignment rate Time searching: 00:12:54 Overall time: 00:12:54 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_rmdupse_core] 10865607 / 42404754 = 0.2562 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 03:27:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX146994/SRX146994.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX146994/SRX146994.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX146994/SRX146994.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX146994/SRX146994.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 03:27:40: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:27:40: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:27:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX146994/SRX146994.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX146994/SRX146994.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX146994/SRX146994.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX146994/SRX146994.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 03:27:40: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:27:40: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:27:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX146994/SRX146994.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX146994/SRX146994.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX146994/SRX146994.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX146994/SRX146994.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 03:27:40: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:27:40: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:27:47: 1000000 INFO @ Mon, 03 Jun 2019 03:27:51: 1000000 INFO @ Mon, 03 Jun 2019 03:27:51: 1000000 INFO @ Mon, 03 Jun 2019 03:27:55: 2000000 INFO @ Mon, 03 Jun 2019 03:28:02: 2000000 INFO @ Mon, 03 Jun 2019 03:28:02: 2000000 INFO @ Mon, 03 Jun 2019 03:28:02: 3000000 INFO @ Mon, 03 Jun 2019 03:28:09: 4000000 INFO @ Mon, 03 Jun 2019 03:28:13: 3000000 INFO @ Mon, 03 Jun 2019 03:28:13: 3000000 INFO @ Mon, 03 Jun 2019 03:28:17: 5000000 INFO @ Mon, 03 Jun 2019 03:28:24: 4000000 INFO @ Mon, 03 Jun 2019 03:28:25: 6000000 INFO @ Mon, 03 Jun 2019 03:28:25: 4000000 INFO @ Mon, 03 Jun 2019 03:28:34: 7000000 INFO @ Mon, 03 Jun 2019 03:28:36: 5000000 INFO @ Mon, 03 Jun 2019 03:28:38: 5000000 INFO @ Mon, 03 Jun 2019 03:28:42: 8000000 INFO @ Mon, 03 Jun 2019 03:28:47: 6000000 INFO @ Mon, 03 Jun 2019 03:28:48: 6000000 INFO @ Mon, 03 Jun 2019 03:28:50: 9000000 INFO @ Mon, 03 Jun 2019 03:28:57: 10000000 INFO @ Mon, 03 Jun 2019 03:28:59: 7000000 INFO @ Mon, 03 Jun 2019 03:28:59: 7000000 INFO @ Mon, 03 Jun 2019 03:29:05: 11000000 INFO @ Mon, 03 Jun 2019 03:29:09: 8000000 INFO @ Mon, 03 Jun 2019 03:29:09: 8000000 INFO @ Mon, 03 Jun 2019 03:29:12: 12000000 INFO @ Mon, 03 Jun 2019 03:29:19: 13000000 INFO @ Mon, 03 Jun 2019 03:29:19: 9000000 INFO @ Mon, 03 Jun 2019 03:29:19: 9000000 INFO @ Mon, 03 Jun 2019 03:29:27: 14000000 INFO @ Mon, 03 Jun 2019 03:29:29: 10000000 INFO @ Mon, 03 Jun 2019 03:29:29: 10000000 INFO @ Mon, 03 Jun 2019 03:29:35: 15000000 INFO @ Mon, 03 Jun 2019 03:29:39: 11000000 INFO @ Mon, 03 Jun 2019 03:29:39: 11000000 INFO @ Mon, 03 Jun 2019 03:29:43: 16000000 INFO @ Mon, 03 Jun 2019 03:29:48: 12000000 INFO @ Mon, 03 Jun 2019 03:29:49: 12000000 INFO @ Mon, 03 Jun 2019 03:29:50: 17000000 INFO @ Mon, 03 Jun 2019 03:29:58: 18000000 INFO @ Mon, 03 Jun 2019 03:29:58: 13000000 INFO @ Mon, 03 Jun 2019 03:29:58: 13000000 INFO @ Mon, 03 Jun 2019 03:30:05: 19000000 INFO @ Mon, 03 Jun 2019 03:30:07: 14000000 INFO @ Mon, 03 Jun 2019 03:30:08: 14000000 INFO @ Mon, 03 Jun 2019 03:30:12: 20000000 INFO @ Mon, 03 Jun 2019 03:30:17: 15000000 INFO @ Mon, 03 Jun 2019 03:30:17: 15000000 INFO @ Mon, 03 Jun 2019 03:30:19: 21000000 INFO @ Mon, 03 Jun 2019 03:30:27: 16000000 INFO @ Mon, 03 Jun 2019 03:30:27: 16000000 INFO @ Mon, 03 Jun 2019 03:30:29: 22000000 INFO @ Mon, 03 Jun 2019 03:30:36: 23000000 INFO @ Mon, 03 Jun 2019 03:30:37: 17000000 INFO @ Mon, 03 Jun 2019 03:30:37: 17000000 INFO @ Mon, 03 Jun 2019 03:30:44: 24000000 INFO @ Mon, 03 Jun 2019 03:30:46: 18000000 INFO @ Mon, 03 Jun 2019 03:30:47: 18000000 INFO @ Mon, 03 Jun 2019 03:30:51: 25000000 INFO @ Mon, 03 Jun 2019 03:30:56: 19000000 INFO @ Mon, 03 Jun 2019 03:30:56: 19000000 INFO @ Mon, 03 Jun 2019 03:30:59: 26000000 INFO @ Mon, 03 Jun 2019 03:31:05: 20000000 INFO @ Mon, 03 Jun 2019 03:31:06: 20000000 INFO @ Mon, 03 Jun 2019 03:31:06: 27000000 INFO @ Mon, 03 Jun 2019 03:31:13: 28000000 INFO @ Mon, 03 Jun 2019 03:31:15: 21000000 INFO @ Mon, 03 Jun 2019 03:31:16: 21000000 INFO @ Mon, 03 Jun 2019 03:31:21: 29000000 INFO @ Mon, 03 Jun 2019 03:31:26: 22000000 INFO @ Mon, 03 Jun 2019 03:31:26: 22000000 INFO @ Mon, 03 Jun 2019 03:31:30: 30000000 INFO @ Mon, 03 Jun 2019 03:31:36: 23000000 INFO @ Mon, 03 Jun 2019 03:31:36: 23000000 INFO @ Mon, 03 Jun 2019 03:31:37: 31000000 INFO @ Mon, 03 Jun 2019 03:31:42: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 03:31:42: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 03:31:42: #1 total tags in treatment: 31539147 INFO @ Mon, 03 Jun 2019 03:31:42: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:31:42: #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 03:31:42: #1 tags after filtering in treatment: 31539147 INFO @ Mon, 03 Jun 2019 03:31:42: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:31:42: #1 finished! INFO @ Mon, 03 Jun 2019 03:31:42: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:31:42: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:31:45: #2 number of paired peaks: 266 WARNING @ Mon, 03 Jun 2019 03:31:45: Fewer paired peaks (266) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 266 pairs to build model! INFO @ Mon, 03 Jun 2019 03:31:45: start model_add_line... INFO @ Mon, 03 Jun 2019 03:31:45: start X-correlation... INFO @ Mon, 03 Jun 2019 03:31:45: end of X-cor INFO @ Mon, 03 Jun 2019 03:31:45: #2 finished! INFO @ Mon, 03 Jun 2019 03:31:45: #2 predicted fragment length is 1 bps INFO @ Mon, 03 Jun 2019 03:31:45: #2 alternative fragment length(s) may be 1,25 bps INFO @ Mon, 03 Jun 2019 03:31:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX146994/SRX146994.20_model.r WARNING @ Mon, 03 Jun 2019 03:31:45: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 03:31:45: #2 You may need to consider one of the other alternative d(s): 1,25 WARNING @ Mon, 03 Jun 2019 03:31:45: #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 03:31:45: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:31:45: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:31:45: 24000000 INFO @ Mon, 03 Jun 2019 03:31:46: 24000000 INFO @ Mon, 03 Jun 2019 03:31:55: 25000000 INFO @ Mon, 03 Jun 2019 03:31:55: 25000000 INFO @ Mon, 03 Jun 2019 03:32:05: 26000000 INFO @ Mon, 03 Jun 2019 03:32:05: 26000000 INFO @ Mon, 03 Jun 2019 03:32:14: 27000000 INFO @ Mon, 03 Jun 2019 03:32:15: 27000000 INFO @ Mon, 03 Jun 2019 03:32:24: 28000000 INFO @ Mon, 03 Jun 2019 03:32:24: 28000000 INFO @ Mon, 03 Jun 2019 03:32:34: 29000000 INFO @ Mon, 03 Jun 2019 03:32:34: 29000000 INFO @ Mon, 03 Jun 2019 03:32:43: 30000000 INFO @ Mon, 03 Jun 2019 03:32:44: 30000000 INFO @ Mon, 03 Jun 2019 03:32:51: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:32:53: 31000000 INFO @ Mon, 03 Jun 2019 03:32:53: 31000000 INFO @ Mon, 03 Jun 2019 03:32:58: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 03:32:58: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 03:32:58: #1 total tags in treatment: 31539147 INFO @ Mon, 03 Jun 2019 03:32:58: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:32:58: #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 03:32:58: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 03:32:58: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 03:32:58: #1 total tags in treatment: 31539147 INFO @ Mon, 03 Jun 2019 03:32:58: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:32:58: #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 03:32:59: #1 tags after filtering in treatment: 31539147 INFO @ Mon, 03 Jun 2019 03:32:59: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:32:59: #1 finished! INFO @ Mon, 03 Jun 2019 03:32:59: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:32:59: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:32:59: #1 tags after filtering in treatment: 31539147 INFO @ Mon, 03 Jun 2019 03:32:59: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:32:59: #1 finished! INFO @ Mon, 03 Jun 2019 03:32:59: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:32:59: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:33:01: #2 number of paired peaks: 266 WARNING @ Mon, 03 Jun 2019 03:33:01: Fewer paired peaks (266) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 266 pairs to build model! INFO @ Mon, 03 Jun 2019 03:33:01: start model_add_line... INFO @ Mon, 03 Jun 2019 03:33:02: start X-correlation... INFO @ Mon, 03 Jun 2019 03:33:02: end of X-cor INFO @ Mon, 03 Jun 2019 03:33:02: #2 finished! INFO @ Mon, 03 Jun 2019 03:33:02: #2 predicted fragment length is 1 bps INFO @ Mon, 03 Jun 2019 03:33:02: #2 alternative fragment length(s) may be 1,25 bps INFO @ Mon, 03 Jun 2019 03:33:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX146994/SRX146994.10_model.r WARNING @ Mon, 03 Jun 2019 03:33:02: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 03:33:02: #2 You may need to consider one of the other alternative d(s): 1,25 WARNING @ Mon, 03 Jun 2019 03:33:02: #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 03:33:02: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:33:02: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:33:02: #2 number of paired peaks: 266 WARNING @ Mon, 03 Jun 2019 03:33:02: Fewer paired peaks (266) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 266 pairs to build model! INFO @ Mon, 03 Jun 2019 03:33:02: start model_add_line... INFO @ Mon, 03 Jun 2019 03:33:02: start X-correlation... INFO @ Mon, 03 Jun 2019 03:33:02: end of X-cor INFO @ Mon, 03 Jun 2019 03:33:02: #2 finished! INFO @ Mon, 03 Jun 2019 03:33:02: #2 predicted fragment length is 1 bps INFO @ Mon, 03 Jun 2019 03:33:02: #2 alternative fragment length(s) may be 1,25 bps INFO @ Mon, 03 Jun 2019 03:33:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX146994/SRX146994.05_model.r WARNING @ Mon, 03 Jun 2019 03:33:02: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 03:33:02: #2 You may need to consider one of the other alternative d(s): 1,25 WARNING @ Mon, 03 Jun 2019 03:33:02: #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 03:33:02: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:33:02: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:33:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX146994/SRX146994.20_peaks.xls INFO @ Mon, 03 Jun 2019 03:33:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX146994/SRX146994.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:33:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX146994/SRX146994.20_summits.bed INFO @ Mon, 03 Jun 2019 03:33:22: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 03:34:07: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:34:07: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:34:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX146994/SRX146994.10_peaks.xls INFO @ Mon, 03 Jun 2019 03:34:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX146994/SRX146994.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:34:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX146994/SRX146994.10_summits.bed INFO @ Mon, 03 Jun 2019 03:34:36: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 03:34:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX146994/SRX146994.05_peaks.xls INFO @ Mon, 03 Jun 2019 03:34:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX146994/SRX146994.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:34:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX146994/SRX146994.05_summits.bed INFO @ Mon, 03 Jun 2019 03:34:38: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。