Job ID = 1301286 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 24,256,281 reads read : 24,256,281 reads written : 24,256,281 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: 00:05:56 24256281 reads; of these: 24256281 (100.00%) were unpaired; of these: 6111127 (25.19%) aligned 0 times 15253743 (62.89%) aligned exactly 1 time 2891411 (11.92%) aligned >1 times 74.81% overall alignment rate Time searching: 00:05:56 Overall time: 00:05:56 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] 11984545 / 18145154 = 0.6605 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 20:05:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX485211/SRX485211.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX485211/SRX485211.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX485211/SRX485211.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX485211/SRX485211.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 20:05:27: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:05:27: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:05:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX485211/SRX485211.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX485211/SRX485211.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX485211/SRX485211.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX485211/SRX485211.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 20:05:27: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:05:27: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:05:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX485211/SRX485211.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX485211/SRX485211.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX485211/SRX485211.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX485211/SRX485211.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 20:05:27: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:05:27: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:05:36: 1000000 INFO @ Mon, 03 Jun 2019 20:05:37: 1000000 INFO @ Mon, 03 Jun 2019 20:05:40: 1000000 INFO @ Mon, 03 Jun 2019 20:05:44: 2000000 INFO @ Mon, 03 Jun 2019 20:05:47: 2000000 INFO @ Mon, 03 Jun 2019 20:05:53: 3000000 INFO @ Mon, 03 Jun 2019 20:05:54: 2000000 INFO @ Mon, 03 Jun 2019 20:05:56: 3000000 INFO @ Mon, 03 Jun 2019 20:06:01: 4000000 INFO @ Mon, 03 Jun 2019 20:06:06: 4000000 INFO @ Mon, 03 Jun 2019 20:06:07: 3000000 INFO @ Mon, 03 Jun 2019 20:06:10: 5000000 INFO @ Mon, 03 Jun 2019 20:06:16: 5000000 INFO @ Mon, 03 Jun 2019 20:06:18: 6000000 INFO @ Mon, 03 Jun 2019 20:06:19: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 20:06:19: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 20:06:19: #1 total tags in treatment: 6160609 INFO @ Mon, 03 Jun 2019 20:06:19: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:06:19: #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 20:06:20: #1 tags after filtering in treatment: 6160609 INFO @ Mon, 03 Jun 2019 20:06:20: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:06:20: #1 finished! INFO @ Mon, 03 Jun 2019 20:06:20: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:06:20: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:06:20: 4000000 INFO @ Mon, 03 Jun 2019 20:06:20: #2 number of paired peaks: 981 WARNING @ Mon, 03 Jun 2019 20:06:20: Fewer paired peaks (981) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 981 pairs to build model! INFO @ Mon, 03 Jun 2019 20:06:20: start model_add_line... INFO @ Mon, 03 Jun 2019 20:06:20: start X-correlation... INFO @ Mon, 03 Jun 2019 20:06:20: end of X-cor INFO @ Mon, 03 Jun 2019 20:06:20: #2 finished! INFO @ Mon, 03 Jun 2019 20:06:20: #2 predicted fragment length is 184 bps INFO @ Mon, 03 Jun 2019 20:06:20: #2 alternative fragment length(s) may be 184 bps INFO @ Mon, 03 Jun 2019 20:06:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX485211/SRX485211.20_model.r INFO @ Mon, 03 Jun 2019 20:06:20: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:06:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:06:25: 6000000 INFO @ Mon, 03 Jun 2019 20:06:27: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 20:06:27: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 20:06:27: #1 total tags in treatment: 6160609 INFO @ Mon, 03 Jun 2019 20:06:27: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:06:27: #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 20:06:27: #1 tags after filtering in treatment: 6160609 INFO @ Mon, 03 Jun 2019 20:06:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:06:27: #1 finished! INFO @ Mon, 03 Jun 2019 20:06:27: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:06:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:06:28: #2 number of paired peaks: 981 WARNING @ Mon, 03 Jun 2019 20:06:28: Fewer paired peaks (981) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 981 pairs to build model! INFO @ Mon, 03 Jun 2019 20:06:28: start model_add_line... INFO @ Mon, 03 Jun 2019 20:06:28: start X-correlation... INFO @ Mon, 03 Jun 2019 20:06:28: end of X-cor INFO @ Mon, 03 Jun 2019 20:06:28: #2 finished! INFO @ Mon, 03 Jun 2019 20:06:28: #2 predicted fragment length is 184 bps INFO @ Mon, 03 Jun 2019 20:06:28: #2 alternative fragment length(s) may be 184 bps INFO @ Mon, 03 Jun 2019 20:06:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX485211/SRX485211.05_model.r INFO @ Mon, 03 Jun 2019 20:06:28: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:06:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:06:33: 5000000 INFO @ Mon, 03 Jun 2019 20:06:40: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:06:46: 6000000 INFO @ Mon, 03 Jun 2019 20:06:47: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:06:47: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 20:06:47: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 20:06:47: #1 total tags in treatment: 6160609 INFO @ Mon, 03 Jun 2019 20:06:47: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:06:47: #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 20:06:47: #1 tags after filtering in treatment: 6160609 INFO @ Mon, 03 Jun 2019 20:06:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:06:47: #1 finished! INFO @ Mon, 03 Jun 2019 20:06:47: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:06:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:06:48: #2 number of paired peaks: 981 WARNING @ Mon, 03 Jun 2019 20:06:48: Fewer paired peaks (981) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 981 pairs to build model! INFO @ Mon, 03 Jun 2019 20:06:48: start model_add_line... INFO @ Mon, 03 Jun 2019 20:06:48: start X-correlation... INFO @ Mon, 03 Jun 2019 20:06:48: end of X-cor INFO @ Mon, 03 Jun 2019 20:06:48: #2 finished! INFO @ Mon, 03 Jun 2019 20:06:48: #2 predicted fragment length is 184 bps INFO @ Mon, 03 Jun 2019 20:06:48: #2 alternative fragment length(s) may be 184 bps INFO @ Mon, 03 Jun 2019 20:06:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX485211/SRX485211.10_model.r INFO @ Mon, 03 Jun 2019 20:06:48: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:06:48: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:06:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX485211/SRX485211.20_peaks.xls INFO @ Mon, 03 Jun 2019 20:06:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX485211/SRX485211.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:06:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX485211/SRX485211.20_summits.bed INFO @ Mon, 03 Jun 2019 20:06:49: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1122 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 20:06:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX485211/SRX485211.05_peaks.xls INFO @ Mon, 03 Jun 2019 20:06:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX485211/SRX485211.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:06:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX485211/SRX485211.05_summits.bed INFO @ Mon, 03 Jun 2019 20:06:56: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3491 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 20:07:08: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:07:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX485211/SRX485211.10_peaks.xls INFO @ Mon, 03 Jun 2019 20:07:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX485211/SRX485211.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:07:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX485211/SRX485211.10_summits.bed INFO @ Mon, 03 Jun 2019 20:07:17: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1883 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。