Job ID = 1295568 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 34,617,023 reads read : 34,617,023 reads written : 34,617,023 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: 00:05:51 34617023 reads; of these: 34617023 (100.00%) were unpaired; of these: 21658617 (62.57%) aligned 0 times 9280447 (26.81%) aligned exactly 1 time 3677959 (10.62%) aligned >1 times 37.43% overall alignment rate Time searching: 00:05:51 Overall time: 00:05:51 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_rmdupse_core] 4493187 / 12958406 = 0.3467 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 14:33:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX367041/SRX367041.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX367041/SRX367041.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX367041/SRX367041.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX367041/SRX367041.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 14:33:43: #1 read tag files... INFO @ Mon, 03 Jun 2019 14:33:43: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 14:33:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX367041/SRX367041.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX367041/SRX367041.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX367041/SRX367041.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX367041/SRX367041.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 14:33:43: #1 read tag files... INFO @ Mon, 03 Jun 2019 14:33:43: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 14:33:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX367041/SRX367041.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX367041/SRX367041.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX367041/SRX367041.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX367041/SRX367041.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 14:33:43: #1 read tag files... INFO @ Mon, 03 Jun 2019 14:33:43: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 14:33:50: 1000000 INFO @ Mon, 03 Jun 2019 14:33:51: 1000000 INFO @ Mon, 03 Jun 2019 14:33:53: 1000000 INFO @ Mon, 03 Jun 2019 14:33:58: 2000000 INFO @ Mon, 03 Jun 2019 14:33:59: 2000000 INFO @ Mon, 03 Jun 2019 14:34:02: 2000000 INFO @ Mon, 03 Jun 2019 14:34:05: 3000000 INFO @ Mon, 03 Jun 2019 14:34:07: 3000000 INFO @ Mon, 03 Jun 2019 14:34:11: 3000000 INFO @ Mon, 03 Jun 2019 14:34:12: 4000000 INFO @ Mon, 03 Jun 2019 14:34:15: 4000000 INFO @ Mon, 03 Jun 2019 14:34:19: 5000000 INFO @ Mon, 03 Jun 2019 14:34:20: 4000000 INFO @ Mon, 03 Jun 2019 14:34:22: 5000000 INFO @ Mon, 03 Jun 2019 14:34:26: 6000000 INFO @ Mon, 03 Jun 2019 14:34:29: 5000000 INFO @ Mon, 03 Jun 2019 14:34:30: 6000000 INFO @ Mon, 03 Jun 2019 14:34:33: 7000000 INFO @ Mon, 03 Jun 2019 14:34:37: 7000000 INFO @ Mon, 03 Jun 2019 14:34:38: 6000000 INFO @ Mon, 03 Jun 2019 14:34:40: 8000000 INFO @ Mon, 03 Jun 2019 14:34:43: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 14:34:43: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 14:34:43: #1 total tags in treatment: 8465219 INFO @ Mon, 03 Jun 2019 14:34:43: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 14:34:43: #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 14:34:44: #1 tags after filtering in treatment: 8465219 INFO @ Mon, 03 Jun 2019 14:34:44: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 14:34:44: #1 finished! INFO @ Mon, 03 Jun 2019 14:34:44: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 14:34:44: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 14:34:44: 8000000 INFO @ Mon, 03 Jun 2019 14:34:44: #2 number of paired peaks: 478 WARNING @ Mon, 03 Jun 2019 14:34:44: Fewer paired peaks (478) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 478 pairs to build model! INFO @ Mon, 03 Jun 2019 14:34:44: start model_add_line... INFO @ Mon, 03 Jun 2019 14:34:45: start X-correlation... INFO @ Mon, 03 Jun 2019 14:34:45: end of X-cor INFO @ Mon, 03 Jun 2019 14:34:45: #2 finished! INFO @ Mon, 03 Jun 2019 14:34:45: #2 predicted fragment length is 39 bps INFO @ Mon, 03 Jun 2019 14:34:45: #2 alternative fragment length(s) may be 39 bps INFO @ Mon, 03 Jun 2019 14:34:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX367041/SRX367041.20_model.r WARNING @ Mon, 03 Jun 2019 14:34:45: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 14:34:45: #2 You may need to consider one of the other alternative d(s): 39 WARNING @ Mon, 03 Jun 2019 14:34:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 14:34:45: #3 Call peaks... INFO @ Mon, 03 Jun 2019 14:34:45: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 14:34:47: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 14:34:47: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 14:34:47: #1 total tags in treatment: 8465219 INFO @ Mon, 03 Jun 2019 14:34:47: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 14:34:47: #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 14:34:48: 7000000 INFO @ Mon, 03 Jun 2019 14:34:48: #1 tags after filtering in treatment: 8465219 INFO @ Mon, 03 Jun 2019 14:34:48: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 14:34:48: #1 finished! INFO @ Mon, 03 Jun 2019 14:34:48: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 14:34:48: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 14:34:48: #2 number of paired peaks: 478 WARNING @ Mon, 03 Jun 2019 14:34:48: Fewer paired peaks (478) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 478 pairs to build model! INFO @ Mon, 03 Jun 2019 14:34:48: start model_add_line... INFO @ Mon, 03 Jun 2019 14:34:49: start X-correlation... INFO @ Mon, 03 Jun 2019 14:34:49: end of X-cor INFO @ Mon, 03 Jun 2019 14:34:49: #2 finished! INFO @ Mon, 03 Jun 2019 14:34:49: #2 predicted fragment length is 39 bps INFO @ Mon, 03 Jun 2019 14:34:49: #2 alternative fragment length(s) may be 39 bps INFO @ Mon, 03 Jun 2019 14:34:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX367041/SRX367041.05_model.r WARNING @ Mon, 03 Jun 2019 14:34:49: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 14:34:49: #2 You may need to consider one of the other alternative d(s): 39 WARNING @ Mon, 03 Jun 2019 14:34:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 14:34:49: #3 Call peaks... INFO @ Mon, 03 Jun 2019 14:34:49: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 14:34:56: 8000000 INFO @ Mon, 03 Jun 2019 14:35:00: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 14:35:00: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 14:35:00: #1 total tags in treatment: 8465219 INFO @ Mon, 03 Jun 2019 14:35:00: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 14:35:00: #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 14:35:00: #1 tags after filtering in treatment: 8465219 INFO @ Mon, 03 Jun 2019 14:35:00: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 14:35:00: #1 finished! INFO @ Mon, 03 Jun 2019 14:35:00: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 14:35:00: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 14:35:01: #2 number of paired peaks: 478 WARNING @ Mon, 03 Jun 2019 14:35:01: Fewer paired peaks (478) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 478 pairs to build model! INFO @ Mon, 03 Jun 2019 14:35:01: start model_add_line... INFO @ Mon, 03 Jun 2019 14:35:01: start X-correlation... INFO @ Mon, 03 Jun 2019 14:35:01: end of X-cor INFO @ Mon, 03 Jun 2019 14:35:01: #2 finished! INFO @ Mon, 03 Jun 2019 14:35:01: #2 predicted fragment length is 39 bps INFO @ Mon, 03 Jun 2019 14:35:01: #2 alternative fragment length(s) may be 39 bps INFO @ Mon, 03 Jun 2019 14:35:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX367041/SRX367041.10_model.r WARNING @ Mon, 03 Jun 2019 14:35:01: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 14:35:01: #2 You may need to consider one of the other alternative d(s): 39 WARNING @ Mon, 03 Jun 2019 14:35:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 14:35:01: #3 Call peaks... INFO @ Mon, 03 Jun 2019 14:35:01: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 14:35:09: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 14:35:13: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 14:35:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX367041/SRX367041.20_peaks.xls INFO @ Mon, 03 Jun 2019 14:35:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX367041/SRX367041.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 14:35:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX367041/SRX367041.20_summits.bed INFO @ Mon, 03 Jun 2019 14:35:20: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (631 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 14:35:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX367041/SRX367041.05_peaks.xls INFO @ Mon, 03 Jun 2019 14:35:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX367041/SRX367041.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 14:35:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX367041/SRX367041.05_summits.bed INFO @ Mon, 03 Jun 2019 14:35:25: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3151 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 14:35:26: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 14:35:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX367041/SRX367041.10_peaks.xls INFO @ Mon, 03 Jun 2019 14:35:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX367041/SRX367041.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 14:35:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX367041/SRX367041.10_summits.bed INFO @ Mon, 03 Jun 2019 14:35:38: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1417 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。