Job ID = 1293781 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 18,188,898 reads read : 18,188,898 reads written : 18,188,898 spots read : 22,003,233 reads read : 22,003,233 reads written : 22,003,233 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: 00:00:01 Multiseed full-index search: 00:11:21 40192131 reads; of these: 40192131 (100.00%) were unpaired; of these: 838094 (2.09%) aligned 0 times 34908528 (86.85%) aligned exactly 1 time 4445509 (11.06%) aligned >1 times 97.91% overall alignment rate Time searching: 00:11:22 Overall time: 00:11:22 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] 21711257 / 39354037 = 0.5517 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 02:41:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX113330/SRX113330.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX113330/SRX113330.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX113330/SRX113330.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX113330/SRX113330.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 02:41:33: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:41:33: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:41:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX113330/SRX113330.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX113330/SRX113330.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX113330/SRX113330.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX113330/SRX113330.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 02:41:33: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:41:33: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:41:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX113330/SRX113330.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX113330/SRX113330.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX113330/SRX113330.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX113330/SRX113330.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 02:41:33: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:41:33: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:41:43: 1000000 INFO @ Mon, 03 Jun 2019 02:41:44: 1000000 INFO @ Mon, 03 Jun 2019 02:41:44: 1000000 INFO @ Mon, 03 Jun 2019 02:41:52: 2000000 INFO @ Mon, 03 Jun 2019 02:41:53: 2000000 INFO @ Mon, 03 Jun 2019 02:41:54: 2000000 INFO @ Mon, 03 Jun 2019 02:42:01: 3000000 INFO @ Mon, 03 Jun 2019 02:42:02: 3000000 INFO @ Mon, 03 Jun 2019 02:42:03: 3000000 INFO @ Mon, 03 Jun 2019 02:42:10: 4000000 INFO @ Mon, 03 Jun 2019 02:42:12: 4000000 INFO @ Mon, 03 Jun 2019 02:42:13: 4000000 INFO @ Mon, 03 Jun 2019 02:42:20: 5000000 INFO @ Mon, 03 Jun 2019 02:42:22: 5000000 INFO @ Mon, 03 Jun 2019 02:42:23: 5000000 INFO @ Mon, 03 Jun 2019 02:42:30: 6000000 INFO @ Mon, 03 Jun 2019 02:42:32: 6000000 INFO @ Mon, 03 Jun 2019 02:42:34: 6000000 INFO @ Mon, 03 Jun 2019 02:42:40: 7000000 INFO @ Mon, 03 Jun 2019 02:42:42: 7000000 INFO @ Mon, 03 Jun 2019 02:42:44: 7000000 INFO @ Mon, 03 Jun 2019 02:42:49: 8000000 INFO @ Mon, 03 Jun 2019 02:42:51: 8000000 INFO @ Mon, 03 Jun 2019 02:42:54: 8000000 INFO @ Mon, 03 Jun 2019 02:42:59: 9000000 INFO @ Mon, 03 Jun 2019 02:43:01: 9000000 INFO @ Mon, 03 Jun 2019 02:43:04: 9000000 INFO @ Mon, 03 Jun 2019 02:43:08: 10000000 INFO @ Mon, 03 Jun 2019 02:43:10: 10000000 INFO @ Mon, 03 Jun 2019 02:43:13: 10000000 INFO @ Mon, 03 Jun 2019 02:43:17: 11000000 INFO @ Mon, 03 Jun 2019 02:43:20: 11000000 INFO @ Mon, 03 Jun 2019 02:43:23: 11000000 INFO @ Mon, 03 Jun 2019 02:43:27: 12000000 INFO @ Mon, 03 Jun 2019 02:43:29: 12000000 INFO @ Mon, 03 Jun 2019 02:43:33: 12000000 INFO @ Mon, 03 Jun 2019 02:43:36: 13000000 INFO @ Mon, 03 Jun 2019 02:43:39: 13000000 INFO @ Mon, 03 Jun 2019 02:43:42: 13000000 INFO @ Mon, 03 Jun 2019 02:43:45: 14000000 INFO @ Mon, 03 Jun 2019 02:43:48: 14000000 INFO @ Mon, 03 Jun 2019 02:43:52: 14000000 INFO @ Mon, 03 Jun 2019 02:43:55: 15000000 INFO @ Mon, 03 Jun 2019 02:43:58: 15000000 INFO @ Mon, 03 Jun 2019 02:44:02: 15000000 INFO @ Mon, 03 Jun 2019 02:44:04: 16000000 INFO @ Mon, 03 Jun 2019 02:44:07: 16000000 INFO @ Mon, 03 Jun 2019 02:44:11: 16000000 INFO @ Mon, 03 Jun 2019 02:44:13: 17000000 INFO @ Mon, 03 Jun 2019 02:44:16: 17000000 INFO @ Mon, 03 Jun 2019 02:44:19: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 02:44:19: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 02:44:19: #1 total tags in treatment: 17642780 INFO @ Mon, 03 Jun 2019 02:44:19: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:44:19: #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 02:44:19: #1 tags after filtering in treatment: 17642780 INFO @ Mon, 03 Jun 2019 02:44:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:44:19: #1 finished! INFO @ Mon, 03 Jun 2019 02:44:19: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:44:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:44:21: 17000000 INFO @ Mon, 03 Jun 2019 02:44:22: #2 number of paired peaks: 1546 INFO @ Mon, 03 Jun 2019 02:44:22: start model_add_line... INFO @ Mon, 03 Jun 2019 02:44:22: start X-correlation... INFO @ Mon, 03 Jun 2019 02:44:22: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 02:44:22: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 02:44:22: #1 total tags in treatment: 17642780 INFO @ Mon, 03 Jun 2019 02:44:22: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:44:22: #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 02:44:22: end of X-cor INFO @ Mon, 03 Jun 2019 02:44:22: #2 finished! INFO @ Mon, 03 Jun 2019 02:44:22: #2 predicted fragment length is 2 bps INFO @ Mon, 03 Jun 2019 02:44:22: #2 alternative fragment length(s) may be 2 bps INFO @ Mon, 03 Jun 2019 02:44:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX113330/SRX113330.10_model.r WARNING @ Mon, 03 Jun 2019 02:44:22: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 02:44:22: #2 You may need to consider one of the other alternative d(s): 2 WARNING @ Mon, 03 Jun 2019 02:44:22: #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 02:44:22: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:44:22: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:44:22: #1 tags after filtering in treatment: 17642780 INFO @ Mon, 03 Jun 2019 02:44:22: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:44:22: #1 finished! INFO @ Mon, 03 Jun 2019 02:44:22: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:44:22: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:44:24: #2 number of paired peaks: 1546 INFO @ Mon, 03 Jun 2019 02:44:24: start model_add_line... INFO @ Mon, 03 Jun 2019 02:44:24: start X-correlation... INFO @ Mon, 03 Jun 2019 02:44:24: end of X-cor INFO @ Mon, 03 Jun 2019 02:44:24: #2 finished! INFO @ Mon, 03 Jun 2019 02:44:24: #2 predicted fragment length is 2 bps INFO @ Mon, 03 Jun 2019 02:44:24: #2 alternative fragment length(s) may be 2 bps INFO @ Mon, 03 Jun 2019 02:44:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX113330/SRX113330.05_model.r WARNING @ Mon, 03 Jun 2019 02:44:24: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 02:44:24: #2 You may need to consider one of the other alternative d(s): 2 WARNING @ Mon, 03 Jun 2019 02:44:24: #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 02:44:24: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:44:24: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:44:27: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 02:44:27: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 02:44:27: #1 total tags in treatment: 17642780 INFO @ Mon, 03 Jun 2019 02:44:27: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:44:27: #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 02:44:27: #1 tags after filtering in treatment: 17642780 INFO @ Mon, 03 Jun 2019 02:44:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:44:27: #1 finished! INFO @ Mon, 03 Jun 2019 02:44:27: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:44:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:44:29: #2 number of paired peaks: 1546 INFO @ Mon, 03 Jun 2019 02:44:29: start model_add_line... INFO @ Mon, 03 Jun 2019 02:44:30: start X-correlation... INFO @ Mon, 03 Jun 2019 02:44:30: end of X-cor INFO @ Mon, 03 Jun 2019 02:44:30: #2 finished! INFO @ Mon, 03 Jun 2019 02:44:30: #2 predicted fragment length is 2 bps INFO @ Mon, 03 Jun 2019 02:44:30: #2 alternative fragment length(s) may be 2 bps INFO @ Mon, 03 Jun 2019 02:44:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX113330/SRX113330.20_model.r WARNING @ Mon, 03 Jun 2019 02:44:30: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 02:44:30: #2 You may need to consider one of the other alternative d(s): 2 WARNING @ Mon, 03 Jun 2019 02:44:30: #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 02:44:30: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:44:30: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:45:08: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:45:10: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:45:16: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:45:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX113330/SRX113330.10_peaks.xls INFO @ Mon, 03 Jun 2019 02:45:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX113330/SRX113330.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:45:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX113330/SRX113330.10_summits.bed INFO @ Mon, 03 Jun 2019 02:45:29: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 02:45:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX113330/SRX113330.05_peaks.xls INFO @ Mon, 03 Jun 2019 02:45:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX113330/SRX113330.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:45:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX113330/SRX113330.05_summits.bed INFO @ Mon, 03 Jun 2019 02:45:31: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 02:45:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX113330/SRX113330.20_peaks.xls INFO @ Mon, 03 Jun 2019 02:45:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX113330/SRX113330.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:45:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX113330/SRX113330.20_summits.bed INFO @ Mon, 03 Jun 2019 02:45:37: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。