Job ID = 1293957 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 13,804,609 reads read : 13,804,609 reads written : 13,804,609 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: 00:03:55 13804609 reads; of these: 13804609 (100.00%) were unpaired; of these: 738004 (5.35%) aligned 0 times 11523959 (83.48%) aligned exactly 1 time 1542646 (11.17%) aligned >1 times 94.65% overall alignment rate Time searching: 00:03:55 Overall time: 00:03:55 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] 3809629 / 13066605 = 0.2916 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 03:46:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX152091/SRX152091.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX152091/SRX152091.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX152091/SRX152091.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX152091/SRX152091.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 03:46:00: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:46:00: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:46:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX152091/SRX152091.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX152091/SRX152091.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX152091/SRX152091.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX152091/SRX152091.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 03:46:00: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:46:00: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:46:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX152091/SRX152091.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX152091/SRX152091.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX152091/SRX152091.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX152091/SRX152091.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 03:46:00: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:46:00: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:46:07: 1000000 INFO @ Mon, 03 Jun 2019 03:46:08: 1000000 INFO @ Mon, 03 Jun 2019 03:46:09: 1000000 INFO @ Mon, 03 Jun 2019 03:46:14: 2000000 INFO @ Mon, 03 Jun 2019 03:46:15: 2000000 INFO @ Mon, 03 Jun 2019 03:46:17: 2000000 INFO @ Mon, 03 Jun 2019 03:46:21: 3000000 INFO @ Mon, 03 Jun 2019 03:46:22: 3000000 INFO @ Mon, 03 Jun 2019 03:46:25: 3000000 INFO @ Mon, 03 Jun 2019 03:46:27: 4000000 INFO @ Mon, 03 Jun 2019 03:46:29: 4000000 INFO @ Mon, 03 Jun 2019 03:46:33: 4000000 INFO @ Mon, 03 Jun 2019 03:46:34: 5000000 INFO @ Mon, 03 Jun 2019 03:46:36: 5000000 INFO @ Mon, 03 Jun 2019 03:46:40: 6000000 INFO @ Mon, 03 Jun 2019 03:46:40: 5000000 INFO @ Mon, 03 Jun 2019 03:46:43: 6000000 INFO @ Mon, 03 Jun 2019 03:46:46: 7000000 INFO @ Mon, 03 Jun 2019 03:46:48: 6000000 INFO @ Mon, 03 Jun 2019 03:46:50: 7000000 INFO @ Mon, 03 Jun 2019 03:46:53: 8000000 INFO @ Mon, 03 Jun 2019 03:46:56: 7000000 INFO @ Mon, 03 Jun 2019 03:46:57: 8000000 INFO @ Mon, 03 Jun 2019 03:46:59: 9000000 INFO @ Mon, 03 Jun 2019 03:47:01: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 03:47:01: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 03:47:01: #1 total tags in treatment: 9256976 INFO @ Mon, 03 Jun 2019 03:47:01: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:47:01: #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 03:47:01: #1 tags after filtering in treatment: 9256976 INFO @ Mon, 03 Jun 2019 03:47:01: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:47:01: #1 finished! INFO @ Mon, 03 Jun 2019 03:47:01: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:47:01: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:47:02: #2 number of paired peaks: 1953 INFO @ Mon, 03 Jun 2019 03:47:02: start model_add_line... INFO @ Mon, 03 Jun 2019 03:47:02: start X-correlation... INFO @ Mon, 03 Jun 2019 03:47:02: end of X-cor INFO @ Mon, 03 Jun 2019 03:47:02: #2 finished! INFO @ Mon, 03 Jun 2019 03:47:02: #2 predicted fragment length is 35 bps INFO @ Mon, 03 Jun 2019 03:47:02: #2 alternative fragment length(s) may be 4,35 bps INFO @ Mon, 03 Jun 2019 03:47:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX152091/SRX152091.20_model.r WARNING @ Mon, 03 Jun 2019 03:47:02: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 03:47:02: #2 You may need to consider one of the other alternative d(s): 4,35 WARNING @ Mon, 03 Jun 2019 03:47:02: #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 03:47:02: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:47:02: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:47:03: 8000000 INFO @ Mon, 03 Jun 2019 03:47:04: 9000000 INFO @ Mon, 03 Jun 2019 03:47:06: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 03:47:06: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 03:47:06: #1 total tags in treatment: 9256976 INFO @ Mon, 03 Jun 2019 03:47:06: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:47:06: #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 03:47:07: #1 tags after filtering in treatment: 9256976 INFO @ Mon, 03 Jun 2019 03:47:07: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:47:07: #1 finished! INFO @ Mon, 03 Jun 2019 03:47:07: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:47:07: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:47:08: #2 number of paired peaks: 1953 INFO @ Mon, 03 Jun 2019 03:47:08: start model_add_line... INFO @ Mon, 03 Jun 2019 03:47:08: start X-correlation... INFO @ Mon, 03 Jun 2019 03:47:08: end of X-cor INFO @ Mon, 03 Jun 2019 03:47:08: #2 finished! INFO @ Mon, 03 Jun 2019 03:47:08: #2 predicted fragment length is 35 bps INFO @ Mon, 03 Jun 2019 03:47:08: #2 alternative fragment length(s) may be 4,35 bps INFO @ Mon, 03 Jun 2019 03:47:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX152091/SRX152091.05_model.r WARNING @ Mon, 03 Jun 2019 03:47:08: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 03:47:08: #2 You may need to consider one of the other alternative d(s): 4,35 WARNING @ Mon, 03 Jun 2019 03:47:08: #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 03:47:08: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:47:08: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:47:11: 9000000 INFO @ Mon, 03 Jun 2019 03:47:13: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 03:47:13: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 03:47:13: #1 total tags in treatment: 9256976 INFO @ Mon, 03 Jun 2019 03:47:13: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:47:13: #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 03:47:13: #1 tags after filtering in treatment: 9256976 INFO @ Mon, 03 Jun 2019 03:47:13: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:47:13: #1 finished! INFO @ Mon, 03 Jun 2019 03:47:13: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:47:13: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:47:14: #2 number of paired peaks: 1953 INFO @ Mon, 03 Jun 2019 03:47:14: start model_add_line... INFO @ Mon, 03 Jun 2019 03:47:14: start X-correlation... INFO @ Mon, 03 Jun 2019 03:47:14: end of X-cor INFO @ Mon, 03 Jun 2019 03:47:14: #2 finished! INFO @ Mon, 03 Jun 2019 03:47:14: #2 predicted fragment length is 35 bps INFO @ Mon, 03 Jun 2019 03:47:14: #2 alternative fragment length(s) may be 4,35 bps INFO @ Mon, 03 Jun 2019 03:47:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX152091/SRX152091.10_model.r WARNING @ Mon, 03 Jun 2019 03:47:14: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 03:47:14: #2 You may need to consider one of the other alternative d(s): 4,35 WARNING @ Mon, 03 Jun 2019 03:47:14: #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 03:47:14: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:47:14: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:47:28: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:47:36: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:47:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX152091/SRX152091.20_peaks.xls INFO @ Mon, 03 Jun 2019 03:47:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX152091/SRX152091.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:47:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX152091/SRX152091.20_summits.bed INFO @ Mon, 03 Jun 2019 03:47:40: Done! pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (5 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 03:47:41: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:47:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX152091/SRX152091.05_peaks.xls INFO @ Mon, 03 Jun 2019 03:47:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX152091/SRX152091.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:47:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX152091/SRX152091.05_summits.bed INFO @ Mon, 03 Jun 2019 03:47:49: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3846 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 03:47:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX152091/SRX152091.10_peaks.xls INFO @ Mon, 03 Jun 2019 03:47:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX152091/SRX152091.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:47:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX152091/SRX152091.10_summits.bed INFO @ Mon, 03 Jun 2019 03:47:53: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1176 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。