Job ID = 1305939 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 37,981,047 reads read : 37,981,047 reads written : 37,981,047 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: 00:43:13 37981047 reads; of these: 37981047 (100.00%) were unpaired; of these: 1778639 (4.68%) aligned 0 times 16067262 (42.30%) aligned exactly 1 time 20135146 (53.01%) aligned >1 times 95.32% overall alignment rate Time searching: 00:43:13 Overall time: 00:43:13 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 16 files... [bam_rmdupse_core] 24414853 / 36202408 = 0.6744 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 22:36:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495311/SRX495311.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495311/SRX495311.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495311/SRX495311.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495311/SRX495311.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 22:36:39: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:36:39: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:36:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495311/SRX495311.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495311/SRX495311.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495311/SRX495311.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495311/SRX495311.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 22:36:39: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:36:39: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:36:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495311/SRX495311.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495311/SRX495311.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495311/SRX495311.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495311/SRX495311.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 22:36:39: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:36:39: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:36:49: 1000000 INFO @ Mon, 03 Jun 2019 22:36:49: 1000000 INFO @ Mon, 03 Jun 2019 22:36:49: 1000000 INFO @ Mon, 03 Jun 2019 22:36:59: 2000000 INFO @ Mon, 03 Jun 2019 22:36:59: 2000000 INFO @ Mon, 03 Jun 2019 22:37:00: 2000000 INFO @ Mon, 03 Jun 2019 22:37:08: 3000000 INFO @ Mon, 03 Jun 2019 22:37:09: 3000000 INFO @ Mon, 03 Jun 2019 22:37:10: 3000000 INFO @ Mon, 03 Jun 2019 22:37:18: 4000000 INFO @ Mon, 03 Jun 2019 22:37:19: 4000000 INFO @ Mon, 03 Jun 2019 22:37:20: 4000000 INFO @ Mon, 03 Jun 2019 22:37:27: 5000000 INFO @ Mon, 03 Jun 2019 22:37:29: 5000000 INFO @ Mon, 03 Jun 2019 22:37:29: 5000000 INFO @ Mon, 03 Jun 2019 22:37:36: 6000000 INFO @ Mon, 03 Jun 2019 22:37:39: 6000000 INFO @ Mon, 03 Jun 2019 22:37:39: 6000000 INFO @ Mon, 03 Jun 2019 22:37:45: 7000000 INFO @ Mon, 03 Jun 2019 22:37:49: 7000000 INFO @ Mon, 03 Jun 2019 22:37:49: 7000000 INFO @ Mon, 03 Jun 2019 22:37:54: 8000000 INFO @ Mon, 03 Jun 2019 22:37:59: 8000000 INFO @ Mon, 03 Jun 2019 22:37:59: 8000000 INFO @ Mon, 03 Jun 2019 22:38:03: 9000000 INFO @ Mon, 03 Jun 2019 22:38:08: 9000000 INFO @ Mon, 03 Jun 2019 22:38:09: 9000000 INFO @ Mon, 03 Jun 2019 22:38:12: 10000000 INFO @ Mon, 03 Jun 2019 22:38:18: 10000000 INFO @ Mon, 03 Jun 2019 22:38:18: 10000000 INFO @ Mon, 03 Jun 2019 22:38:21: 11000000 INFO @ Mon, 03 Jun 2019 22:38:28: 11000000 INFO @ Mon, 03 Jun 2019 22:38:28: 11000000 INFO @ Mon, 03 Jun 2019 22:38:29: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 22:38:29: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 22:38:29: #1 total tags in treatment: 11787555 INFO @ Mon, 03 Jun 2019 22:38:29: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:38:29: #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 22:38:29: #1 tags after filtering in treatment: 11787555 INFO @ Mon, 03 Jun 2019 22:38:29: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:38:29: #1 finished! INFO @ Mon, 03 Jun 2019 22:38:29: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:38:29: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:38:30: #2 number of paired peaks: 2147 INFO @ Mon, 03 Jun 2019 22:38:30: start model_add_line... INFO @ Mon, 03 Jun 2019 22:38:31: start X-correlation... INFO @ Mon, 03 Jun 2019 22:38:31: end of X-cor INFO @ Mon, 03 Jun 2019 22:38:31: #2 finished! INFO @ Mon, 03 Jun 2019 22:38:31: #2 predicted fragment length is 44 bps INFO @ Mon, 03 Jun 2019 22:38:31: #2 alternative fragment length(s) may be 44 bps INFO @ Mon, 03 Jun 2019 22:38:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX495311/SRX495311.10_model.r WARNING @ Mon, 03 Jun 2019 22:38:31: #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 22:38:31: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Mon, 03 Jun 2019 22:38:31: #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 22:38:31: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:38:31: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:38:35: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 22:38:35: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 22:38:35: #1 total tags in treatment: 11787555 INFO @ Mon, 03 Jun 2019 22:38:35: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:38:35: #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 22:38:35: #1 tags after filtering in treatment: 11787555 INFO @ Mon, 03 Jun 2019 22:38:35: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:38:35: #1 finished! INFO @ Mon, 03 Jun 2019 22:38:35: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:38:35: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:38:36: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 22:38:36: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 22:38:36: #1 total tags in treatment: 11787555 INFO @ Mon, 03 Jun 2019 22:38:36: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:38:36: #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 22:38:36: #1 tags after filtering in treatment: 11787555 INFO @ Mon, 03 Jun 2019 22:38:36: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:38:36: #1 finished! INFO @ Mon, 03 Jun 2019 22:38:36: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:38:36: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:38:37: #2 number of paired peaks: 2147 INFO @ Mon, 03 Jun 2019 22:38:37: start model_add_line... INFO @ Mon, 03 Jun 2019 22:38:37: start X-correlation... INFO @ Mon, 03 Jun 2019 22:38:37: end of X-cor INFO @ Mon, 03 Jun 2019 22:38:37: #2 finished! INFO @ Mon, 03 Jun 2019 22:38:37: #2 predicted fragment length is 44 bps INFO @ Mon, 03 Jun 2019 22:38:37: #2 alternative fragment length(s) may be 44 bps INFO @ Mon, 03 Jun 2019 22:38:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX495311/SRX495311.05_model.r WARNING @ Mon, 03 Jun 2019 22:38:37: #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 22:38:37: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Mon, 03 Jun 2019 22:38:37: #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 22:38:37: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:38:37: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:38:38: #2 number of paired peaks: 2147 INFO @ Mon, 03 Jun 2019 22:38:38: start model_add_line... INFO @ Mon, 03 Jun 2019 22:38:38: start X-correlation... INFO @ Mon, 03 Jun 2019 22:38:38: end of X-cor INFO @ Mon, 03 Jun 2019 22:38:38: #2 finished! INFO @ Mon, 03 Jun 2019 22:38:38: #2 predicted fragment length is 44 bps INFO @ Mon, 03 Jun 2019 22:38:38: #2 alternative fragment length(s) may be 44 bps INFO @ Mon, 03 Jun 2019 22:38:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX495311/SRX495311.20_model.r WARNING @ Mon, 03 Jun 2019 22:38:38: #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 22:38:38: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Mon, 03 Jun 2019 22:38:38: #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 22:38:38: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:38:38: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:39:07: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:39:13: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:39:13: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:39:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX495311/SRX495311.10_peaks.xls INFO @ Mon, 03 Jun 2019 22:39:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX495311/SRX495311.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:39:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX495311/SRX495311.10_summits.bed INFO @ Mon, 03 Jun 2019 22:39:25: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (6242 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:39:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX495311/SRX495311.05_peaks.xls INFO @ Mon, 03 Jun 2019 22:39:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX495311/SRX495311.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:39:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX495311/SRX495311.05_summits.bed INFO @ Mon, 03 Jun 2019 22:39:31: Done! pass1 - making usageList (15 chroms): 5 millis pass2 - checking and writing primary data (9135 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:39:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX495311/SRX495311.20_peaks.xls INFO @ Mon, 03 Jun 2019 22:39:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX495311/SRX495311.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:39:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX495311/SRX495311.20_summits.bed INFO @ Mon, 03 Jun 2019 22:39:32: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (3363 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。