Job ID = 1294006 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 18,406,223 reads read : 18,406,223 reads written : 18,406,223 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: 00:07:07 18406223 reads; of these: 18406223 (100.00%) were unpaired; of these: 484657 (2.63%) aligned 0 times 11776062 (63.98%) aligned exactly 1 time 6145504 (33.39%) aligned >1 times 97.37% overall alignment rate Time searching: 00:07:07 Overall time: 00:07:07 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] 3244589 / 17921566 = 0.1810 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 04:10:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX160146/SRX160146.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX160146/SRX160146.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX160146/SRX160146.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX160146/SRX160146.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 04:10:46: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:10:46: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:10:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX160146/SRX160146.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX160146/SRX160146.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX160146/SRX160146.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX160146/SRX160146.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 04:10:46: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:10:46: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:10:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX160146/SRX160146.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX160146/SRX160146.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX160146/SRX160146.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX160146/SRX160146.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 04:10:46: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:10:46: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:10:53: 1000000 INFO @ Mon, 03 Jun 2019 04:10:54: 1000000 INFO @ Mon, 03 Jun 2019 04:10:54: 1000000 INFO @ Mon, 03 Jun 2019 04:10:59: 2000000 INFO @ Mon, 03 Jun 2019 04:11:01: 2000000 INFO @ Mon, 03 Jun 2019 04:11:01: 2000000 INFO @ Mon, 03 Jun 2019 04:11:06: 3000000 INFO @ Mon, 03 Jun 2019 04:11:08: 3000000 INFO @ Mon, 03 Jun 2019 04:11:09: 3000000 INFO @ Mon, 03 Jun 2019 04:11:12: 4000000 INFO @ Mon, 03 Jun 2019 04:11:15: 4000000 INFO @ Mon, 03 Jun 2019 04:11:16: 4000000 INFO @ Mon, 03 Jun 2019 04:11:19: 5000000 INFO @ Mon, 03 Jun 2019 04:11:22: 5000000 INFO @ Mon, 03 Jun 2019 04:11:23: 5000000 INFO @ Mon, 03 Jun 2019 04:11:25: 6000000 INFO @ Mon, 03 Jun 2019 04:11:30: 6000000 INFO @ Mon, 03 Jun 2019 04:11:30: 6000000 INFO @ Mon, 03 Jun 2019 04:11:31: 7000000 INFO @ Mon, 03 Jun 2019 04:11:37: 7000000 INFO @ Mon, 03 Jun 2019 04:11:37: 7000000 INFO @ Mon, 03 Jun 2019 04:11:38: 8000000 INFO @ Mon, 03 Jun 2019 04:11:44: 8000000 INFO @ Mon, 03 Jun 2019 04:11:44: 9000000 INFO @ Mon, 03 Jun 2019 04:11:44: 8000000 INFO @ Mon, 03 Jun 2019 04:11:51: 10000000 INFO @ Mon, 03 Jun 2019 04:11:51: 9000000 INFO @ Mon, 03 Jun 2019 04:11:52: 9000000 INFO @ Mon, 03 Jun 2019 04:11:57: 11000000 INFO @ Mon, 03 Jun 2019 04:11:58: 10000000 INFO @ Mon, 03 Jun 2019 04:11:59: 10000000 INFO @ Mon, 03 Jun 2019 04:12:03: 12000000 INFO @ Mon, 03 Jun 2019 04:12:05: 11000000 INFO @ Mon, 03 Jun 2019 04:12:06: 11000000 INFO @ Mon, 03 Jun 2019 04:12:10: 13000000 INFO @ Mon, 03 Jun 2019 04:12:12: 12000000 INFO @ Mon, 03 Jun 2019 04:12:13: 12000000 INFO @ Mon, 03 Jun 2019 04:12:16: 14000000 INFO @ Mon, 03 Jun 2019 04:12:20: 13000000 INFO @ Mon, 03 Jun 2019 04:12:20: 13000000 INFO @ Mon, 03 Jun 2019 04:12:21: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 04:12:21: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 04:12:21: #1 total tags in treatment: 14676977 INFO @ Mon, 03 Jun 2019 04:12:21: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:12:21: #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 04:12:21: #1 tags after filtering in treatment: 14676977 INFO @ Mon, 03 Jun 2019 04:12:21: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:12:21: #1 finished! INFO @ Mon, 03 Jun 2019 04:12:21: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:12:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:12:22: #2 number of paired peaks: 883 WARNING @ Mon, 03 Jun 2019 04:12:22: Fewer paired peaks (883) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 883 pairs to build model! INFO @ Mon, 03 Jun 2019 04:12:22: start model_add_line... INFO @ Mon, 03 Jun 2019 04:12:22: start X-correlation... INFO @ Mon, 03 Jun 2019 04:12:22: end of X-cor INFO @ Mon, 03 Jun 2019 04:12:22: #2 finished! INFO @ Mon, 03 Jun 2019 04:12:22: #2 predicted fragment length is 77 bps INFO @ Mon, 03 Jun 2019 04:12:22: #2 alternative fragment length(s) may be 4,77 bps INFO @ Mon, 03 Jun 2019 04:12:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX160146/SRX160146.10_model.r INFO @ Mon, 03 Jun 2019 04:12:22: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:12:22: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:12:27: 14000000 INFO @ Mon, 03 Jun 2019 04:12:27: 14000000 INFO @ Mon, 03 Jun 2019 04:12:32: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 04:12:32: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 04:12:32: #1 total tags in treatment: 14676977 INFO @ Mon, 03 Jun 2019 04:12:32: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:12:32: #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 04:12:32: #1 tags after filtering in treatment: 14676977 INFO @ Mon, 03 Jun 2019 04:12:32: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:12:32: #1 finished! INFO @ Mon, 03 Jun 2019 04:12:32: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:12:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:12:32: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 04:12:32: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 04:12:32: #1 total tags in treatment: 14676977 INFO @ Mon, 03 Jun 2019 04:12:32: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:12:32: #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 04:12:32: #1 tags after filtering in treatment: 14676977 INFO @ Mon, 03 Jun 2019 04:12:32: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:12:32: #1 finished! INFO @ Mon, 03 Jun 2019 04:12:32: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:12:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:12:33: #2 number of paired peaks: 883 WARNING @ Mon, 03 Jun 2019 04:12:33: Fewer paired peaks (883) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 883 pairs to build model! INFO @ Mon, 03 Jun 2019 04:12:33: start model_add_line... INFO @ Mon, 03 Jun 2019 04:12:33: start X-correlation... INFO @ Mon, 03 Jun 2019 04:12:33: end of X-cor INFO @ Mon, 03 Jun 2019 04:12:33: #2 finished! INFO @ Mon, 03 Jun 2019 04:12:33: #2 predicted fragment length is 77 bps INFO @ Mon, 03 Jun 2019 04:12:33: #2 alternative fragment length(s) may be 4,77 bps INFO @ Mon, 03 Jun 2019 04:12:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX160146/SRX160146.20_model.r INFO @ Mon, 03 Jun 2019 04:12:33: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:12:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:12:34: #2 number of paired peaks: 883 WARNING @ Mon, 03 Jun 2019 04:12:34: Fewer paired peaks (883) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 883 pairs to build model! INFO @ Mon, 03 Jun 2019 04:12:34: start model_add_line... INFO @ Mon, 03 Jun 2019 04:12:34: start X-correlation... INFO @ Mon, 03 Jun 2019 04:12:34: end of X-cor INFO @ Mon, 03 Jun 2019 04:12:34: #2 finished! INFO @ Mon, 03 Jun 2019 04:12:34: #2 predicted fragment length is 77 bps INFO @ Mon, 03 Jun 2019 04:12:34: #2 alternative fragment length(s) may be 4,77 bps INFO @ Mon, 03 Jun 2019 04:12:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX160146/SRX160146.05_model.r INFO @ Mon, 03 Jun 2019 04:12:34: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:12:34: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:13:03: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:13:14: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:13:14: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:13:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX160146/SRX160146.10_peaks.xls INFO @ Mon, 03 Jun 2019 04:13:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX160146/SRX160146.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:13:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX160146/SRX160146.10_summits.bed INFO @ Mon, 03 Jun 2019 04:13:23: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2187 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 04:13:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX160146/SRX160146.05_peaks.xls INFO @ Mon, 03 Jun 2019 04:13:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX160146/SRX160146.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:13:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX160146/SRX160146.05_summits.bed INFO @ Mon, 03 Jun 2019 04:13:34: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3614 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 04:13:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX160146/SRX160146.20_peaks.xls INFO @ Mon, 03 Jun 2019 04:13:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX160146/SRX160146.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:13:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX160146/SRX160146.20_summits.bed INFO @ Mon, 03 Jun 2019 04:13:35: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1301 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。