Job ID = 1294387 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 19,172,821 reads read : 19,172,821 reads written : 19,172,821 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: 00:08:53 19172821 reads; of these: 19172821 (100.00%) were unpaired; of these: 728089 (3.80%) aligned 0 times 12514293 (65.27%) aligned exactly 1 time 5930439 (30.93%) aligned >1 times 96.20% overall alignment rate Time searching: 00:08:53 Overall time: 00:08:53 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] 2854587 / 18444732 = 0.1548 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 07:26:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287566/SRX287566.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287566/SRX287566.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287566/SRX287566.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287566/SRX287566.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 07:26:58: #1 read tag files... INFO @ Mon, 03 Jun 2019 07:26:58: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 07:26:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287566/SRX287566.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287566/SRX287566.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287566/SRX287566.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287566/SRX287566.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 07:26:58: #1 read tag files... INFO @ Mon, 03 Jun 2019 07:26:58: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 07:26:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287566/SRX287566.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287566/SRX287566.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287566/SRX287566.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287566/SRX287566.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 07:26:58: #1 read tag files... INFO @ Mon, 03 Jun 2019 07:26:58: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 07:27:08: 1000000 INFO @ Mon, 03 Jun 2019 07:27:08: 1000000 INFO @ Mon, 03 Jun 2019 07:27:08: 1000000 INFO @ Mon, 03 Jun 2019 07:27:17: 2000000 INFO @ Mon, 03 Jun 2019 07:27:18: 2000000 INFO @ Mon, 03 Jun 2019 07:27:18: 2000000 INFO @ Mon, 03 Jun 2019 07:27:26: 3000000 INFO @ Mon, 03 Jun 2019 07:27:28: 3000000 INFO @ Mon, 03 Jun 2019 07:27:29: 3000000 INFO @ Mon, 03 Jun 2019 07:27:37: 4000000 INFO @ Mon, 03 Jun 2019 07:27:37: 4000000 INFO @ Mon, 03 Jun 2019 07:27:39: 4000000 INFO @ Mon, 03 Jun 2019 07:27:47: 5000000 INFO @ Mon, 03 Jun 2019 07:27:48: 5000000 INFO @ Mon, 03 Jun 2019 07:27:50: 5000000 INFO @ Mon, 03 Jun 2019 07:27:56: 6000000 INFO @ Mon, 03 Jun 2019 07:27:58: 6000000 INFO @ Mon, 03 Jun 2019 07:28:01: 6000000 INFO @ Mon, 03 Jun 2019 07:28:05: 7000000 INFO @ Mon, 03 Jun 2019 07:28:09: 7000000 INFO @ Mon, 03 Jun 2019 07:28:11: 7000000 INFO @ Mon, 03 Jun 2019 07:28:14: 8000000 INFO @ Mon, 03 Jun 2019 07:28:20: 8000000 INFO @ Mon, 03 Jun 2019 07:28:22: 8000000 INFO @ Mon, 03 Jun 2019 07:28:23: 9000000 INFO @ Mon, 03 Jun 2019 07:28:30: 9000000 INFO @ Mon, 03 Jun 2019 07:28:33: 10000000 INFO @ Mon, 03 Jun 2019 07:28:33: 9000000 INFO @ Mon, 03 Jun 2019 07:28:41: 10000000 INFO @ Mon, 03 Jun 2019 07:28:42: 11000000 INFO @ Mon, 03 Jun 2019 07:28:43: 10000000 INFO @ Mon, 03 Jun 2019 07:28:51: 12000000 INFO @ Mon, 03 Jun 2019 07:28:52: 11000000 INFO @ Mon, 03 Jun 2019 07:28:54: 11000000 INFO @ Mon, 03 Jun 2019 07:29:00: 13000000 INFO @ Mon, 03 Jun 2019 07:29:02: 12000000 INFO @ Mon, 03 Jun 2019 07:29:05: 12000000 INFO @ Mon, 03 Jun 2019 07:29:10: 14000000 INFO @ Mon, 03 Jun 2019 07:29:13: 13000000 INFO @ Mon, 03 Jun 2019 07:29:15: 13000000 INFO @ Mon, 03 Jun 2019 07:29:19: 15000000 INFO @ Mon, 03 Jun 2019 07:29:24: 14000000 INFO @ Mon, 03 Jun 2019 07:29:24: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 07:29:24: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 07:29:24: #1 total tags in treatment: 15590145 INFO @ Mon, 03 Jun 2019 07:29:24: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 07:29:24: #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 07:29:24: #1 tags after filtering in treatment: 15590145 INFO @ Mon, 03 Jun 2019 07:29:24: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 07:29:24: #1 finished! INFO @ Mon, 03 Jun 2019 07:29:24: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 07:29:24: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 07:29:26: 14000000 INFO @ Mon, 03 Jun 2019 07:29:26: #2 number of paired peaks: 249 WARNING @ Mon, 03 Jun 2019 07:29:26: Fewer paired peaks (249) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 249 pairs to build model! INFO @ Mon, 03 Jun 2019 07:29:26: start model_add_line... INFO @ Mon, 03 Jun 2019 07:29:26: start X-correlation... INFO @ Mon, 03 Jun 2019 07:29:26: end of X-cor INFO @ Mon, 03 Jun 2019 07:29:26: #2 finished! INFO @ Mon, 03 Jun 2019 07:29:26: #2 predicted fragment length is 44 bps INFO @ Mon, 03 Jun 2019 07:29:26: #2 alternative fragment length(s) may be 44 bps INFO @ Mon, 03 Jun 2019 07:29:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287566/SRX287566.10_model.r WARNING @ Mon, 03 Jun 2019 07:29:26: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 07:29:26: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Mon, 03 Jun 2019 07:29:26: #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 07:29:26: #3 Call peaks... INFO @ Mon, 03 Jun 2019 07:29:26: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 07:29:33: 15000000 INFO @ Mon, 03 Jun 2019 07:29:35: 15000000 INFO @ Mon, 03 Jun 2019 07:29:39: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 07:29:39: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 07:29:39: #1 total tags in treatment: 15590145 INFO @ Mon, 03 Jun 2019 07:29:39: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 07:29:39: #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 07:29:39: #1 tags after filtering in treatment: 15590145 INFO @ Mon, 03 Jun 2019 07:29:39: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 07:29:39: #1 finished! INFO @ Mon, 03 Jun 2019 07:29:39: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 07:29:39: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 07:29:41: #2 number of paired peaks: 249 WARNING @ Mon, 03 Jun 2019 07:29:41: Fewer paired peaks (249) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 249 pairs to build model! INFO @ Mon, 03 Jun 2019 07:29:41: start model_add_line... INFO @ Mon, 03 Jun 2019 07:29:41: start X-correlation... INFO @ Mon, 03 Jun 2019 07:29:41: end of X-cor INFO @ Mon, 03 Jun 2019 07:29:41: #2 finished! INFO @ Mon, 03 Jun 2019 07:29:41: #2 predicted fragment length is 44 bps INFO @ Mon, 03 Jun 2019 07:29:41: #2 alternative fragment length(s) may be 44 bps INFO @ Mon, 03 Jun 2019 07:29:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287566/SRX287566.20_model.r WARNING @ Mon, 03 Jun 2019 07:29:41: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 07:29:41: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Mon, 03 Jun 2019 07:29:41: #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 07:29:41: #3 Call peaks... INFO @ Mon, 03 Jun 2019 07:29:41: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 07:29:41: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 07:29:41: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 07:29:41: #1 total tags in treatment: 15590145 INFO @ Mon, 03 Jun 2019 07:29:41: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 07:29:41: #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 07:29:41: #1 tags after filtering in treatment: 15590145 INFO @ Mon, 03 Jun 2019 07:29:41: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 07:29:41: #1 finished! INFO @ Mon, 03 Jun 2019 07:29:41: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 07:29:41: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 07:29:42: #2 number of paired peaks: 249 WARNING @ Mon, 03 Jun 2019 07:29:42: Fewer paired peaks (249) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 249 pairs to build model! INFO @ Mon, 03 Jun 2019 07:29:42: start model_add_line... INFO @ Mon, 03 Jun 2019 07:29:42: start X-correlation... INFO @ Mon, 03 Jun 2019 07:29:43: end of X-cor INFO @ Mon, 03 Jun 2019 07:29:43: #2 finished! INFO @ Mon, 03 Jun 2019 07:29:43: #2 predicted fragment length is 44 bps INFO @ Mon, 03 Jun 2019 07:29:43: #2 alternative fragment length(s) may be 44 bps INFO @ Mon, 03 Jun 2019 07:29:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287566/SRX287566.05_model.r WARNING @ Mon, 03 Jun 2019 07:29:43: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 07:29:43: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Mon, 03 Jun 2019 07:29:43: #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 07:29:43: #3 Call peaks... INFO @ Mon, 03 Jun 2019 07:29:43: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 07:30:06: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 07:30:21: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 07:30:23: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 07:30:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287566/SRX287566.10_peaks.xls INFO @ Mon, 03 Jun 2019 07:30:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287566/SRX287566.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 07:30:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287566/SRX287566.10_summits.bed INFO @ Mon, 03 Jun 2019 07:30:26: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1659 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 07:30:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287566/SRX287566.20_peaks.xls INFO @ Mon, 03 Jun 2019 07:30:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287566/SRX287566.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 07:30:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287566/SRX287566.20_summits.bed INFO @ Mon, 03 Jun 2019 07:30:41: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1262 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 07:30:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287566/SRX287566.05_peaks.xls INFO @ Mon, 03 Jun 2019 07:30:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287566/SRX287566.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 07:30:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287566/SRX287566.05_summits.bed INFO @ Mon, 03 Jun 2019 07:30:43: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1992 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。