Job ID = 1293927 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 24,821,883 reads read : 24,821,883 reads written : 24,821,883 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: 00:09:02 24821883 reads; of these: 24821883 (100.00%) were unpaired; of these: 1069073 (4.31%) aligned 0 times 15719154 (63.33%) aligned exactly 1 time 8033656 (32.37%) aligned >1 times 95.69% overall alignment rate Time searching: 00:09:02 Overall time: 00:09:02 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] 4318142 / 23752810 = 0.1818 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 03:31:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX149199/SRX149199.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX149199/SRX149199.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX149199/SRX149199.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX149199/SRX149199.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 03:31:11: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:31:11: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:31:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX149199/SRX149199.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX149199/SRX149199.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX149199/SRX149199.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX149199/SRX149199.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 03:31:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX149199/SRX149199.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX149199/SRX149199.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX149199/SRX149199.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX149199/SRX149199.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 03:31:11: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:31:11: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:31:11: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:31:11: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:31:20: 1000000 INFO @ Mon, 03 Jun 2019 03:31:21: 1000000 INFO @ Mon, 03 Jun 2019 03:31:21: 1000000 INFO @ Mon, 03 Jun 2019 03:31:28: 2000000 INFO @ Mon, 03 Jun 2019 03:31:31: 2000000 INFO @ Mon, 03 Jun 2019 03:31:31: 2000000 INFO @ Mon, 03 Jun 2019 03:31:37: 3000000 INFO @ Mon, 03 Jun 2019 03:31:41: 3000000 INFO @ Mon, 03 Jun 2019 03:31:41: 3000000 INFO @ Mon, 03 Jun 2019 03:31:46: 4000000 INFO @ Mon, 03 Jun 2019 03:31:51: 4000000 INFO @ Mon, 03 Jun 2019 03:31:51: 4000000 INFO @ Mon, 03 Jun 2019 03:31:54: 5000000 INFO @ Mon, 03 Jun 2019 03:32:00: 5000000 INFO @ Mon, 03 Jun 2019 03:32:00: 5000000 INFO @ Mon, 03 Jun 2019 03:32:03: 6000000 INFO @ Mon, 03 Jun 2019 03:32:10: 6000000 INFO @ Mon, 03 Jun 2019 03:32:10: 6000000 INFO @ Mon, 03 Jun 2019 03:32:11: 7000000 INFO @ Mon, 03 Jun 2019 03:32:20: 8000000 INFO @ Mon, 03 Jun 2019 03:32:20: 7000000 INFO @ Mon, 03 Jun 2019 03:32:20: 7000000 INFO @ Mon, 03 Jun 2019 03:32:28: 9000000 INFO @ Mon, 03 Jun 2019 03:32:30: 8000000 INFO @ Mon, 03 Jun 2019 03:32:30: 8000000 INFO @ Mon, 03 Jun 2019 03:32:36: 10000000 INFO @ Mon, 03 Jun 2019 03:32:39: 9000000 INFO @ Mon, 03 Jun 2019 03:32:39: 9000000 INFO @ Mon, 03 Jun 2019 03:32:45: 11000000 INFO @ Mon, 03 Jun 2019 03:32:49: 10000000 INFO @ Mon, 03 Jun 2019 03:32:49: 10000000 INFO @ Mon, 03 Jun 2019 03:32:53: 12000000 INFO @ Mon, 03 Jun 2019 03:32:58: 11000000 INFO @ Mon, 03 Jun 2019 03:32:59: 11000000 INFO @ Mon, 03 Jun 2019 03:33:01: 13000000 INFO @ Mon, 03 Jun 2019 03:33:07: 12000000 INFO @ Mon, 03 Jun 2019 03:33:08: 12000000 INFO @ Mon, 03 Jun 2019 03:33:10: 14000000 INFO @ Mon, 03 Jun 2019 03:33:17: 13000000 INFO @ Mon, 03 Jun 2019 03:33:17: 13000000 INFO @ Mon, 03 Jun 2019 03:33:18: 15000000 INFO @ Mon, 03 Jun 2019 03:33:26: 14000000 INFO @ Mon, 03 Jun 2019 03:33:27: 14000000 INFO @ Mon, 03 Jun 2019 03:33:27: 16000000 INFO @ Mon, 03 Jun 2019 03:33:35: 17000000 INFO @ Mon, 03 Jun 2019 03:33:36: 15000000 INFO @ Mon, 03 Jun 2019 03:33:36: 15000000 INFO @ Mon, 03 Jun 2019 03:33:43: 18000000 INFO @ Mon, 03 Jun 2019 03:33:45: 16000000 INFO @ Mon, 03 Jun 2019 03:33:45: 16000000 INFO @ Mon, 03 Jun 2019 03:33:52: 19000000 INFO @ Mon, 03 Jun 2019 03:33:54: 17000000 INFO @ Mon, 03 Jun 2019 03:33:55: 17000000 INFO @ Mon, 03 Jun 2019 03:33:56: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 03:33:56: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 03:33:56: #1 total tags in treatment: 19434668 INFO @ Mon, 03 Jun 2019 03:33:56: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:33:56: #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 03:33:56: #1 tags after filtering in treatment: 19434668 INFO @ Mon, 03 Jun 2019 03:33:56: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:33:56: #1 finished! INFO @ Mon, 03 Jun 2019 03:33:56: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:33:56: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:33:58: #2 number of paired peaks: 465 WARNING @ Mon, 03 Jun 2019 03:33:58: Fewer paired peaks (465) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 465 pairs to build model! INFO @ Mon, 03 Jun 2019 03:33:58: start model_add_line... INFO @ Mon, 03 Jun 2019 03:33:58: start X-correlation... INFO @ Mon, 03 Jun 2019 03:33:58: end of X-cor INFO @ Mon, 03 Jun 2019 03:33:58: #2 finished! INFO @ Mon, 03 Jun 2019 03:33:58: #2 predicted fragment length is 35 bps INFO @ Mon, 03 Jun 2019 03:33:58: #2 alternative fragment length(s) may be 2,35,544,560,572,595 bps INFO @ Mon, 03 Jun 2019 03:33:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX149199/SRX149199.20_model.r WARNING @ Mon, 03 Jun 2019 03:33:58: #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 03:33:58: #2 You may need to consider one of the other alternative d(s): 2,35,544,560,572,595 WARNING @ Mon, 03 Jun 2019 03:33:58: #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 03:33:58: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:33:58: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:34:03: 18000000 INFO @ Mon, 03 Jun 2019 03:34:05: 18000000 INFO @ Mon, 03 Jun 2019 03:34:13: 19000000 INFO @ Mon, 03 Jun 2019 03:34:14: 19000000 INFO @ Mon, 03 Jun 2019 03:34:17: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 03:34:17: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 03:34:17: #1 total tags in treatment: 19434668 INFO @ Mon, 03 Jun 2019 03:34:17: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:34:17: #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 03:34:17: #1 tags after filtering in treatment: 19434668 INFO @ Mon, 03 Jun 2019 03:34:17: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:34:17: #1 finished! INFO @ Mon, 03 Jun 2019 03:34:17: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:34:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:34:18: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 03:34:18: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 03:34:18: #1 total tags in treatment: 19434668 INFO @ Mon, 03 Jun 2019 03:34:18: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:34:18: #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 03:34:19: #1 tags after filtering in treatment: 19434668 INFO @ Mon, 03 Jun 2019 03:34:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:34:19: #1 finished! INFO @ Mon, 03 Jun 2019 03:34:19: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:34:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:34:19: #2 number of paired peaks: 465 WARNING @ Mon, 03 Jun 2019 03:34:19: Fewer paired peaks (465) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 465 pairs to build model! INFO @ Mon, 03 Jun 2019 03:34:19: start model_add_line... INFO @ Mon, 03 Jun 2019 03:34:19: start X-correlation... INFO @ Mon, 03 Jun 2019 03:34:19: end of X-cor INFO @ Mon, 03 Jun 2019 03:34:19: #2 finished! INFO @ Mon, 03 Jun 2019 03:34:19: #2 predicted fragment length is 35 bps INFO @ Mon, 03 Jun 2019 03:34:19: #2 alternative fragment length(s) may be 2,35,544,560,572,595 bps INFO @ Mon, 03 Jun 2019 03:34:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX149199/SRX149199.10_model.r WARNING @ Mon, 03 Jun 2019 03:34:19: #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 03:34:19: #2 You may need to consider one of the other alternative d(s): 2,35,544,560,572,595 WARNING @ Mon, 03 Jun 2019 03:34:19: #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 03:34:19: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:34:19: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:34:20: #2 number of paired peaks: 465 WARNING @ Mon, 03 Jun 2019 03:34:20: Fewer paired peaks (465) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 465 pairs to build model! INFO @ Mon, 03 Jun 2019 03:34:20: start model_add_line... INFO @ Mon, 03 Jun 2019 03:34:21: start X-correlation... INFO @ Mon, 03 Jun 2019 03:34:21: end of X-cor INFO @ Mon, 03 Jun 2019 03:34:21: #2 finished! INFO @ Mon, 03 Jun 2019 03:34:21: #2 predicted fragment length is 35 bps INFO @ Mon, 03 Jun 2019 03:34:21: #2 alternative fragment length(s) may be 2,35,544,560,572,595 bps INFO @ Mon, 03 Jun 2019 03:34:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX149199/SRX149199.05_model.r WARNING @ Mon, 03 Jun 2019 03:34:21: #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 03:34:21: #2 You may need to consider one of the other alternative d(s): 2,35,544,560,572,595 WARNING @ Mon, 03 Jun 2019 03:34:21: #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 03:34:21: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:34:21: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:34:47: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:35:08: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:35:10: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:35:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX149199/SRX149199.20_peaks.xls INFO @ Mon, 03 Jun 2019 03:35:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX149199/SRX149199.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:35:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX149199/SRX149199.20_summits.bed INFO @ Mon, 03 Jun 2019 03:35:10: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (506 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 03:35:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX149199/SRX149199.10_peaks.xls INFO @ Mon, 03 Jun 2019 03:35:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX149199/SRX149199.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:35:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX149199/SRX149199.10_summits.bed INFO @ Mon, 03 Jun 2019 03:35:32: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (2444 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 03:35:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX149199/SRX149199.05_peaks.xls INFO @ Mon, 03 Jun 2019 03:35:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX149199/SRX149199.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:35:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX149199/SRX149199.05_summits.bed INFO @ Mon, 03 Jun 2019 03:35:33: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3907 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。