Job ID = 1293282 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 36,475,879 reads read : 36,475,879 reads written : 36,475,879 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: 00:06:42 36475879 reads; of these: 36475879 (100.00%) were unpaired; of these: 3444655 (9.44%) aligned 0 times 29679501 (81.37%) aligned exactly 1 time 3351723 (9.19%) aligned >1 times 90.56% overall alignment rate Time searching: 00:06:42 Overall time: 00:06:42 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 12 files... [bam_rmdupse_core] 20987919 / 33031224 = 0.6354 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 @ Sun, 02 Jun 2019 23:02:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX011418/ERX011418.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX011418/ERX011418.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX011418/ERX011418.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX011418/ERX011418.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 @ Sun, 02 Jun 2019 23:02:57: #1 read tag files... INFO @ Sun, 02 Jun 2019 23:02:57: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 23:02:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX011418/ERX011418.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX011418/ERX011418.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX011418/ERX011418.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX011418/ERX011418.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 @ Sun, 02 Jun 2019 23:02:58: #1 read tag files... INFO @ Sun, 02 Jun 2019 23:02:58: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 23:02:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX011418/ERX011418.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX011418/ERX011418.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX011418/ERX011418.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX011418/ERX011418.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 @ Sun, 02 Jun 2019 23:02:58: #1 read tag files... INFO @ Sun, 02 Jun 2019 23:02:58: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 23:03:06: 1000000 INFO @ Sun, 02 Jun 2019 23:03:06: 1000000 INFO @ Sun, 02 Jun 2019 23:03:09: 1000000 INFO @ Sun, 02 Jun 2019 23:03:14: 2000000 INFO @ Sun, 02 Jun 2019 23:03:16: 2000000 INFO @ Sun, 02 Jun 2019 23:03:20: 2000000 INFO @ Sun, 02 Jun 2019 23:03:23: 3000000 INFO @ Sun, 02 Jun 2019 23:03:25: 3000000 INFO @ Sun, 02 Jun 2019 23:03:30: 3000000 INFO @ Sun, 02 Jun 2019 23:03:31: 4000000 INFO @ Sun, 02 Jun 2019 23:03:33: 4000000 INFO @ Sun, 02 Jun 2019 23:03:39: 5000000 INFO @ Sun, 02 Jun 2019 23:03:41: 4000000 INFO @ Sun, 02 Jun 2019 23:03:42: 5000000 INFO @ Sun, 02 Jun 2019 23:03:47: 6000000 INFO @ Sun, 02 Jun 2019 23:03:51: 6000000 INFO @ Sun, 02 Jun 2019 23:03:51: 5000000 INFO @ Sun, 02 Jun 2019 23:03:56: 7000000 INFO @ Sun, 02 Jun 2019 23:03:59: 7000000 INFO @ Sun, 02 Jun 2019 23:04:02: 6000000 INFO @ Sun, 02 Jun 2019 23:04:04: 8000000 INFO @ Sun, 02 Jun 2019 23:04:08: 8000000 INFO @ Sun, 02 Jun 2019 23:04:12: 9000000 INFO @ Sun, 02 Jun 2019 23:04:12: 7000000 INFO @ Sun, 02 Jun 2019 23:04:17: 9000000 INFO @ Sun, 02 Jun 2019 23:04:20: 10000000 INFO @ Sun, 02 Jun 2019 23:04:22: 8000000 INFO @ Sun, 02 Jun 2019 23:04:25: 10000000 INFO @ Sun, 02 Jun 2019 23:04:28: 11000000 INFO @ Sun, 02 Jun 2019 23:04:32: 9000000 INFO @ Sun, 02 Jun 2019 23:04:34: 11000000 INFO @ Sun, 02 Jun 2019 23:04:36: 12000000 INFO @ Sun, 02 Jun 2019 23:04:37: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 23:04:37: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 23:04:37: #1 total tags in treatment: 12043305 INFO @ Sun, 02 Jun 2019 23:04:37: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 23:04:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 23:04:37: #1 tags after filtering in treatment: 12043305 INFO @ Sun, 02 Jun 2019 23:04:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 23:04:37: #1 finished! INFO @ Sun, 02 Jun 2019 23:04:37: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 23:04:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 23:04:39: #2 number of paired peaks: 5141 INFO @ Sun, 02 Jun 2019 23:04:39: start model_add_line... INFO @ Sun, 02 Jun 2019 23:04:39: start X-correlation... INFO @ Sun, 02 Jun 2019 23:04:39: end of X-cor INFO @ Sun, 02 Jun 2019 23:04:39: #2 finished! INFO @ Sun, 02 Jun 2019 23:04:39: #2 predicted fragment length is 58 bps INFO @ Sun, 02 Jun 2019 23:04:39: #2 alternative fragment length(s) may be 4,58 bps INFO @ Sun, 02 Jun 2019 23:04:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX011418/ERX011418.05_model.r WARNING @ Sun, 02 Jun 2019 23:04:39: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 23:04:39: #2 You may need to consider one of the other alternative d(s): 4,58 WARNING @ Sun, 02 Jun 2019 23:04:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 23:04:39: #3 Call peaks... INFO @ Sun, 02 Jun 2019 23:04:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 23:04:43: 12000000 INFO @ Sun, 02 Jun 2019 23:04:43: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 23:04:43: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 23:04:43: #1 total tags in treatment: 12043305 INFO @ Sun, 02 Jun 2019 23:04:43: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 23:04:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 23:04:43: 10000000 INFO @ Sun, 02 Jun 2019 23:04:43: #1 tags after filtering in treatment: 12043305 INFO @ Sun, 02 Jun 2019 23:04:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 23:04:43: #1 finished! INFO @ Sun, 02 Jun 2019 23:04:43: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 23:04:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 23:04:45: #2 number of paired peaks: 5141 INFO @ Sun, 02 Jun 2019 23:04:45: start model_add_line... INFO @ Sun, 02 Jun 2019 23:04:45: start X-correlation... INFO @ Sun, 02 Jun 2019 23:04:45: end of X-cor INFO @ Sun, 02 Jun 2019 23:04:45: #2 finished! INFO @ Sun, 02 Jun 2019 23:04:45: #2 predicted fragment length is 58 bps INFO @ Sun, 02 Jun 2019 23:04:45: #2 alternative fragment length(s) may be 4,58 bps INFO @ Sun, 02 Jun 2019 23:04:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX011418/ERX011418.10_model.r WARNING @ Sun, 02 Jun 2019 23:04:45: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 23:04:45: #2 You may need to consider one of the other alternative d(s): 4,58 WARNING @ Sun, 02 Jun 2019 23:04:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 23:04:45: #3 Call peaks... INFO @ Sun, 02 Jun 2019 23:04:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 23:04:54: 11000000 INFO @ Sun, 02 Jun 2019 23:05:04: 12000000 INFO @ Sun, 02 Jun 2019 23:05:04: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 23:05:04: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 23:05:04: #1 total tags in treatment: 12043305 INFO @ Sun, 02 Jun 2019 23:05:04: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 23:05:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 23:05:05: #1 tags after filtering in treatment: 12043305 INFO @ Sun, 02 Jun 2019 23:05:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 23:05:05: #1 finished! INFO @ Sun, 02 Jun 2019 23:05:05: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 23:05:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 23:05:06: #2 number of paired peaks: 5141 INFO @ Sun, 02 Jun 2019 23:05:06: start model_add_line... INFO @ Sun, 02 Jun 2019 23:05:06: start X-correlation... INFO @ Sun, 02 Jun 2019 23:05:06: end of X-cor INFO @ Sun, 02 Jun 2019 23:05:06: #2 finished! INFO @ Sun, 02 Jun 2019 23:05:06: #2 predicted fragment length is 58 bps INFO @ Sun, 02 Jun 2019 23:05:06: #2 alternative fragment length(s) may be 4,58 bps INFO @ Sun, 02 Jun 2019 23:05:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX011418/ERX011418.20_model.r WARNING @ Sun, 02 Jun 2019 23:05:06: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 23:05:06: #2 You may need to consider one of the other alternative d(s): 4,58 WARNING @ Sun, 02 Jun 2019 23:05:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 23:05:06: #3 Call peaks... INFO @ Sun, 02 Jun 2019 23:05:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 23:05:12: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 23:05:19: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 23:05:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX011418/ERX011418.05_peaks.xls INFO @ Sun, 02 Jun 2019 23:05:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX011418/ERX011418.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 23:05:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX011418/ERX011418.05_summits.bed INFO @ Sun, 02 Jun 2019 23:05:29: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (12768 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 23:05:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX011418/ERX011418.10_peaks.xls INFO @ Sun, 02 Jun 2019 23:05:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX011418/ERX011418.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 23:05:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX011418/ERX011418.10_summits.bed INFO @ Sun, 02 Jun 2019 23:05:36: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (5414 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 23:05:40: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 23:05:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX011418/ERX011418.20_peaks.xls INFO @ Sun, 02 Jun 2019 23:05:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX011418/ERX011418.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 23:05:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX011418/ERX011418.20_summits.bed INFO @ Sun, 02 Jun 2019 23:05:57: Done! pass1 - making usageList (11 chroms): 2 millis pass2 - checking and writing primary data (1494 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。