Job ID = 2590830 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 33,839,220 reads read : 67,678,440 reads written : 33,839,220 reads 0-length : 33,839,220 rm: cannot remove ‘[DSE]RR*’: 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:11:21 33839220 reads; of these: 33839220 (100.00%) were unpaired; of these: 9766366 (28.86%) aligned 0 times 17585714 (51.97%) aligned exactly 1 time 6487140 (19.17%) aligned >1 times 71.14% overall alignment rate Time searching: 00:11:22 Overall time: 00:11:22 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 12 files... [bam_rmdupse_core] 15649150 / 24072854 = 0.6501 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, 12 Aug 2019 23:49:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011069/SRX5011069.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011069/SRX5011069.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011069/SRX5011069.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011069/SRX5011069.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, 12 Aug 2019 23:49:19: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:49:19: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:49:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011069/SRX5011069.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011069/SRX5011069.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011069/SRX5011069.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011069/SRX5011069.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, 12 Aug 2019 23:49:20: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:49:20: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:49:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011069/SRX5011069.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011069/SRX5011069.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011069/SRX5011069.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011069/SRX5011069.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, 12 Aug 2019 23:49:21: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:49:21: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:49:30: 1000000 INFO @ Mon, 12 Aug 2019 23:49:30: 1000000 INFO @ Mon, 12 Aug 2019 23:49:32: 1000000 INFO @ Mon, 12 Aug 2019 23:49:39: 2000000 INFO @ Mon, 12 Aug 2019 23:49:41: 2000000 INFO @ Mon, 12 Aug 2019 23:49:42: 2000000 INFO @ Mon, 12 Aug 2019 23:49:49: 3000000 INFO @ Mon, 12 Aug 2019 23:49:52: 3000000 INFO @ Mon, 12 Aug 2019 23:49:53: 3000000 INFO @ Mon, 12 Aug 2019 23:49:58: 4000000 INFO @ Mon, 12 Aug 2019 23:50:03: 4000000 INFO @ Mon, 12 Aug 2019 23:50:04: 4000000 INFO @ Mon, 12 Aug 2019 23:50:07: 5000000 INFO @ Mon, 12 Aug 2019 23:50:13: 5000000 INFO @ Mon, 12 Aug 2019 23:50:13: 5000000 INFO @ Mon, 12 Aug 2019 23:50:16: 6000000 INFO @ Mon, 12 Aug 2019 23:50:21: 6000000 INFO @ Mon, 12 Aug 2019 23:50:22: 6000000 INFO @ Mon, 12 Aug 2019 23:50:26: 7000000 INFO @ Mon, 12 Aug 2019 23:50:28: 7000000 INFO @ Mon, 12 Aug 2019 23:50:32: 7000000 INFO @ Mon, 12 Aug 2019 23:50:34: 8000000 INFO @ Mon, 12 Aug 2019 23:50:36: 8000000 INFO @ Mon, 12 Aug 2019 23:50:38: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:50:38: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:50:38: #1 total tags in treatment: 8423704 INFO @ Mon, 12 Aug 2019 23:50:38: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:50:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 23:50:38: #1 tags after filtering in treatment: 8423704 INFO @ Mon, 12 Aug 2019 23:50:38: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:50:38: #1 finished! INFO @ Mon, 12 Aug 2019 23:50:38: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:50:38: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:50:39: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:50:39: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:50:39: #1 total tags in treatment: 8423704 INFO @ Mon, 12 Aug 2019 23:50:39: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:50:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 23:50:39: #1 tags after filtering in treatment: 8423704 INFO @ Mon, 12 Aug 2019 23:50:39: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:50:39: #1 finished! INFO @ Mon, 12 Aug 2019 23:50:39: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:50:39: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:50:39: #2 number of paired peaks: 2599 INFO @ Mon, 12 Aug 2019 23:50:39: start model_add_line... INFO @ Mon, 12 Aug 2019 23:50:39: start X-correlation... INFO @ Mon, 12 Aug 2019 23:50:39: end of X-cor INFO @ Mon, 12 Aug 2019 23:50:39: #2 finished! INFO @ Mon, 12 Aug 2019 23:50:39: #2 predicted fragment length is 64 bps INFO @ Mon, 12 Aug 2019 23:50:39: #2 alternative fragment length(s) may be 64 bps INFO @ Mon, 12 Aug 2019 23:50:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011069/SRX5011069.10_model.r WARNING @ Mon, 12 Aug 2019 23:50:39: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:50:39: #2 You may need to consider one of the other alternative d(s): 64 WARNING @ Mon, 12 Aug 2019 23:50:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 23:50:39: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:50:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:50:40: #2 number of paired peaks: 2599 INFO @ Mon, 12 Aug 2019 23:50:40: start model_add_line... INFO @ Mon, 12 Aug 2019 23:50:40: start X-correlation... INFO @ Mon, 12 Aug 2019 23:50:40: end of X-cor INFO @ Mon, 12 Aug 2019 23:50:40: #2 finished! INFO @ Mon, 12 Aug 2019 23:50:40: #2 predicted fragment length is 64 bps INFO @ Mon, 12 Aug 2019 23:50:40: #2 alternative fragment length(s) may be 64 bps INFO @ Mon, 12 Aug 2019 23:50:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011069/SRX5011069.05_model.r WARNING @ Mon, 12 Aug 2019 23:50:40: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:50:40: #2 You may need to consider one of the other alternative d(s): 64 WARNING @ Mon, 12 Aug 2019 23:50:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 23:50:40: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:50:40: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:50:41: 8000000 INFO @ Mon, 12 Aug 2019 23:50:45: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:50:45: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:50:45: #1 total tags in treatment: 8423704 INFO @ Mon, 12 Aug 2019 23:50:45: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:50:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 23:50:45: #1 tags after filtering in treatment: 8423704 INFO @ Mon, 12 Aug 2019 23:50:45: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:50:45: #1 finished! INFO @ Mon, 12 Aug 2019 23:50:45: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:50:45: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:50:46: #2 number of paired peaks: 2599 INFO @ Mon, 12 Aug 2019 23:50:46: start model_add_line... INFO @ Mon, 12 Aug 2019 23:50:46: start X-correlation... INFO @ Mon, 12 Aug 2019 23:50:46: end of X-cor INFO @ Mon, 12 Aug 2019 23:50:46: #2 finished! INFO @ Mon, 12 Aug 2019 23:50:46: #2 predicted fragment length is 64 bps INFO @ Mon, 12 Aug 2019 23:50:46: #2 alternative fragment length(s) may be 64 bps INFO @ Mon, 12 Aug 2019 23:50:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011069/SRX5011069.20_model.r WARNING @ Mon, 12 Aug 2019 23:50:46: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:50:46: #2 You may need to consider one of the other alternative d(s): 64 WARNING @ Mon, 12 Aug 2019 23:50:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 23:50:46: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:50:46: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:51:05: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:51:05: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:51:11: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:51:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011069/SRX5011069.10_peaks.xls INFO @ Mon, 12 Aug 2019 23:51:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011069/SRX5011069.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:51:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011069/SRX5011069.10_summits.bed INFO @ Mon, 12 Aug 2019 23:51:18: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3994 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:51:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011069/SRX5011069.05_peaks.xls INFO @ Mon, 12 Aug 2019 23:51:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011069/SRX5011069.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:51:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011069/SRX5011069.05_summits.bed INFO @ Mon, 12 Aug 2019 23:51:18: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7315 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:51:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011069/SRX5011069.20_peaks.xls INFO @ Mon, 12 Aug 2019 23:51:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011069/SRX5011069.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:51:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011069/SRX5011069.20_summits.bed INFO @ Mon, 12 Aug 2019 23:51:23: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (2246 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。