Job ID = 1295025 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 17,913,665 reads read : 17,913,665 reads written : 17,913,665 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: 00:07:15 17913665 reads; of these: 17913665 (100.00%) were unpaired; of these: 724402 (4.04%) aligned 0 times 11839829 (66.09%) aligned exactly 1 time 5349434 (29.86%) aligned >1 times 95.96% overall alignment rate Time searching: 00:07:15 Overall time: 00:07:15 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] 1634779 / 17189263 = 0.0951 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 11:39:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX306195/SRX306195.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX306195/SRX306195.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX306195/SRX306195.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX306195/SRX306195.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 11:39:40: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:39:40: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:39:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX306195/SRX306195.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX306195/SRX306195.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX306195/SRX306195.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX306195/SRX306195.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 11:39:40: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:39:40: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:39:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX306195/SRX306195.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX306195/SRX306195.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX306195/SRX306195.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX306195/SRX306195.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 11:39:40: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:39:40: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:39:48: 1000000 INFO @ Mon, 03 Jun 2019 11:39:48: 1000000 INFO @ Mon, 03 Jun 2019 11:39:48: 1000000 INFO @ Mon, 03 Jun 2019 11:39:55: 2000000 INFO @ Mon, 03 Jun 2019 11:39:56: 2000000 INFO @ Mon, 03 Jun 2019 11:39:56: 2000000 INFO @ Mon, 03 Jun 2019 11:40:02: 3000000 INFO @ Mon, 03 Jun 2019 11:40:04: 3000000 INFO @ Mon, 03 Jun 2019 11:40:04: 3000000 INFO @ Mon, 03 Jun 2019 11:40:09: 4000000 INFO @ Mon, 03 Jun 2019 11:40:11: 4000000 INFO @ Mon, 03 Jun 2019 11:40:12: 4000000 INFO @ Mon, 03 Jun 2019 11:40:16: 5000000 INFO @ Mon, 03 Jun 2019 11:40:19: 5000000 INFO @ Mon, 03 Jun 2019 11:40:19: 5000000 INFO @ Mon, 03 Jun 2019 11:40:23: 6000000 INFO @ Mon, 03 Jun 2019 11:40:27: 6000000 INFO @ Mon, 03 Jun 2019 11:40:27: 6000000 INFO @ Mon, 03 Jun 2019 11:40:30: 7000000 INFO @ Mon, 03 Jun 2019 11:40:35: 7000000 INFO @ Mon, 03 Jun 2019 11:40:35: 7000000 INFO @ Mon, 03 Jun 2019 11:40:37: 8000000 INFO @ Mon, 03 Jun 2019 11:40:42: 8000000 INFO @ Mon, 03 Jun 2019 11:40:42: 8000000 INFO @ Mon, 03 Jun 2019 11:40:44: 9000000 INFO @ Mon, 03 Jun 2019 11:40:50: 9000000 INFO @ Mon, 03 Jun 2019 11:40:50: 9000000 INFO @ Mon, 03 Jun 2019 11:40:51: 10000000 INFO @ Mon, 03 Jun 2019 11:40:58: 10000000 INFO @ Mon, 03 Jun 2019 11:40:58: 10000000 INFO @ Mon, 03 Jun 2019 11:40:59: 11000000 INFO @ Mon, 03 Jun 2019 11:41:05: 11000000 INFO @ Mon, 03 Jun 2019 11:41:06: 12000000 INFO @ Mon, 03 Jun 2019 11:41:06: 11000000 INFO @ Mon, 03 Jun 2019 11:41:13: 12000000 INFO @ Mon, 03 Jun 2019 11:41:13: 13000000 INFO @ Mon, 03 Jun 2019 11:41:14: 12000000 INFO @ Mon, 03 Jun 2019 11:41:20: 13000000 INFO @ Mon, 03 Jun 2019 11:41:21: 14000000 INFO @ Mon, 03 Jun 2019 11:41:22: 13000000 INFO @ Mon, 03 Jun 2019 11:41:28: 14000000 INFO @ Mon, 03 Jun 2019 11:41:28: 15000000 INFO @ Mon, 03 Jun 2019 11:41:29: 14000000 INFO @ Mon, 03 Jun 2019 11:41:33: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 11:41:33: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 11:41:33: #1 total tags in treatment: 15554484 INFO @ Mon, 03 Jun 2019 11:41:33: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:41:33: #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 11:41:33: #1 tags after filtering in treatment: 15554484 INFO @ Mon, 03 Jun 2019 11:41:33: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:41:33: #1 finished! INFO @ Mon, 03 Jun 2019 11:41:33: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:41:33: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:41:35: #2 number of paired peaks: 437 WARNING @ Mon, 03 Jun 2019 11:41:35: Fewer paired peaks (437) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 437 pairs to build model! INFO @ Mon, 03 Jun 2019 11:41:35: start model_add_line... INFO @ Mon, 03 Jun 2019 11:41:35: start X-correlation... INFO @ Mon, 03 Jun 2019 11:41:35: end of X-cor INFO @ Mon, 03 Jun 2019 11:41:35: #2 finished! INFO @ Mon, 03 Jun 2019 11:41:35: #2 predicted fragment length is 48 bps INFO @ Mon, 03 Jun 2019 11:41:35: #2 alternative fragment length(s) may be 3,48 bps INFO @ Mon, 03 Jun 2019 11:41:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX306195/SRX306195.05_model.r WARNING @ Mon, 03 Jun 2019 11:41:35: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 11:41:35: #2 You may need to consider one of the other alternative d(s): 3,48 WARNING @ Mon, 03 Jun 2019 11:41:35: #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 11:41:35: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:41:35: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:41:35: 15000000 INFO @ Mon, 03 Jun 2019 11:41:37: 15000000 INFO @ Mon, 03 Jun 2019 11:41:40: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 11:41:40: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 11:41:40: #1 total tags in treatment: 15554484 INFO @ Mon, 03 Jun 2019 11:41:40: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:41:40: #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 11:41:40: #1 tags after filtering in treatment: 15554484 INFO @ Mon, 03 Jun 2019 11:41:40: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:41:40: #1 finished! INFO @ Mon, 03 Jun 2019 11:41:40: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:41:40: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:41:41: #2 number of paired peaks: 437 WARNING @ Mon, 03 Jun 2019 11:41:41: Fewer paired peaks (437) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 437 pairs to build model! INFO @ Mon, 03 Jun 2019 11:41:41: start model_add_line... INFO @ Mon, 03 Jun 2019 11:41:41: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 11:41:41: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 11:41:41: #1 total tags in treatment: 15554484 INFO @ Mon, 03 Jun 2019 11:41:41: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:41:41: #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 11:41:41: start X-correlation... INFO @ Mon, 03 Jun 2019 11:41:41: end of X-cor INFO @ Mon, 03 Jun 2019 11:41:41: #2 finished! INFO @ Mon, 03 Jun 2019 11:41:41: #2 predicted fragment length is 48 bps INFO @ Mon, 03 Jun 2019 11:41:41: #2 alternative fragment length(s) may be 3,48 bps INFO @ Mon, 03 Jun 2019 11:41:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX306195/SRX306195.20_model.r WARNING @ Mon, 03 Jun 2019 11:41:41: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 11:41:41: #2 You may need to consider one of the other alternative d(s): 3,48 WARNING @ Mon, 03 Jun 2019 11:41:41: #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 11:41:41: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:41:41: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:41:42: #1 tags after filtering in treatment: 15554484 INFO @ Mon, 03 Jun 2019 11:41:42: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:41:42: #1 finished! INFO @ Mon, 03 Jun 2019 11:41:42: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:41:42: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:41:43: #2 number of paired peaks: 437 WARNING @ Mon, 03 Jun 2019 11:41:43: Fewer paired peaks (437) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 437 pairs to build model! INFO @ Mon, 03 Jun 2019 11:41:43: start model_add_line... INFO @ Mon, 03 Jun 2019 11:41:43: start X-correlation... INFO @ Mon, 03 Jun 2019 11:41:43: end of X-cor INFO @ Mon, 03 Jun 2019 11:41:43: #2 finished! INFO @ Mon, 03 Jun 2019 11:41:43: #2 predicted fragment length is 48 bps INFO @ Mon, 03 Jun 2019 11:41:43: #2 alternative fragment length(s) may be 3,48 bps INFO @ Mon, 03 Jun 2019 11:41:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX306195/SRX306195.10_model.r WARNING @ Mon, 03 Jun 2019 11:41:43: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 11:41:43: #2 You may need to consider one of the other alternative d(s): 3,48 WARNING @ Mon, 03 Jun 2019 11:41:43: #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 11:41:43: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:41:43: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:42:17: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:42:23: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:42:25: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:42:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX306195/SRX306195.05_peaks.xls INFO @ Mon, 03 Jun 2019 11:42:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX306195/SRX306195.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:42:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX306195/SRX306195.05_summits.bed INFO @ Mon, 03 Jun 2019 11:42:37: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3012 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:42:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX306195/SRX306195.20_peaks.xls INFO @ Mon, 03 Jun 2019 11:42:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX306195/SRX306195.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:42:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX306195/SRX306195.20_summits.bed INFO @ Mon, 03 Jun 2019 11:42:44: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (832 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:42:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX306195/SRX306195.10_peaks.xls INFO @ Mon, 03 Jun 2019 11:42:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX306195/SRX306195.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:42:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX306195/SRX306195.10_summits.bed INFO @ Mon, 03 Jun 2019 11:42:45: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1907 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。