Job ID = 2590371 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 14,583,801 reads read : 29,167,602 reads written : 14,583,801 reads 0-length : 14,583,801 spots read : 14,472,446 reads read : 28,944,892 reads written : 14,472,446 reads 0-length : 14,472,446 spots read : 14,455,423 reads read : 28,910,846 reads written : 14,455,423 reads 0-length : 14,455,423 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: 00:11:37 43511670 reads; of these: 43511670 (100.00%) were unpaired; of these: 1373465 (3.16%) aligned 0 times 35286795 (81.10%) aligned exactly 1 time 6851410 (15.75%) aligned >1 times 96.84% overall alignment rate Time searching: 00:11:37 Overall time: 00:11:37 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_rmdupse_core] 9063296 / 42138205 = 0.2151 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 21:41:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981643/SRX3981643.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981643/SRX3981643.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981643/SRX3981643.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981643/SRX3981643.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 21:41:25: #1 read tag files... INFO @ Mon, 12 Aug 2019 21:41:25: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 21:41:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981643/SRX3981643.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981643/SRX3981643.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981643/SRX3981643.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981643/SRX3981643.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 21:41:26: #1 read tag files... INFO @ Mon, 12 Aug 2019 21:41:26: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 21:41:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981643/SRX3981643.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981643/SRX3981643.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981643/SRX3981643.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981643/SRX3981643.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 21:41:27: #1 read tag files... INFO @ Mon, 12 Aug 2019 21:41:27: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 21:41:34: 1000000 INFO @ Mon, 12 Aug 2019 21:41:35: 1000000 INFO @ Mon, 12 Aug 2019 21:41:36: 1000000 INFO @ Mon, 12 Aug 2019 21:41:43: 2000000 INFO @ Mon, 12 Aug 2019 21:41:44: 2000000 INFO @ Mon, 12 Aug 2019 21:41:47: 2000000 INFO @ Mon, 12 Aug 2019 21:41:51: 3000000 INFO @ Mon, 12 Aug 2019 21:41:55: 3000000 INFO @ Mon, 12 Aug 2019 21:41:58: 3000000 INFO @ Mon, 12 Aug 2019 21:41:58: 4000000 INFO @ Mon, 12 Aug 2019 21:42:05: 4000000 INFO @ Mon, 12 Aug 2019 21:42:06: 5000000 INFO @ Mon, 12 Aug 2019 21:42:07: 4000000 INFO @ Mon, 12 Aug 2019 21:42:14: 6000000 INFO @ Mon, 12 Aug 2019 21:42:15: 5000000 INFO @ Mon, 12 Aug 2019 21:42:17: 5000000 INFO @ Mon, 12 Aug 2019 21:42:22: 7000000 INFO @ Mon, 12 Aug 2019 21:42:25: 6000000 INFO @ Mon, 12 Aug 2019 21:42:27: 6000000 INFO @ Mon, 12 Aug 2019 21:42:31: 8000000 INFO @ Mon, 12 Aug 2019 21:42:35: 7000000 INFO @ Mon, 12 Aug 2019 21:42:38: 7000000 INFO @ Mon, 12 Aug 2019 21:42:39: 9000000 INFO @ Mon, 12 Aug 2019 21:42:46: 8000000 INFO @ Mon, 12 Aug 2019 21:42:48: 10000000 INFO @ Mon, 12 Aug 2019 21:42:48: 8000000 INFO @ Mon, 12 Aug 2019 21:42:55: 11000000 INFO @ Mon, 12 Aug 2019 21:42:56: 9000000 INFO @ Mon, 12 Aug 2019 21:42:59: 9000000 INFO @ Mon, 12 Aug 2019 21:43:03: 12000000 INFO @ Mon, 12 Aug 2019 21:43:06: 10000000 INFO @ Mon, 12 Aug 2019 21:43:09: 10000000 INFO @ Mon, 12 Aug 2019 21:43:11: 13000000 INFO @ Mon, 12 Aug 2019 21:43:16: 11000000 INFO @ Mon, 12 Aug 2019 21:43:18: 11000000 INFO @ Mon, 12 Aug 2019 21:43:19: 14000000 INFO @ Mon, 12 Aug 2019 21:43:26: 12000000 INFO @ Mon, 12 Aug 2019 21:43:27: 15000000 INFO @ Mon, 12 Aug 2019 21:43:28: 12000000 INFO @ Mon, 12 Aug 2019 21:43:35: 16000000 INFO @ Mon, 12 Aug 2019 21:43:35: 13000000 INFO @ Mon, 12 Aug 2019 21:43:38: 13000000 INFO @ Mon, 12 Aug 2019 21:43:42: 17000000 INFO @ Mon, 12 Aug 2019 21:43:45: 14000000 INFO @ Mon, 12 Aug 2019 21:43:47: 14000000 INFO @ Mon, 12 Aug 2019 21:43:50: 18000000 INFO @ Mon, 12 Aug 2019 21:43:55: 15000000 INFO @ Mon, 12 Aug 2019 21:43:57: 15000000 INFO @ Mon, 12 Aug 2019 21:43:58: 19000000 INFO @ Mon, 12 Aug 2019 21:44:04: 16000000 INFO @ Mon, 12 Aug 2019 21:44:06: 20000000 INFO @ Mon, 12 Aug 2019 21:44:06: 16000000 INFO @ Mon, 12 Aug 2019 21:44:14: 17000000 INFO @ Mon, 12 Aug 2019 21:44:14: 21000000 INFO @ Mon, 12 Aug 2019 21:44:16: 17000000 INFO @ Mon, 12 Aug 2019 21:44:22: 22000000 INFO @ Mon, 12 Aug 2019 21:44:24: 18000000 INFO @ Mon, 12 Aug 2019 21:44:26: 18000000 INFO @ Mon, 12 Aug 2019 21:44:30: 23000000 INFO @ Mon, 12 Aug 2019 21:44:33: 19000000 INFO @ Mon, 12 Aug 2019 21:44:35: 19000000 INFO @ Mon, 12 Aug 2019 21:44:39: 24000000 INFO @ Mon, 12 Aug 2019 21:44:42: 20000000 INFO @ Mon, 12 Aug 2019 21:44:44: 20000000 INFO @ Mon, 12 Aug 2019 21:44:47: 25000000 INFO @ Mon, 12 Aug 2019 21:44:52: 21000000 INFO @ Mon, 12 Aug 2019 21:44:54: 21000000 INFO @ Mon, 12 Aug 2019 21:44:56: 26000000 INFO @ Mon, 12 Aug 2019 21:45:02: 22000000 INFO @ Mon, 12 Aug 2019 21:45:04: 22000000 INFO @ Mon, 12 Aug 2019 21:45:05: 27000000 INFO @ Mon, 12 Aug 2019 21:45:11: 23000000 INFO @ Mon, 12 Aug 2019 21:45:13: 23000000 INFO @ Mon, 12 Aug 2019 21:45:14: 28000000 INFO @ Mon, 12 Aug 2019 21:45:19: 24000000 INFO @ Mon, 12 Aug 2019 21:45:21: 24000000 INFO @ Mon, 12 Aug 2019 21:45:22: 29000000 INFO @ Mon, 12 Aug 2019 21:45:27: 25000000 INFO @ Mon, 12 Aug 2019 21:45:29: 25000000 INFO @ Mon, 12 Aug 2019 21:45:31: 30000000 INFO @ Mon, 12 Aug 2019 21:45:35: 26000000 INFO @ Mon, 12 Aug 2019 21:45:37: 26000000 INFO @ Mon, 12 Aug 2019 21:45:39: 31000000 INFO @ Mon, 12 Aug 2019 21:45:43: 27000000 INFO @ Mon, 12 Aug 2019 21:45:45: 27000000 INFO @ Mon, 12 Aug 2019 21:45:47: 32000000 INFO @ Mon, 12 Aug 2019 21:45:51: 28000000 INFO @ Mon, 12 Aug 2019 21:45:53: 28000000 INFO @ Mon, 12 Aug 2019 21:45:55: 33000000 INFO @ Mon, 12 Aug 2019 21:45:56: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 21:45:56: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 21:45:56: #1 total tags in treatment: 33074909 INFO @ Mon, 12 Aug 2019 21:45:56: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:45:56: #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 21:45:56: #1 tags after filtering in treatment: 33074909 INFO @ Mon, 12 Aug 2019 21:45:56: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:45:56: #1 finished! INFO @ Mon, 12 Aug 2019 21:45:56: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:45:56: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:45:59: 29000000 INFO @ Mon, 12 Aug 2019 21:45:59: #2 number of paired peaks: 525 WARNING @ Mon, 12 Aug 2019 21:45:59: Fewer paired peaks (525) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 525 pairs to build model! INFO @ Mon, 12 Aug 2019 21:45:59: start model_add_line... INFO @ Mon, 12 Aug 2019 21:45:59: start X-correlation... INFO @ Mon, 12 Aug 2019 21:45:59: end of X-cor INFO @ Mon, 12 Aug 2019 21:45:59: #2 finished! INFO @ Mon, 12 Aug 2019 21:45:59: #2 predicted fragment length is 1 bps INFO @ Mon, 12 Aug 2019 21:45:59: #2 alternative fragment length(s) may be 1,34,48,50,67,86,108,115,588 bps INFO @ Mon, 12 Aug 2019 21:45:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981643/SRX3981643.20_model.r WARNING @ Mon, 12 Aug 2019 21:45:59: #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, 12 Aug 2019 21:45:59: #2 You may need to consider one of the other alternative d(s): 1,34,48,50,67,86,108,115,588 WARNING @ Mon, 12 Aug 2019 21:45:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 21:45:59: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:45:59: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:46:01: 29000000 INFO @ Mon, 12 Aug 2019 21:46:07: 30000000 INFO @ Mon, 12 Aug 2019 21:46:09: 30000000 INFO @ Mon, 12 Aug 2019 21:46:14: 31000000 INFO @ Mon, 12 Aug 2019 21:46:17: 31000000 INFO @ Mon, 12 Aug 2019 21:46:23: 32000000 INFO @ Mon, 12 Aug 2019 21:46:26: 32000000 INFO @ Mon, 12 Aug 2019 21:46:33: 33000000 INFO @ Mon, 12 Aug 2019 21:46:33: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 21:46:33: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 21:46:33: #1 total tags in treatment: 33074909 INFO @ Mon, 12 Aug 2019 21:46:33: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:46:33: #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 21:46:34: #1 tags after filtering in treatment: 33074909 INFO @ Mon, 12 Aug 2019 21:46:34: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:46:34: #1 finished! INFO @ Mon, 12 Aug 2019 21:46:34: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:46:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:46:35: 33000000 INFO @ Mon, 12 Aug 2019 21:46:36: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 21:46:36: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 21:46:36: #1 total tags in treatment: 33074909 INFO @ Mon, 12 Aug 2019 21:46:36: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:46:36: #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 21:46:37: #1 tags after filtering in treatment: 33074909 INFO @ Mon, 12 Aug 2019 21:46:37: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:46:37: #1 finished! INFO @ Mon, 12 Aug 2019 21:46:37: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:46:37: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:46:37: #2 number of paired peaks: 525 WARNING @ Mon, 12 Aug 2019 21:46:37: Fewer paired peaks (525) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 525 pairs to build model! INFO @ Mon, 12 Aug 2019 21:46:37: start model_add_line... INFO @ Mon, 12 Aug 2019 21:46:37: start X-correlation... INFO @ Mon, 12 Aug 2019 21:46:37: end of X-cor INFO @ Mon, 12 Aug 2019 21:46:37: #2 finished! INFO @ Mon, 12 Aug 2019 21:46:37: #2 predicted fragment length is 1 bps INFO @ Mon, 12 Aug 2019 21:46:37: #2 alternative fragment length(s) may be 1,34,48,50,67,86,108,115,588 bps INFO @ Mon, 12 Aug 2019 21:46:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981643/SRX3981643.05_model.r WARNING @ Mon, 12 Aug 2019 21:46:37: #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, 12 Aug 2019 21:46:37: #2 You may need to consider one of the other alternative d(s): 1,34,48,50,67,86,108,115,588 WARNING @ Mon, 12 Aug 2019 21:46:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 21:46:37: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:46:37: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:46:39: #2 number of paired peaks: 525 WARNING @ Mon, 12 Aug 2019 21:46:39: Fewer paired peaks (525) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 525 pairs to build model! INFO @ Mon, 12 Aug 2019 21:46:39: start model_add_line... INFO @ Mon, 12 Aug 2019 21:46:40: start X-correlation... INFO @ Mon, 12 Aug 2019 21:46:40: end of X-cor INFO @ Mon, 12 Aug 2019 21:46:40: #2 finished! INFO @ Mon, 12 Aug 2019 21:46:40: #2 predicted fragment length is 1 bps INFO @ Mon, 12 Aug 2019 21:46:40: #2 alternative fragment length(s) may be 1,34,48,50,67,86,108,115,588 bps INFO @ Mon, 12 Aug 2019 21:46:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981643/SRX3981643.10_model.r WARNING @ Mon, 12 Aug 2019 21:46:40: #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, 12 Aug 2019 21:46:40: #2 You may need to consider one of the other alternative d(s): 1,34,48,50,67,86,108,115,588 WARNING @ Mon, 12 Aug 2019 21:46:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 21:46:40: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:46:40: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:46:58: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:47:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981643/SRX3981643.20_peaks.xls INFO @ Mon, 12 Aug 2019 21:47:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981643/SRX3981643.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:47:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981643/SRX3981643.20_summits.bed INFO @ Mon, 12 Aug 2019 21:47:25: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 21:47:37: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:47:39: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:48:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981643/SRX3981643.05_peaks.xls INFO @ Mon, 12 Aug 2019 21:48:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981643/SRX3981643.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:48:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981643/SRX3981643.05_summits.bed INFO @ Mon, 12 Aug 2019 21:48:03: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 21:48:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981643/SRX3981643.10_peaks.xls INFO @ Mon, 12 Aug 2019 21:48:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981643/SRX3981643.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:48:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981643/SRX3981643.10_summits.bed INFO @ Mon, 12 Aug 2019 21:48:05: Done! pass1 - making usageList (0 chroms): 2 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。