Job ID = 1294883 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 15,665,769 reads read : 15,665,769 reads written : 15,665,769 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: 00:05:51 15665769 reads; of these: 15665769 (100.00%) were unpaired; of these: 773595 (4.94%) aligned 0 times 11476917 (73.26%) aligned exactly 1 time 3415257 (21.80%) aligned >1 times 95.06% overall alignment rate Time searching: 00:05:51 Overall time: 00:05:51 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] 1399806 / 14892174 = 0.0940 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 10:49:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287961/SRX287961.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287961/SRX287961.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287961/SRX287961.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287961/SRX287961.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 10:49:55: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:49:55: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:49:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287961/SRX287961.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287961/SRX287961.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287961/SRX287961.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287961/SRX287961.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 10:49:55: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:49:55: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:49:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287961/SRX287961.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287961/SRX287961.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287961/SRX287961.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287961/SRX287961.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 10:49:55: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:49:55: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:50:02: 1000000 INFO @ Mon, 03 Jun 2019 10:50:02: 1000000 INFO @ Mon, 03 Jun 2019 10:50:02: 1000000 INFO @ Mon, 03 Jun 2019 10:50:10: 2000000 INFO @ Mon, 03 Jun 2019 10:50:10: 2000000 INFO @ Mon, 03 Jun 2019 10:50:10: 2000000 INFO @ Mon, 03 Jun 2019 10:50:17: 3000000 INFO @ Mon, 03 Jun 2019 10:50:17: 3000000 INFO @ Mon, 03 Jun 2019 10:50:18: 3000000 INFO @ Mon, 03 Jun 2019 10:50:24: 4000000 INFO @ Mon, 03 Jun 2019 10:50:24: 4000000 INFO @ Mon, 03 Jun 2019 10:50:26: 4000000 INFO @ Mon, 03 Jun 2019 10:50:31: 5000000 INFO @ Mon, 03 Jun 2019 10:50:31: 5000000 INFO @ Mon, 03 Jun 2019 10:50:33: 5000000 INFO @ Mon, 03 Jun 2019 10:50:38: 6000000 INFO @ Mon, 03 Jun 2019 10:50:38: 6000000 INFO @ Mon, 03 Jun 2019 10:50:40: 6000000 INFO @ Mon, 03 Jun 2019 10:50:44: 7000000 INFO @ Mon, 03 Jun 2019 10:50:45: 7000000 INFO @ Mon, 03 Jun 2019 10:50:47: 7000000 INFO @ Mon, 03 Jun 2019 10:50:50: 8000000 INFO @ Mon, 03 Jun 2019 10:50:51: 8000000 INFO @ Mon, 03 Jun 2019 10:50:54: 8000000 INFO @ Mon, 03 Jun 2019 10:50:57: 9000000 INFO @ Mon, 03 Jun 2019 10:50:57: 9000000 INFO @ Mon, 03 Jun 2019 10:51:01: 9000000 INFO @ Mon, 03 Jun 2019 10:51:03: 10000000 INFO @ Mon, 03 Jun 2019 10:51:04: 10000000 INFO @ Mon, 03 Jun 2019 10:51:08: 10000000 INFO @ Mon, 03 Jun 2019 10:51:10: 11000000 INFO @ Mon, 03 Jun 2019 10:51:10: 11000000 INFO @ Mon, 03 Jun 2019 10:51:16: 12000000 INFO @ Mon, 03 Jun 2019 10:51:17: 11000000 INFO @ Mon, 03 Jun 2019 10:51:17: 12000000 INFO @ Mon, 03 Jun 2019 10:51:23: 13000000 INFO @ Mon, 03 Jun 2019 10:51:23: 13000000 INFO @ Mon, 03 Jun 2019 10:51:24: 12000000 INFO @ Mon, 03 Jun 2019 10:51:27: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:51:27: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:51:27: #1 total tags in treatment: 13492368 INFO @ Mon, 03 Jun 2019 10:51:27: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:51:27: #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 10:51:27: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:51:27: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:51:27: #1 total tags in treatment: 13492368 INFO @ Mon, 03 Jun 2019 10:51:27: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:51:27: #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 10:51:27: #1 tags after filtering in treatment: 13492368 INFO @ Mon, 03 Jun 2019 10:51:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:51:27: #1 finished! INFO @ Mon, 03 Jun 2019 10:51:27: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:51:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:51:27: #1 tags after filtering in treatment: 13492368 INFO @ Mon, 03 Jun 2019 10:51:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:51:27: #1 finished! INFO @ Mon, 03 Jun 2019 10:51:27: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:51:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:51:28: #2 number of paired peaks: 611 WARNING @ Mon, 03 Jun 2019 10:51:28: Fewer paired peaks (611) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 611 pairs to build model! INFO @ Mon, 03 Jun 2019 10:51:28: start model_add_line... INFO @ Mon, 03 Jun 2019 10:51:28: #2 number of paired peaks: 611 WARNING @ Mon, 03 Jun 2019 10:51:28: Fewer paired peaks (611) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 611 pairs to build model! INFO @ Mon, 03 Jun 2019 10:51:28: start model_add_line... INFO @ Mon, 03 Jun 2019 10:51:28: start X-correlation... INFO @ Mon, 03 Jun 2019 10:51:28: end of X-cor INFO @ Mon, 03 Jun 2019 10:51:28: #2 finished! INFO @ Mon, 03 Jun 2019 10:51:28: #2 predicted fragment length is 178 bps INFO @ Mon, 03 Jun 2019 10:51:28: #2 alternative fragment length(s) may be 178 bps INFO @ Mon, 03 Jun 2019 10:51:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287961/SRX287961.20_model.r INFO @ Mon, 03 Jun 2019 10:51:28: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:51:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:51:28: start X-correlation... INFO @ Mon, 03 Jun 2019 10:51:28: end of X-cor INFO @ Mon, 03 Jun 2019 10:51:28: #2 finished! INFO @ Mon, 03 Jun 2019 10:51:28: #2 predicted fragment length is 178 bps INFO @ Mon, 03 Jun 2019 10:51:28: #2 alternative fragment length(s) may be 178 bps INFO @ Mon, 03 Jun 2019 10:51:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287961/SRX287961.10_model.r INFO @ Mon, 03 Jun 2019 10:51:28: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:51:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:51:31: 13000000 INFO @ Mon, 03 Jun 2019 10:51:34: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:51:34: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:51:34: #1 total tags in treatment: 13492368 INFO @ Mon, 03 Jun 2019 10:51:34: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:51:34: #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 10:51:35: #1 tags after filtering in treatment: 13492368 INFO @ Mon, 03 Jun 2019 10:51:35: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:51:35: #1 finished! INFO @ Mon, 03 Jun 2019 10:51:35: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:51:35: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:51:36: #2 number of paired peaks: 611 WARNING @ Mon, 03 Jun 2019 10:51:36: Fewer paired peaks (611) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 611 pairs to build model! INFO @ Mon, 03 Jun 2019 10:51:36: start model_add_line... INFO @ Mon, 03 Jun 2019 10:51:36: start X-correlation... INFO @ Mon, 03 Jun 2019 10:51:36: end of X-cor INFO @ Mon, 03 Jun 2019 10:51:36: #2 finished! INFO @ Mon, 03 Jun 2019 10:51:36: #2 predicted fragment length is 178 bps INFO @ Mon, 03 Jun 2019 10:51:36: #2 alternative fragment length(s) may be 178 bps INFO @ Mon, 03 Jun 2019 10:51:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287961/SRX287961.05_model.r INFO @ Mon, 03 Jun 2019 10:51:36: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:51:36: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:52:07: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:52:07: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:52:16: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:52:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287961/SRX287961.10_peaks.xls INFO @ Mon, 03 Jun 2019 10:52:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287961/SRX287961.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:52:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287961/SRX287961.10_summits.bed INFO @ Mon, 03 Jun 2019 10:52:27: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5599 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:52:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287961/SRX287961.20_peaks.xls INFO @ Mon, 03 Jun 2019 10:52:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287961/SRX287961.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:52:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287961/SRX287961.20_summits.bed INFO @ Mon, 03 Jun 2019 10:52:28: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3114 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:52:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287961/SRX287961.05_peaks.xls INFO @ Mon, 03 Jun 2019 10:52:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287961/SRX287961.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:52:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287961/SRX287961.05_summits.bed INFO @ Mon, 03 Jun 2019 10:52:36: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7974 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。