Job ID = 2590328 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 19,188,196 reads read : 19,188,196 reads written : 19,188,196 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1024307.sra.cache’: 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: 00:04:54 19188196 reads; of these: 19188196 (100.00%) were unpaired; of these: 2992212 (15.59%) aligned 0 times 12016107 (62.62%) aligned exactly 1 time 4179877 (21.78%) aligned >1 times 84.41% overall alignment rate Time searching: 00:04:54 Overall time: 00:04:54 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 8 files... [bam_rmdupse_core] 1800029 / 16195984 = 0.1111 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 20:51:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX373351/SRX373351.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX373351/SRX373351.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX373351/SRX373351.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX373351/SRX373351.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 20:51:24: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:51:24: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:51:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX373351/SRX373351.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX373351/SRX373351.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX373351/SRX373351.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX373351/SRX373351.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 20:51:25: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:51:25: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:51:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX373351/SRX373351.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX373351/SRX373351.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX373351/SRX373351.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX373351/SRX373351.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 20:51:26: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:51:26: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:51:32: 1000000 INFO @ Mon, 12 Aug 2019 20:51:33: 1000000 INFO @ Mon, 12 Aug 2019 20:51:33: 1000000 INFO @ Mon, 12 Aug 2019 20:51:40: 2000000 INFO @ Mon, 12 Aug 2019 20:51:40: 2000000 INFO @ Mon, 12 Aug 2019 20:51:41: 2000000 INFO @ Mon, 12 Aug 2019 20:51:47: 3000000 INFO @ Mon, 12 Aug 2019 20:51:48: 3000000 INFO @ Mon, 12 Aug 2019 20:51:49: 3000000 INFO @ Mon, 12 Aug 2019 20:51:54: 4000000 INFO @ Mon, 12 Aug 2019 20:51:56: 4000000 INFO @ Mon, 12 Aug 2019 20:51:57: 4000000 INFO @ Mon, 12 Aug 2019 20:52:01: 5000000 INFO @ Mon, 12 Aug 2019 20:52:03: 5000000 INFO @ Mon, 12 Aug 2019 20:52:06: 5000000 INFO @ Mon, 12 Aug 2019 20:52:09: 6000000 INFO @ Mon, 12 Aug 2019 20:52:11: 6000000 INFO @ Mon, 12 Aug 2019 20:52:15: 6000000 INFO @ Mon, 12 Aug 2019 20:52:16: 7000000 INFO @ Mon, 12 Aug 2019 20:52:19: 7000000 INFO @ Mon, 12 Aug 2019 20:52:23: 8000000 INFO @ Mon, 12 Aug 2019 20:52:23: 7000000 INFO @ Mon, 12 Aug 2019 20:52:27: 8000000 INFO @ Mon, 12 Aug 2019 20:52:30: 9000000 INFO @ Mon, 12 Aug 2019 20:52:32: 8000000 INFO @ Mon, 12 Aug 2019 20:52:35: 9000000 INFO @ Mon, 12 Aug 2019 20:52:37: 10000000 INFO @ Mon, 12 Aug 2019 20:52:42: 9000000 INFO @ Mon, 12 Aug 2019 20:52:43: 10000000 INFO @ Mon, 12 Aug 2019 20:52:44: 11000000 INFO @ Mon, 12 Aug 2019 20:52:51: 10000000 INFO @ Mon, 12 Aug 2019 20:52:51: 11000000 INFO @ Mon, 12 Aug 2019 20:52:51: 12000000 INFO @ Mon, 12 Aug 2019 20:52:59: 13000000 INFO @ Mon, 12 Aug 2019 20:52:59: 12000000 INFO @ Mon, 12 Aug 2019 20:53:00: 11000000 INFO @ Mon, 12 Aug 2019 20:53:06: 14000000 INFO @ Mon, 12 Aug 2019 20:53:07: 13000000 INFO @ Mon, 12 Aug 2019 20:53:09: #1 tag size is determined as 36 bps INFO @ Mon, 12 Aug 2019 20:53:09: #1 tag size = 36 INFO @ Mon, 12 Aug 2019 20:53:09: #1 total tags in treatment: 14395955 INFO @ Mon, 12 Aug 2019 20:53:09: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:53:09: #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 20:53:09: #1 tags after filtering in treatment: 14395955 INFO @ Mon, 12 Aug 2019 20:53:09: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:53:09: #1 finished! INFO @ Mon, 12 Aug 2019 20:53:09: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:53:09: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:53:09: 12000000 INFO @ Mon, 12 Aug 2019 20:53:10: #2 number of paired peaks: 723 WARNING @ Mon, 12 Aug 2019 20:53:10: Fewer paired peaks (723) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 723 pairs to build model! INFO @ Mon, 12 Aug 2019 20:53:10: start model_add_line... INFO @ Mon, 12 Aug 2019 20:53:10: start X-correlation... INFO @ Mon, 12 Aug 2019 20:53:10: end of X-cor INFO @ Mon, 12 Aug 2019 20:53:10: #2 finished! INFO @ Mon, 12 Aug 2019 20:53:10: #2 predicted fragment length is 127 bps INFO @ Mon, 12 Aug 2019 20:53:10: #2 alternative fragment length(s) may be 127 bps INFO @ Mon, 12 Aug 2019 20:53:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX373351/SRX373351.20_model.r INFO @ Mon, 12 Aug 2019 20:53:10: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:53:10: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:53:14: 14000000 INFO @ Mon, 12 Aug 2019 20:53:17: #1 tag size is determined as 36 bps INFO @ Mon, 12 Aug 2019 20:53:17: #1 tag size = 36 INFO @ Mon, 12 Aug 2019 20:53:17: #1 total tags in treatment: 14395955 INFO @ Mon, 12 Aug 2019 20:53:17: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:53:17: #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 20:53:18: #1 tags after filtering in treatment: 14395955 INFO @ Mon, 12 Aug 2019 20:53:18: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:53:18: #1 finished! INFO @ Mon, 12 Aug 2019 20:53:18: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:53:18: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:53:18: 13000000 INFO @ Mon, 12 Aug 2019 20:53:19: #2 number of paired peaks: 723 WARNING @ Mon, 12 Aug 2019 20:53:19: Fewer paired peaks (723) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 723 pairs to build model! INFO @ Mon, 12 Aug 2019 20:53:19: start model_add_line... INFO @ Mon, 12 Aug 2019 20:53:19: start X-correlation... INFO @ Mon, 12 Aug 2019 20:53:19: end of X-cor INFO @ Mon, 12 Aug 2019 20:53:19: #2 finished! INFO @ Mon, 12 Aug 2019 20:53:19: #2 predicted fragment length is 127 bps INFO @ Mon, 12 Aug 2019 20:53:19: #2 alternative fragment length(s) may be 127 bps INFO @ Mon, 12 Aug 2019 20:53:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX373351/SRX373351.05_model.r INFO @ Mon, 12 Aug 2019 20:53:19: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:53:19: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:53:27: 14000000 INFO @ Mon, 12 Aug 2019 20:53:30: #1 tag size is determined as 36 bps INFO @ Mon, 12 Aug 2019 20:53:30: #1 tag size = 36 INFO @ Mon, 12 Aug 2019 20:53:30: #1 total tags in treatment: 14395955 INFO @ Mon, 12 Aug 2019 20:53:30: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:53:30: #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 20:53:30: #1 tags after filtering in treatment: 14395955 INFO @ Mon, 12 Aug 2019 20:53:30: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:53:30: #1 finished! INFO @ Mon, 12 Aug 2019 20:53:30: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:53:30: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:53:32: #2 number of paired peaks: 723 WARNING @ Mon, 12 Aug 2019 20:53:32: Fewer paired peaks (723) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 723 pairs to build model! INFO @ Mon, 12 Aug 2019 20:53:32: start model_add_line... INFO @ Mon, 12 Aug 2019 20:53:32: start X-correlation... INFO @ Mon, 12 Aug 2019 20:53:32: end of X-cor INFO @ Mon, 12 Aug 2019 20:53:32: #2 finished! INFO @ Mon, 12 Aug 2019 20:53:32: #2 predicted fragment length is 127 bps INFO @ Mon, 12 Aug 2019 20:53:32: #2 alternative fragment length(s) may be 127 bps INFO @ Mon, 12 Aug 2019 20:53:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX373351/SRX373351.10_model.r INFO @ Mon, 12 Aug 2019 20:53:32: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:53:32: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:53:51: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:54:00: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:54:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX373351/SRX373351.20_peaks.xls INFO @ Mon, 12 Aug 2019 20:54:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX373351/SRX373351.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:54:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX373351/SRX373351.20_summits.bed INFO @ Mon, 12 Aug 2019 20:54:11: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1008 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:54:12: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:54:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX373351/SRX373351.05_peaks.xls INFO @ Mon, 12 Aug 2019 20:54:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX373351/SRX373351.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:54:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX373351/SRX373351.05_summits.bed INFO @ Mon, 12 Aug 2019 20:54:19: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3977 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:54:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX373351/SRX373351.10_peaks.xls INFO @ Mon, 12 Aug 2019 20:54:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX373351/SRX373351.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:54:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX373351/SRX373351.10_summits.bed INFO @ Mon, 12 Aug 2019 20:54:32: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2299 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。