Job ID = 1295755 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 46,465,514 reads read : 46,465,514 reads written : 46,465,514 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: 00:12:50 46465514 reads; of these: 46465514 (100.00%) were unpaired; of these: 7099695 (15.28%) aligned 0 times 28965955 (62.34%) aligned exactly 1 time 10399864 (22.38%) aligned >1 times 84.72% overall alignment rate Time searching: 00:12:50 Overall time: 00:12:50 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] 6027695 / 39365819 = 0.1531 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 15:45:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX447394/SRX447394.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX447394/SRX447394.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX447394/SRX447394.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX447394/SRX447394.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 15:45:10: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:45:10: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:45:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX447394/SRX447394.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX447394/SRX447394.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX447394/SRX447394.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX447394/SRX447394.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 15:45:10: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:45:10: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:45:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX447394/SRX447394.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX447394/SRX447394.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX447394/SRX447394.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX447394/SRX447394.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 15:45:10: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:45:10: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:45:18: 1000000 INFO @ Mon, 03 Jun 2019 15:45:20: 1000000 INFO @ Mon, 03 Jun 2019 15:45:20: 1000000 INFO @ Mon, 03 Jun 2019 15:45:27: 2000000 INFO @ Mon, 03 Jun 2019 15:45:29: 2000000 INFO @ Mon, 03 Jun 2019 15:45:29: 2000000 INFO @ Mon, 03 Jun 2019 15:45:35: 3000000 INFO @ Mon, 03 Jun 2019 15:45:38: 3000000 INFO @ Mon, 03 Jun 2019 15:45:38: 3000000 INFO @ Mon, 03 Jun 2019 15:45:43: 4000000 INFO @ Mon, 03 Jun 2019 15:45:47: 4000000 INFO @ Mon, 03 Jun 2019 15:45:47: 4000000 INFO @ Mon, 03 Jun 2019 15:45:51: 5000000 INFO @ Mon, 03 Jun 2019 15:45:58: 5000000 INFO @ Mon, 03 Jun 2019 15:45:58: 5000000 INFO @ Mon, 03 Jun 2019 15:45:59: 6000000 INFO @ Mon, 03 Jun 2019 15:46:08: 7000000 INFO @ Mon, 03 Jun 2019 15:46:08: 6000000 INFO @ Mon, 03 Jun 2019 15:46:08: 6000000 INFO @ Mon, 03 Jun 2019 15:46:15: 8000000 INFO @ Mon, 03 Jun 2019 15:46:17: 7000000 INFO @ Mon, 03 Jun 2019 15:46:18: 7000000 INFO @ Mon, 03 Jun 2019 15:46:23: 9000000 INFO @ Mon, 03 Jun 2019 15:46:28: 8000000 INFO @ Mon, 03 Jun 2019 15:46:29: 8000000 INFO @ Mon, 03 Jun 2019 15:46:30: 10000000 INFO @ Mon, 03 Jun 2019 15:46:38: 9000000 INFO @ Mon, 03 Jun 2019 15:46:39: 9000000 INFO @ Mon, 03 Jun 2019 15:46:39: 11000000 INFO @ Mon, 03 Jun 2019 15:46:47: 12000000 INFO @ Mon, 03 Jun 2019 15:46:49: 10000000 INFO @ Mon, 03 Jun 2019 15:46:49: 10000000 INFO @ Mon, 03 Jun 2019 15:46:54: 13000000 INFO @ Mon, 03 Jun 2019 15:46:59: 11000000 INFO @ Mon, 03 Jun 2019 15:47:00: 11000000 INFO @ Mon, 03 Jun 2019 15:47:02: 14000000 INFO @ Mon, 03 Jun 2019 15:47:09: 12000000 INFO @ Mon, 03 Jun 2019 15:47:10: 15000000 INFO @ Mon, 03 Jun 2019 15:47:10: 12000000 INFO @ Mon, 03 Jun 2019 15:47:17: 16000000 INFO @ Mon, 03 Jun 2019 15:47:20: 13000000 INFO @ Mon, 03 Jun 2019 15:47:21: 13000000 INFO @ Mon, 03 Jun 2019 15:47:25: 17000000 INFO @ Mon, 03 Jun 2019 15:47:30: 14000000 INFO @ Mon, 03 Jun 2019 15:47:31: 14000000 INFO @ Mon, 03 Jun 2019 15:47:32: 18000000 INFO @ Mon, 03 Jun 2019 15:47:41: 19000000 INFO @ Mon, 03 Jun 2019 15:47:41: 15000000 INFO @ Mon, 03 Jun 2019 15:47:41: 15000000 INFO @ Mon, 03 Jun 2019 15:47:48: 20000000 INFO @ Mon, 03 Jun 2019 15:47:51: 16000000 INFO @ Mon, 03 Jun 2019 15:47:51: 16000000 INFO @ Mon, 03 Jun 2019 15:47:56: 21000000 INFO @ Mon, 03 Jun 2019 15:48:01: 17000000 INFO @ Mon, 03 Jun 2019 15:48:01: 17000000 INFO @ Mon, 03 Jun 2019 15:48:04: 22000000 INFO @ Mon, 03 Jun 2019 15:48:11: 18000000 INFO @ Mon, 03 Jun 2019 15:48:12: 18000000 INFO @ Mon, 03 Jun 2019 15:48:13: 23000000 INFO @ Mon, 03 Jun 2019 15:48:21: 19000000 INFO @ Mon, 03 Jun 2019 15:48:21: 24000000 INFO @ Mon, 03 Jun 2019 15:48:22: 19000000 INFO @ Mon, 03 Jun 2019 15:48:30: 25000000 INFO @ Mon, 03 Jun 2019 15:48:31: 20000000 INFO @ Mon, 03 Jun 2019 15:48:31: 20000000 INFO @ Mon, 03 Jun 2019 15:48:37: 26000000 INFO @ Mon, 03 Jun 2019 15:48:41: 21000000 INFO @ Mon, 03 Jun 2019 15:48:41: 21000000 INFO @ Mon, 03 Jun 2019 15:48:46: 27000000 INFO @ Mon, 03 Jun 2019 15:48:50: 22000000 INFO @ Mon, 03 Jun 2019 15:48:51: 22000000 INFO @ Mon, 03 Jun 2019 15:48:55: 28000000 INFO @ Mon, 03 Jun 2019 15:49:00: 23000000 INFO @ Mon, 03 Jun 2019 15:49:00: 23000000 INFO @ Mon, 03 Jun 2019 15:49:03: 29000000 INFO @ Mon, 03 Jun 2019 15:49:10: 24000000 INFO @ Mon, 03 Jun 2019 15:49:10: 24000000 INFO @ Mon, 03 Jun 2019 15:49:11: 30000000 INFO @ Mon, 03 Jun 2019 15:49:19: 31000000 INFO @ Mon, 03 Jun 2019 15:49:20: 25000000 INFO @ Mon, 03 Jun 2019 15:49:20: 25000000 INFO @ Mon, 03 Jun 2019 15:49:28: 32000000 INFO @ Mon, 03 Jun 2019 15:49:30: 26000000 INFO @ Mon, 03 Jun 2019 15:49:30: 26000000 INFO @ Mon, 03 Jun 2019 15:49:35: 33000000 INFO @ Mon, 03 Jun 2019 15:49:38: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 15:49:38: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 15:49:38: #1 total tags in treatment: 33338124 INFO @ Mon, 03 Jun 2019 15:49:38: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:49:38: #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 15:49:39: #1 tags after filtering in treatment: 33338124 INFO @ Mon, 03 Jun 2019 15:49:39: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 15:49:39: #1 finished! INFO @ Mon, 03 Jun 2019 15:49:39: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:49:39: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:49:40: 27000000 INFO @ Mon, 03 Jun 2019 15:49:41: 27000000 INFO @ Mon, 03 Jun 2019 15:49:42: #2 number of paired peaks: 166 WARNING @ Mon, 03 Jun 2019 15:49:42: Fewer paired peaks (166) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 166 pairs to build model! INFO @ Mon, 03 Jun 2019 15:49:42: start model_add_line... INFO @ Mon, 03 Jun 2019 15:49:42: start X-correlation... INFO @ Mon, 03 Jun 2019 15:49:42: end of X-cor INFO @ Mon, 03 Jun 2019 15:49:42: #2 finished! INFO @ Mon, 03 Jun 2019 15:49:42: #2 predicted fragment length is 1 bps INFO @ Mon, 03 Jun 2019 15:49:42: #2 alternative fragment length(s) may be 1,18,583 bps INFO @ Mon, 03 Jun 2019 15:49:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX447394/SRX447394.10_model.r WARNING @ Mon, 03 Jun 2019 15:49:42: #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 15:49:42: #2 You may need to consider one of the other alternative d(s): 1,18,583 WARNING @ Mon, 03 Jun 2019 15:49:42: #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 15:49:42: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:49:42: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:49:49: 28000000 INFO @ Mon, 03 Jun 2019 15:49:50: 28000000 INFO @ Mon, 03 Jun 2019 15:49:59: 29000000 INFO @ Mon, 03 Jun 2019 15:50:01: 29000000 INFO @ Mon, 03 Jun 2019 15:50:08: 30000000 INFO @ Mon, 03 Jun 2019 15:50:10: 30000000 INFO @ Mon, 03 Jun 2019 15:50:18: 31000000 INFO @ Mon, 03 Jun 2019 15:50:21: 31000000 INFO @ Mon, 03 Jun 2019 15:50:28: 32000000 INFO @ Mon, 03 Jun 2019 15:50:31: 32000000 INFO @ Mon, 03 Jun 2019 15:50:38: 33000000 INFO @ Mon, 03 Jun 2019 15:50:40: 33000000 INFO @ Mon, 03 Jun 2019 15:50:41: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 15:50:41: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 15:50:41: #1 total tags in treatment: 33338124 INFO @ Mon, 03 Jun 2019 15:50:41: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:50:41: #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 15:50:42: #1 tags after filtering in treatment: 33338124 INFO @ Mon, 03 Jun 2019 15:50:42: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 15:50:42: #1 finished! INFO @ Mon, 03 Jun 2019 15:50:42: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:50:42: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:50:43: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 15:50:43: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 15:50:43: #1 total tags in treatment: 33338124 INFO @ Mon, 03 Jun 2019 15:50:43: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:50:43: #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 15:50:44: #1 tags after filtering in treatment: 33338124 INFO @ Mon, 03 Jun 2019 15:50:44: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 15:50:44: #1 finished! INFO @ Mon, 03 Jun 2019 15:50:44: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:50:44: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:50:45: #2 number of paired peaks: 166 WARNING @ Mon, 03 Jun 2019 15:50:45: Fewer paired peaks (166) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 166 pairs to build model! INFO @ Mon, 03 Jun 2019 15:50:45: start model_add_line... INFO @ Mon, 03 Jun 2019 15:50:45: start X-correlation... INFO @ Mon, 03 Jun 2019 15:50:45: end of X-cor INFO @ Mon, 03 Jun 2019 15:50:45: #2 finished! INFO @ Mon, 03 Jun 2019 15:50:45: #2 predicted fragment length is 1 bps INFO @ Mon, 03 Jun 2019 15:50:45: #2 alternative fragment length(s) may be 1,18,583 bps INFO @ Mon, 03 Jun 2019 15:50:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX447394/SRX447394.05_model.r WARNING @ Mon, 03 Jun 2019 15:50:45: #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 15:50:45: #2 You may need to consider one of the other alternative d(s): 1,18,583 WARNING @ Mon, 03 Jun 2019 15:50:45: #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 15:50:45: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:50:45: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:50:47: #2 number of paired peaks: 166 WARNING @ Mon, 03 Jun 2019 15:50:47: Fewer paired peaks (166) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 166 pairs to build model! INFO @ Mon, 03 Jun 2019 15:50:47: start model_add_line... INFO @ Mon, 03 Jun 2019 15:50:47: start X-correlation... INFO @ Mon, 03 Jun 2019 15:50:47: end of X-cor INFO @ Mon, 03 Jun 2019 15:50:47: #2 finished! INFO @ Mon, 03 Jun 2019 15:50:47: #2 predicted fragment length is 1 bps INFO @ Mon, 03 Jun 2019 15:50:47: #2 alternative fragment length(s) may be 1,18,583 bps INFO @ Mon, 03 Jun 2019 15:50:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX447394/SRX447394.20_model.r WARNING @ Mon, 03 Jun 2019 15:50:47: #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 15:50:47: #2 You may need to consider one of the other alternative d(s): 1,18,583 WARNING @ Mon, 03 Jun 2019 15:50:47: #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 15:50:47: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:50:47: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:50:53: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:51:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX447394/SRX447394.10_peaks.xls INFO @ Mon, 03 Jun 2019 15:51:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX447394/SRX447394.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:51:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX447394/SRX447394.10_summits.bed INFO @ Mon, 03 Jun 2019 15:51:25: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 15:51:56: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:51:57: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:52:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX447394/SRX447394.05_peaks.xls INFO @ Mon, 03 Jun 2019 15:52:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX447394/SRX447394.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:52:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX447394/SRX447394.05_summits.bed INFO @ Mon, 03 Jun 2019 15:52:28: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 15:52:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX447394/SRX447394.20_peaks.xls INFO @ Mon, 03 Jun 2019 15:52:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX447394/SRX447394.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:52:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX447394/SRX447394.20_summits.bed INFO @ Mon, 03 Jun 2019 15:52:29: 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。