Job ID = 1293270 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 25,880,232 reads read : 25,880,232 reads written : 25,880,232 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: 00:05:58 25880232 reads; of these: 25880232 (100.00%) were unpaired; of these: 757158 (2.93%) aligned 0 times 21360448 (82.54%) aligned exactly 1 time 3762626 (14.54%) aligned >1 times 97.07% overall alignment rate Time searching: 00:05:58 Overall time: 00:05:58 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] 6956870 / 25123074 = 0.2769 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 @ Sun, 02 Jun 2019 22:58:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX011409/ERX011409.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX011409/ERX011409.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX011409/ERX011409.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX011409/ERX011409.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 @ Sun, 02 Jun 2019 22:58:12: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:58:12: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:58:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX011409/ERX011409.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX011409/ERX011409.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX011409/ERX011409.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX011409/ERX011409.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 @ Sun, 02 Jun 2019 22:58:12: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:58:12: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:58:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX011409/ERX011409.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX011409/ERX011409.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX011409/ERX011409.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX011409/ERX011409.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 @ Sun, 02 Jun 2019 22:58:12: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:58:12: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:58:20: 1000000 INFO @ Sun, 02 Jun 2019 22:58:21: 1000000 INFO @ Sun, 02 Jun 2019 22:58:21: 1000000 INFO @ Sun, 02 Jun 2019 22:58:28: 2000000 INFO @ Sun, 02 Jun 2019 22:58:28: 2000000 INFO @ Sun, 02 Jun 2019 22:58:29: 2000000 INFO @ Sun, 02 Jun 2019 22:58:36: 3000000 INFO @ Sun, 02 Jun 2019 22:58:37: 3000000 INFO @ Sun, 02 Jun 2019 22:58:37: 3000000 INFO @ Sun, 02 Jun 2019 22:58:44: 4000000 INFO @ Sun, 02 Jun 2019 22:58:45: 4000000 INFO @ Sun, 02 Jun 2019 22:58:45: 4000000 INFO @ Sun, 02 Jun 2019 22:58:52: 5000000 INFO @ Sun, 02 Jun 2019 22:58:53: 5000000 INFO @ Sun, 02 Jun 2019 22:58:53: 5000000 INFO @ Sun, 02 Jun 2019 22:59:00: 6000000 INFO @ Sun, 02 Jun 2019 22:59:01: 6000000 INFO @ Sun, 02 Jun 2019 22:59:01: 6000000 INFO @ Sun, 02 Jun 2019 22:59:07: 7000000 INFO @ Sun, 02 Jun 2019 22:59:08: 7000000 INFO @ Sun, 02 Jun 2019 22:59:09: 7000000 INFO @ Sun, 02 Jun 2019 22:59:15: 8000000 INFO @ Sun, 02 Jun 2019 22:59:16: 8000000 INFO @ Sun, 02 Jun 2019 22:59:16: 8000000 INFO @ Sun, 02 Jun 2019 22:59:22: 9000000 INFO @ Sun, 02 Jun 2019 22:59:24: 9000000 INFO @ Sun, 02 Jun 2019 22:59:24: 9000000 INFO @ Sun, 02 Jun 2019 22:59:30: 10000000 INFO @ Sun, 02 Jun 2019 22:59:32: 10000000 INFO @ Sun, 02 Jun 2019 22:59:32: 10000000 INFO @ Sun, 02 Jun 2019 22:59:37: 11000000 INFO @ Sun, 02 Jun 2019 22:59:39: 11000000 INFO @ Sun, 02 Jun 2019 22:59:40: 11000000 INFO @ Sun, 02 Jun 2019 22:59:45: 12000000 INFO @ Sun, 02 Jun 2019 22:59:47: 12000000 INFO @ Sun, 02 Jun 2019 22:59:47: 12000000 INFO @ Sun, 02 Jun 2019 22:59:52: 13000000 INFO @ Sun, 02 Jun 2019 22:59:54: 13000000 INFO @ Sun, 02 Jun 2019 22:59:54: 13000000 INFO @ Sun, 02 Jun 2019 23:00:00: 14000000 INFO @ Sun, 02 Jun 2019 23:00:02: 14000000 INFO @ Sun, 02 Jun 2019 23:00:02: 14000000 INFO @ Sun, 02 Jun 2019 23:00:07: 15000000 INFO @ Sun, 02 Jun 2019 23:00:09: 15000000 INFO @ Sun, 02 Jun 2019 23:00:10: 15000000 INFO @ Sun, 02 Jun 2019 23:00:15: 16000000 INFO @ Sun, 02 Jun 2019 23:00:17: 16000000 INFO @ Sun, 02 Jun 2019 23:00:17: 16000000 INFO @ Sun, 02 Jun 2019 23:00:22: 17000000 INFO @ Sun, 02 Jun 2019 23:00:24: 17000000 INFO @ Sun, 02 Jun 2019 23:00:24: 17000000 INFO @ Sun, 02 Jun 2019 23:00:30: 18000000 INFO @ Sun, 02 Jun 2019 23:00:31: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 23:00:31: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 23:00:31: #1 total tags in treatment: 18166204 INFO @ Sun, 02 Jun 2019 23:00:31: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 23:00:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 23:00:32: #1 tags after filtering in treatment: 18166204 INFO @ Sun, 02 Jun 2019 23:00:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 23:00:32: #1 finished! INFO @ Sun, 02 Jun 2019 23:00:32: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 23:00:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 23:00:32: 18000000 INFO @ Sun, 02 Jun 2019 23:00:32: 18000000 INFO @ Sun, 02 Jun 2019 23:00:33: #2 number of paired peaks: 862 WARNING @ Sun, 02 Jun 2019 23:00:33: Fewer paired peaks (862) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 862 pairs to build model! INFO @ Sun, 02 Jun 2019 23:00:33: start model_add_line... INFO @ Sun, 02 Jun 2019 23:00:33: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 23:00:33: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 23:00:33: #1 total tags in treatment: 18166204 INFO @ Sun, 02 Jun 2019 23:00:33: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 23:00:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 23:00:33: start X-correlation... INFO @ Sun, 02 Jun 2019 23:00:33: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 23:00:33: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 23:00:33: #1 total tags in treatment: 18166204 INFO @ Sun, 02 Jun 2019 23:00:33: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 23:00:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 23:00:33: end of X-cor INFO @ Sun, 02 Jun 2019 23:00:33: #2 finished! INFO @ Sun, 02 Jun 2019 23:00:33: #2 predicted fragment length is 183 bps INFO @ Sun, 02 Jun 2019 23:00:33: #2 alternative fragment length(s) may be 183 bps INFO @ Sun, 02 Jun 2019 23:00:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX011409/ERX011409.05_model.r INFO @ Sun, 02 Jun 2019 23:00:33: #3 Call peaks... INFO @ Sun, 02 Jun 2019 23:00:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 23:00:34: #1 tags after filtering in treatment: 18166204 INFO @ Sun, 02 Jun 2019 23:00:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 23:00:34: #1 finished! INFO @ Sun, 02 Jun 2019 23:00:34: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 23:00:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 23:00:34: #1 tags after filtering in treatment: 18166204 INFO @ Sun, 02 Jun 2019 23:00:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 23:00:34: #1 finished! INFO @ Sun, 02 Jun 2019 23:00:34: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 23:00:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 23:00:35: #2 number of paired peaks: 862 WARNING @ Sun, 02 Jun 2019 23:00:35: Fewer paired peaks (862) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 862 pairs to build model! INFO @ Sun, 02 Jun 2019 23:00:35: start model_add_line... INFO @ Sun, 02 Jun 2019 23:00:36: #2 number of paired peaks: 862 WARNING @ Sun, 02 Jun 2019 23:00:36: Fewer paired peaks (862) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 862 pairs to build model! INFO @ Sun, 02 Jun 2019 23:00:36: start model_add_line... INFO @ Sun, 02 Jun 2019 23:00:36: start X-correlation... INFO @ Sun, 02 Jun 2019 23:00:36: end of X-cor INFO @ Sun, 02 Jun 2019 23:00:36: #2 finished! INFO @ Sun, 02 Jun 2019 23:00:36: #2 predicted fragment length is 183 bps INFO @ Sun, 02 Jun 2019 23:00:36: #2 alternative fragment length(s) may be 183 bps INFO @ Sun, 02 Jun 2019 23:00:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX011409/ERX011409.10_model.r INFO @ Sun, 02 Jun 2019 23:00:36: #3 Call peaks... INFO @ Sun, 02 Jun 2019 23:00:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 23:00:36: start X-correlation... INFO @ Sun, 02 Jun 2019 23:00:36: end of X-cor INFO @ Sun, 02 Jun 2019 23:00:36: #2 finished! INFO @ Sun, 02 Jun 2019 23:00:36: #2 predicted fragment length is 183 bps INFO @ Sun, 02 Jun 2019 23:00:36: #2 alternative fragment length(s) may be 183 bps INFO @ Sun, 02 Jun 2019 23:00:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX011409/ERX011409.20_model.r INFO @ Sun, 02 Jun 2019 23:00:36: #3 Call peaks... INFO @ Sun, 02 Jun 2019 23:00:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 23:01:25: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 23:01:27: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 23:01:28: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 23:01:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX011409/ERX011409.05_peaks.xls INFO @ Sun, 02 Jun 2019 23:01:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX011409/ERX011409.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 23:01:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX011409/ERX011409.05_summits.bed INFO @ Sun, 02 Jun 2019 23:01:51: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (8645 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 23:01:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX011409/ERX011409.10_peaks.xls INFO @ Sun, 02 Jun 2019 23:01:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX011409/ERX011409.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 23:01:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX011409/ERX011409.10_summits.bed INFO @ Sun, 02 Jun 2019 23:01:52: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6538 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 23:01:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX011409/ERX011409.20_peaks.xls INFO @ Sun, 02 Jun 2019 23:01:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX011409/ERX011409.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 23:01:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX011409/ERX011409.20_summits.bed INFO @ Sun, 02 Jun 2019 23:01:53: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4280 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。