Job ID = 2590298 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 21,575,683 reads read : 21,575,683 reads written : 21,575,683 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: 00:09:51 21575683 reads; of these: 21575683 (100.00%) were unpaired; of these: 2893594 (13.41%) aligned 0 times 11812639 (54.75%) aligned exactly 1 time 6869450 (31.84%) aligned >1 times 86.59% overall alignment rate Time searching: 00:09:52 Overall time: 00:09:52 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] 2372264 / 18682089 = 0.1270 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 20:58:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX318794/SRX318794.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX318794/SRX318794.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX318794/SRX318794.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX318794/SRX318794.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 20:58:21: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:58:21: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:58:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX318794/SRX318794.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX318794/SRX318794.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX318794/SRX318794.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX318794/SRX318794.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 20:58:22: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:58:22: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:58:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX318794/SRX318794.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX318794/SRX318794.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX318794/SRX318794.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX318794/SRX318794.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 20:58:23: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:58:23: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:58:30: 1000000 INFO @ Mon, 12 Aug 2019 20:58:30: 1000000 INFO @ Mon, 12 Aug 2019 20:58:31: 1000000 INFO @ Mon, 12 Aug 2019 20:58:38: 2000000 INFO @ Mon, 12 Aug 2019 20:58:39: 2000000 INFO @ Mon, 12 Aug 2019 20:58:39: 2000000 INFO @ Mon, 12 Aug 2019 20:58:46: 3000000 INFO @ Mon, 12 Aug 2019 20:58:47: 3000000 INFO @ Mon, 12 Aug 2019 20:58:47: 3000000 INFO @ Mon, 12 Aug 2019 20:58:54: 4000000 INFO @ Mon, 12 Aug 2019 20:58:55: 4000000 INFO @ Mon, 12 Aug 2019 20:58:56: 4000000 INFO @ Mon, 12 Aug 2019 20:59:02: 5000000 INFO @ Mon, 12 Aug 2019 20:59:02: 5000000 INFO @ Mon, 12 Aug 2019 20:59:04: 5000000 INFO @ Mon, 12 Aug 2019 20:59:10: 6000000 INFO @ Mon, 12 Aug 2019 20:59:10: 6000000 INFO @ Mon, 12 Aug 2019 20:59:13: 6000000 INFO @ Mon, 12 Aug 2019 20:59:17: 7000000 INFO @ Mon, 12 Aug 2019 20:59:18: 7000000 INFO @ Mon, 12 Aug 2019 20:59:21: 7000000 INFO @ Mon, 12 Aug 2019 20:59:25: 8000000 INFO @ Mon, 12 Aug 2019 20:59:26: 8000000 INFO @ Mon, 12 Aug 2019 20:59:29: 8000000 INFO @ Mon, 12 Aug 2019 20:59:33: 9000000 INFO @ Mon, 12 Aug 2019 20:59:33: 9000000 INFO @ Mon, 12 Aug 2019 20:59:38: 9000000 INFO @ Mon, 12 Aug 2019 20:59:41: 10000000 INFO @ Mon, 12 Aug 2019 20:59:41: 10000000 INFO @ Mon, 12 Aug 2019 20:59:46: 10000000 INFO @ Mon, 12 Aug 2019 20:59:48: 11000000 INFO @ Mon, 12 Aug 2019 20:59:49: 11000000 INFO @ Mon, 12 Aug 2019 20:59:54: 11000000 INFO @ Mon, 12 Aug 2019 20:59:56: 12000000 INFO @ Mon, 12 Aug 2019 20:59:57: 12000000 INFO @ Mon, 12 Aug 2019 21:00:03: 12000000 INFO @ Mon, 12 Aug 2019 21:00:04: 13000000 INFO @ Mon, 12 Aug 2019 21:00:05: 13000000 INFO @ Mon, 12 Aug 2019 21:00:11: 13000000 INFO @ Mon, 12 Aug 2019 21:00:12: 14000000 INFO @ Mon, 12 Aug 2019 21:00:13: 14000000 INFO @ Mon, 12 Aug 2019 21:00:19: 14000000 INFO @ Mon, 12 Aug 2019 21:00:20: 15000000 INFO @ Mon, 12 Aug 2019 21:00:21: 15000000 INFO @ Mon, 12 Aug 2019 21:00:27: 15000000 INFO @ Mon, 12 Aug 2019 21:00:28: 16000000 INFO @ Mon, 12 Aug 2019 21:00:29: 16000000 INFO @ Mon, 12 Aug 2019 21:00:30: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 21:00:30: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 21:00:30: #1 total tags in treatment: 16309825 INFO @ Mon, 12 Aug 2019 21:00:30: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:00:30: #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 21:00:31: #1 tags after filtering in treatment: 16309825 INFO @ Mon, 12 Aug 2019 21:00:31: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:00:31: #1 finished! INFO @ Mon, 12 Aug 2019 21:00:31: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:00:31: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:00:31: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 21:00:31: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 21:00:31: #1 total tags in treatment: 16309825 INFO @ Mon, 12 Aug 2019 21:00:31: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:00:31: #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 21:00:31: #1 tags after filtering in treatment: 16309825 INFO @ Mon, 12 Aug 2019 21:00:31: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:00:31: #1 finished! INFO @ Mon, 12 Aug 2019 21:00:31: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:00:31: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:00:32: #2 number of paired peaks: 450 WARNING @ Mon, 12 Aug 2019 21:00:32: Fewer paired peaks (450) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 450 pairs to build model! INFO @ Mon, 12 Aug 2019 21:00:32: start model_add_line... INFO @ Mon, 12 Aug 2019 21:00:32: start X-correlation... INFO @ Mon, 12 Aug 2019 21:00:32: end of X-cor INFO @ Mon, 12 Aug 2019 21:00:32: #2 finished! INFO @ Mon, 12 Aug 2019 21:00:32: #2 predicted fragment length is 51 bps INFO @ Mon, 12 Aug 2019 21:00:32: #2 alternative fragment length(s) may be 1,51,561,581,592 bps INFO @ Mon, 12 Aug 2019 21:00:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX318794/SRX318794.20_model.r WARNING @ Mon, 12 Aug 2019 21:00:32: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 21:00:32: #2 You may need to consider one of the other alternative d(s): 1,51,561,581,592 WARNING @ Mon, 12 Aug 2019 21:00:32: #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 21:00:32: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:00:32: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:00:33: #2 number of paired peaks: 450 WARNING @ Mon, 12 Aug 2019 21:00:33: Fewer paired peaks (450) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 450 pairs to build model! INFO @ Mon, 12 Aug 2019 21:00:33: start model_add_line... INFO @ Mon, 12 Aug 2019 21:00:33: start X-correlation... INFO @ Mon, 12 Aug 2019 21:00:33: end of X-cor INFO @ Mon, 12 Aug 2019 21:00:33: #2 finished! INFO @ Mon, 12 Aug 2019 21:00:33: #2 predicted fragment length is 51 bps INFO @ Mon, 12 Aug 2019 21:00:33: #2 alternative fragment length(s) may be 1,51,561,581,592 bps INFO @ Mon, 12 Aug 2019 21:00:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX318794/SRX318794.10_model.r WARNING @ Mon, 12 Aug 2019 21:00:33: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 21:00:33: #2 You may need to consider one of the other alternative d(s): 1,51,561,581,592 WARNING @ Mon, 12 Aug 2019 21:00:33: #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 21:00:33: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:00:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:00:35: 16000000 INFO @ Mon, 12 Aug 2019 21:00:37: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 21:00:37: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 21:00:37: #1 total tags in treatment: 16309825 INFO @ Mon, 12 Aug 2019 21:00:37: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:00:37: #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 21:00:37: #1 tags after filtering in treatment: 16309825 INFO @ Mon, 12 Aug 2019 21:00:37: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:00:37: #1 finished! INFO @ Mon, 12 Aug 2019 21:00:37: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:00:37: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:00:39: #2 number of paired peaks: 450 WARNING @ Mon, 12 Aug 2019 21:00:39: Fewer paired peaks (450) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 450 pairs to build model! INFO @ Mon, 12 Aug 2019 21:00:39: start model_add_line... INFO @ Mon, 12 Aug 2019 21:00:39: start X-correlation... INFO @ Mon, 12 Aug 2019 21:00:39: end of X-cor INFO @ Mon, 12 Aug 2019 21:00:39: #2 finished! INFO @ Mon, 12 Aug 2019 21:00:39: #2 predicted fragment length is 51 bps INFO @ Mon, 12 Aug 2019 21:00:39: #2 alternative fragment length(s) may be 1,51,561,581,592 bps INFO @ Mon, 12 Aug 2019 21:00:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX318794/SRX318794.05_model.r WARNING @ Mon, 12 Aug 2019 21:00:39: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 21:00:39: #2 You may need to consider one of the other alternative d(s): 1,51,561,581,592 WARNING @ Mon, 12 Aug 2019 21:00:39: #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 21:00:39: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:00:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:01:16: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:01:17: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:01:23: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:01:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX318794/SRX318794.20_peaks.xls INFO @ Mon, 12 Aug 2019 21:01:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX318794/SRX318794.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:01:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX318794/SRX318794.20_summits.bed INFO @ Mon, 12 Aug 2019 21:01:37: Done! pass1 - making usageList (10 chroms): 2 millis pass2 - checking and writing primary data (475 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 21:01:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX318794/SRX318794.10_peaks.xls INFO @ Mon, 12 Aug 2019 21:01:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX318794/SRX318794.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:01:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX318794/SRX318794.10_summits.bed INFO @ Mon, 12 Aug 2019 21:01:38: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1276 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 21:01:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX318794/SRX318794.05_peaks.xls INFO @ Mon, 12 Aug 2019 21:01:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX318794/SRX318794.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:01:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX318794/SRX318794.05_summits.bed INFO @ Mon, 12 Aug 2019 21:01:44: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2657 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。