Job ID = 1294903 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 13,690,951 reads read : 13,690,951 reads written : 13,690,951 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: 00:04:09 13690951 reads; of these: 13690951 (100.00%) were unpaired; of these: 1117725 (8.16%) aligned 0 times 10685981 (78.05%) aligned exactly 1 time 1887245 (13.78%) aligned >1 times 91.84% overall alignment rate Time searching: 00:04:09 Overall time: 00:04:09 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] 1305893 / 12573226 = 0.1039 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 10:52:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287978/SRX287978.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287978/SRX287978.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287978/SRX287978.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287978/SRX287978.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 10:52:36: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:52:36: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:52:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287978/SRX287978.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287978/SRX287978.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287978/SRX287978.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287978/SRX287978.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 10:52:37: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:52:37: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:52:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287978/SRX287978.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287978/SRX287978.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287978/SRX287978.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287978/SRX287978.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 10:52:37: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:52:37: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:52:45: 1000000 INFO @ Mon, 03 Jun 2019 10:52:46: 1000000 INFO @ Mon, 03 Jun 2019 10:52:47: 1000000 INFO @ Mon, 03 Jun 2019 10:52:54: 2000000 INFO @ Mon, 03 Jun 2019 10:52:55: 2000000 INFO @ Mon, 03 Jun 2019 10:52:56: 2000000 INFO @ Mon, 03 Jun 2019 10:53:03: 3000000 INFO @ Mon, 03 Jun 2019 10:53:03: 3000000 INFO @ Mon, 03 Jun 2019 10:53:05: 3000000 INFO @ Mon, 03 Jun 2019 10:53:11: 4000000 INFO @ Mon, 03 Jun 2019 10:53:11: 4000000 INFO @ Mon, 03 Jun 2019 10:53:14: 4000000 INFO @ Mon, 03 Jun 2019 10:53:19: 5000000 INFO @ Mon, 03 Jun 2019 10:53:20: 5000000 INFO @ Mon, 03 Jun 2019 10:53:23: 5000000 INFO @ Mon, 03 Jun 2019 10:53:28: 6000000 INFO @ Mon, 03 Jun 2019 10:53:28: 6000000 INFO @ Mon, 03 Jun 2019 10:53:32: 6000000 INFO @ Mon, 03 Jun 2019 10:53:36: 7000000 INFO @ Mon, 03 Jun 2019 10:53:37: 7000000 INFO @ Mon, 03 Jun 2019 10:53:40: 7000000 INFO @ Mon, 03 Jun 2019 10:53:44: 8000000 INFO @ Mon, 03 Jun 2019 10:53:46: 8000000 INFO @ Mon, 03 Jun 2019 10:53:50: 8000000 INFO @ Mon, 03 Jun 2019 10:53:52: 9000000 INFO @ Mon, 03 Jun 2019 10:53:54: 9000000 INFO @ Mon, 03 Jun 2019 10:53:58: 9000000 INFO @ Mon, 03 Jun 2019 10:53:59: 10000000 INFO @ Mon, 03 Jun 2019 10:54:02: 10000000 INFO @ Mon, 03 Jun 2019 10:54:07: 11000000 INFO @ Mon, 03 Jun 2019 10:54:09: 10000000 INFO @ Mon, 03 Jun 2019 10:54:09: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:54:09: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:54:09: #1 total tags in treatment: 11267333 INFO @ Mon, 03 Jun 2019 10:54:09: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:54:09: #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 10:54:09: #1 tags after filtering in treatment: 11267333 INFO @ Mon, 03 Jun 2019 10:54:09: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:54:09: #1 finished! INFO @ Mon, 03 Jun 2019 10:54:09: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:54:09: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:54:10: #2 number of paired peaks: 764 WARNING @ Mon, 03 Jun 2019 10:54:10: Fewer paired peaks (764) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 764 pairs to build model! INFO @ Mon, 03 Jun 2019 10:54:10: start model_add_line... INFO @ Mon, 03 Jun 2019 10:54:10: start X-correlation... INFO @ Mon, 03 Jun 2019 10:54:10: end of X-cor INFO @ Mon, 03 Jun 2019 10:54:10: #2 finished! INFO @ Mon, 03 Jun 2019 10:54:10: #2 predicted fragment length is 201 bps INFO @ Mon, 03 Jun 2019 10:54:10: #2 alternative fragment length(s) may be 201 bps INFO @ Mon, 03 Jun 2019 10:54:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287978/SRX287978.10_model.r INFO @ Mon, 03 Jun 2019 10:54:10: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:54:10: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:54:11: 11000000 INFO @ Mon, 03 Jun 2019 10:54:13: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:54:13: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:54:13: #1 total tags in treatment: 11267333 INFO @ Mon, 03 Jun 2019 10:54:13: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:54:13: #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 10:54:13: #1 tags after filtering in treatment: 11267333 INFO @ Mon, 03 Jun 2019 10:54:13: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:54:13: #1 finished! INFO @ Mon, 03 Jun 2019 10:54:13: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:54:13: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:54:14: #2 number of paired peaks: 764 WARNING @ Mon, 03 Jun 2019 10:54:14: Fewer paired peaks (764) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 764 pairs to build model! INFO @ Mon, 03 Jun 2019 10:54:14: start model_add_line... INFO @ Mon, 03 Jun 2019 10:54:14: start X-correlation... INFO @ Mon, 03 Jun 2019 10:54:14: end of X-cor INFO @ Mon, 03 Jun 2019 10:54:14: #2 finished! INFO @ Mon, 03 Jun 2019 10:54:14: #2 predicted fragment length is 201 bps INFO @ Mon, 03 Jun 2019 10:54:14: #2 alternative fragment length(s) may be 201 bps INFO @ Mon, 03 Jun 2019 10:54:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287978/SRX287978.20_model.r INFO @ Mon, 03 Jun 2019 10:54:14: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:54:14: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:54:17: 11000000 INFO @ Mon, 03 Jun 2019 10:54:19: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:54:19: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:54:19: #1 total tags in treatment: 11267333 INFO @ Mon, 03 Jun 2019 10:54:19: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:54:19: #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 10:54:19: #1 tags after filtering in treatment: 11267333 INFO @ Mon, 03 Jun 2019 10:54:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:54:19: #1 finished! INFO @ Mon, 03 Jun 2019 10:54:19: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:54:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:54:21: #2 number of paired peaks: 764 WARNING @ Mon, 03 Jun 2019 10:54:21: Fewer paired peaks (764) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 764 pairs to build model! INFO @ Mon, 03 Jun 2019 10:54:21: start model_add_line... INFO @ Mon, 03 Jun 2019 10:54:21: start X-correlation... INFO @ Mon, 03 Jun 2019 10:54:21: end of X-cor INFO @ Mon, 03 Jun 2019 10:54:21: #2 finished! INFO @ Mon, 03 Jun 2019 10:54:21: #2 predicted fragment length is 201 bps INFO @ Mon, 03 Jun 2019 10:54:21: #2 alternative fragment length(s) may be 201 bps INFO @ Mon, 03 Jun 2019 10:54:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287978/SRX287978.05_model.r INFO @ Mon, 03 Jun 2019 10:54:21: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:54:21: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:54:45: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:54:50: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:54:58: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:55:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287978/SRX287978.10_peaks.xls INFO @ Mon, 03 Jun 2019 10:55:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287978/SRX287978.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:55:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287978/SRX287978.10_summits.bed INFO @ Mon, 03 Jun 2019 10:55:03: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (2512 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:55:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287978/SRX287978.20_peaks.xls INFO @ Mon, 03 Jun 2019 10:55:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287978/SRX287978.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:55:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287978/SRX287978.20_summits.bed INFO @ Mon, 03 Jun 2019 10:55:07: Done! pass1 - making usageList (9 chroms): 2 millis pass2 - checking and writing primary data (529 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:55:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287978/SRX287978.05_peaks.xls INFO @ Mon, 03 Jun 2019 10:55:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287978/SRX287978.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:55:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287978/SRX287978.05_summits.bed INFO @ Mon, 03 Jun 2019 10:55:17: Done! pass1 - making usageList (13 chroms): 4 millis pass2 - checking and writing primary data (9859 records, 4 fields): 17 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。