Job ID = 1294825 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 13,260,182 reads read : 13,260,182 reads written : 13,260,182 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: 00:04:13 13260182 reads; of these: 13260182 (100.00%) were unpaired; of these: 2148378 (16.20%) aligned 0 times 7821110 (58.98%) aligned exactly 1 time 3290694 (24.82%) aligned >1 times 83.80% overall alignment rate Time searching: 00:04:13 Overall time: 00:04:13 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] 1126475 / 11111804 = 0.1014 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 10:30:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287924/SRX287924.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287924/SRX287924.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287924/SRX287924.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287924/SRX287924.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 10:30:08: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:30:08: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:30:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287924/SRX287924.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287924/SRX287924.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287924/SRX287924.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287924/SRX287924.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 10:30:08: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:30:08: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:30:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287924/SRX287924.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287924/SRX287924.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287924/SRX287924.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287924/SRX287924.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 10:30:08: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:30:08: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:30:16: 1000000 INFO @ Mon, 03 Jun 2019 10:30:16: 1000000 INFO @ Mon, 03 Jun 2019 10:30:18: 1000000 INFO @ Mon, 03 Jun 2019 10:30:24: 2000000 INFO @ Mon, 03 Jun 2019 10:30:24: 2000000 INFO @ Mon, 03 Jun 2019 10:30:27: 2000000 INFO @ Mon, 03 Jun 2019 10:30:32: 3000000 INFO @ Mon, 03 Jun 2019 10:30:32: 3000000 INFO @ Mon, 03 Jun 2019 10:30:37: 3000000 INFO @ Mon, 03 Jun 2019 10:30:39: 4000000 INFO @ Mon, 03 Jun 2019 10:30:39: 4000000 INFO @ Mon, 03 Jun 2019 10:30:46: 4000000 INFO @ Mon, 03 Jun 2019 10:30:47: 5000000 INFO @ Mon, 03 Jun 2019 10:30:47: 5000000 INFO @ Mon, 03 Jun 2019 10:30:55: 6000000 INFO @ Mon, 03 Jun 2019 10:30:55: 6000000 INFO @ Mon, 03 Jun 2019 10:30:55: 5000000 INFO @ Mon, 03 Jun 2019 10:31:03: 7000000 INFO @ Mon, 03 Jun 2019 10:31:03: 7000000 INFO @ Mon, 03 Jun 2019 10:31:05: 6000000 INFO @ Mon, 03 Jun 2019 10:31:11: 8000000 INFO @ Mon, 03 Jun 2019 10:31:11: 8000000 INFO @ Mon, 03 Jun 2019 10:31:14: 7000000 INFO @ Mon, 03 Jun 2019 10:31:19: 9000000 INFO @ Mon, 03 Jun 2019 10:31:19: 9000000 INFO @ Mon, 03 Jun 2019 10:31:23: 8000000 INFO @ Mon, 03 Jun 2019 10:31:26: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:31:26: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:31:26: #1 total tags in treatment: 9985329 INFO @ Mon, 03 Jun 2019 10:31:26: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:31:26: #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 10:31:26: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:31:26: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:31:26: #1 total tags in treatment: 9985329 INFO @ Mon, 03 Jun 2019 10:31:26: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:31:26: #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 10:31:27: #1 tags after filtering in treatment: 9985329 INFO @ Mon, 03 Jun 2019 10:31:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:31:27: #1 finished! INFO @ Mon, 03 Jun 2019 10:31:27: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:31:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:31:27: #1 tags after filtering in treatment: 9985329 INFO @ Mon, 03 Jun 2019 10:31:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:31:27: #1 finished! INFO @ Mon, 03 Jun 2019 10:31:27: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:31:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:31:28: #2 number of paired peaks: 425 WARNING @ Mon, 03 Jun 2019 10:31:28: Fewer paired peaks (425) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 425 pairs to build model! INFO @ Mon, 03 Jun 2019 10:31:28: start model_add_line... INFO @ Mon, 03 Jun 2019 10:31:28: #2 number of paired peaks: 425 WARNING @ Mon, 03 Jun 2019 10:31:28: Fewer paired peaks (425) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 425 pairs to build model! INFO @ Mon, 03 Jun 2019 10:31:28: start model_add_line... INFO @ Mon, 03 Jun 2019 10:31:28: start X-correlation... INFO @ Mon, 03 Jun 2019 10:31:28: end of X-cor INFO @ Mon, 03 Jun 2019 10:31:28: #2 finished! INFO @ Mon, 03 Jun 2019 10:31:28: #2 predicted fragment length is 144 bps INFO @ Mon, 03 Jun 2019 10:31:28: #2 alternative fragment length(s) may be 144 bps INFO @ Mon, 03 Jun 2019 10:31:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287924/SRX287924.10_model.r INFO @ Mon, 03 Jun 2019 10:31:28: start X-correlation... INFO @ Mon, 03 Jun 2019 10:31:28: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:31:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:31:28: end of X-cor INFO @ Mon, 03 Jun 2019 10:31:28: #2 finished! INFO @ Mon, 03 Jun 2019 10:31:28: #2 predicted fragment length is 144 bps INFO @ Mon, 03 Jun 2019 10:31:28: #2 alternative fragment length(s) may be 144 bps INFO @ Mon, 03 Jun 2019 10:31:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287924/SRX287924.20_model.r INFO @ Mon, 03 Jun 2019 10:31:28: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:31:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:31:32: 9000000 INFO @ Mon, 03 Jun 2019 10:31:41: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:31:41: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:31:41: #1 total tags in treatment: 9985329 INFO @ Mon, 03 Jun 2019 10:31:41: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:31:41: #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 10:31:42: #1 tags after filtering in treatment: 9985329 INFO @ Mon, 03 Jun 2019 10:31:42: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:31:42: #1 finished! INFO @ Mon, 03 Jun 2019 10:31:42: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:31:42: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:31:42: #2 number of paired peaks: 425 WARNING @ Mon, 03 Jun 2019 10:31:42: Fewer paired peaks (425) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 425 pairs to build model! INFO @ Mon, 03 Jun 2019 10:31:42: start model_add_line... INFO @ Mon, 03 Jun 2019 10:31:43: start X-correlation... INFO @ Mon, 03 Jun 2019 10:31:43: end of X-cor INFO @ Mon, 03 Jun 2019 10:31:43: #2 finished! INFO @ Mon, 03 Jun 2019 10:31:43: #2 predicted fragment length is 144 bps INFO @ Mon, 03 Jun 2019 10:31:43: #2 alternative fragment length(s) may be 144 bps INFO @ Mon, 03 Jun 2019 10:31:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287924/SRX287924.05_model.r INFO @ Mon, 03 Jun 2019 10:31:43: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:31:43: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:31:57: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:31:57: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:32:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287924/SRX287924.10_peaks.xls INFO @ Mon, 03 Jun 2019 10:32:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287924/SRX287924.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:32:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287924/SRX287924.10_summits.bed INFO @ Mon, 03 Jun 2019 10:32:11: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1405 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:32:12: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:32:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287924/SRX287924.20_peaks.xls INFO @ Mon, 03 Jun 2019 10:32:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287924/SRX287924.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:32:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287924/SRX287924.20_summits.bed INFO @ Mon, 03 Jun 2019 10:32:12: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (656 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:32:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287924/SRX287924.05_peaks.xls INFO @ Mon, 03 Jun 2019 10:32:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287924/SRX287924.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:32:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287924/SRX287924.05_summits.bed INFO @ Mon, 03 Jun 2019 10:32:26: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (2622 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。