Job ID = 11171265 sra ファイルのダウンロード中... Completed: 114849K bytes transferred in 13 seconds (68033K bits/sec), in 1 file. Completed: 113242K bytes transferred in 8 seconds (106682K bits/sec), in 1 file. Completed: 113475K bytes transferred in 5 seconds (170553K bits/sec), in 1 file. Completed: 112982K bytes transferred in 6 seconds (143317K bits/sec), in 1 file. sra ファイルのダウンロードが完了しました。 Read layout: SINGLE fastq に変換中... Read 5973322 spots for /home/okishinya/chipatlas/results/dm3/SRX3020532/SRR5850391.sra Written 5973322 spots for /home/okishinya/chipatlas/results/dm3/SRX3020532/SRR5850391.sra Read 6003388 spots for /home/okishinya/chipatlas/results/dm3/SRX3020532/SRR5850389.sra Written 6003388 spots for /home/okishinya/chipatlas/results/dm3/SRX3020532/SRR5850389.sra Read 6009057 spots for /home/okishinya/chipatlas/results/dm3/SRX3020532/SRR5850390.sra Written 6009057 spots for /home/okishinya/chipatlas/results/dm3/SRX3020532/SRR5850390.sra Read 6084588 spots for /home/okishinya/chipatlas/results/dm3/SRX3020532/SRR5850388.sra Written 6084588 spots for /home/okishinya/chipatlas/results/dm3/SRX3020532/SRR5850388.sra rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません 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: 00:10:30 24070355 reads; of these: 24070355 (100.00%) were unpaired; of these: 727171 (3.02%) aligned 0 times 15349362 (63.77%) aligned exactly 1 time 7993822 (33.21%) aligned >1 times 96.98% overall alignment rate Time searching: 00:10:30 Overall time: 00:10:30 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] 4015528 / 23343184 = 0.1720 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 @ Sat, 08 Sep 2018 13:36:34: # Command line: callpeak -t SRX3020532.bam -f BAM -g dm -n SRX3020532.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3020532.10 # format = BAM # ChIP-seq file = ['SRX3020532.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 @ Sat, 08 Sep 2018 13:36:34: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:36:34: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:36:34: # Command line: callpeak -t SRX3020532.bam -f BAM -g dm -n SRX3020532.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3020532.05 # format = BAM # ChIP-seq file = ['SRX3020532.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 @ Sat, 08 Sep 2018 13:36:34: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:36:34: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:36:34: # Command line: callpeak -t SRX3020532.bam -f BAM -g dm -n SRX3020532.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3020532.20 # format = BAM # ChIP-seq file = ['SRX3020532.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 @ Sat, 08 Sep 2018 13:36:34: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:36:34: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:36:40: 1000000 INFO @ Sat, 08 Sep 2018 13:36:41: 1000000 INFO @ Sat, 08 Sep 2018 13:36:41: 1000000 INFO @ Sat, 08 Sep 2018 13:36:46: 2000000 INFO @ Sat, 08 Sep 2018 13:36:48: 2000000 INFO @ Sat, 08 Sep 2018 13:36:48: 2000000 INFO @ Sat, 08 Sep 2018 13:36:53: 3000000 INFO @ Sat, 08 Sep 2018 13:36:54: 3000000 INFO @ Sat, 08 Sep 2018 13:36:54: 3000000 INFO @ Sat, 08 Sep 2018 13:36:59: 4000000 INFO @ Sat, 08 Sep 2018 13:37:01: 4000000 INFO @ Sat, 08 Sep 2018 13:37:01: 4000000 INFO @ Sat, 08 Sep 2018 13:37:05: 5000000 INFO @ Sat, 08 Sep 2018 13:37:08: 5000000 INFO @ Sat, 08 Sep 2018 13:37:08: 5000000 INFO @ Sat, 08 Sep 2018 13:37:11: 6000000 INFO @ Sat, 08 Sep 2018 13:37:15: 6000000 INFO @ Sat, 08 Sep 2018 13:37:15: 6000000 INFO @ Sat, 08 Sep 2018 13:37:17: 7000000 INFO @ Sat, 08 Sep 2018 13:37:22: 7000000 INFO @ Sat, 08 Sep 2018 13:37:22: 7000000 INFO @ Sat, 08 Sep 2018 13:37:23: 8000000 INFO @ Sat, 08 Sep 2018 13:37:29: 8000000 INFO @ Sat, 08 Sep 2018 13:37:29: 8000000 INFO @ Sat, 08 Sep 2018 13:37:29: 9000000 INFO @ Sat, 08 Sep 2018 13:37:36: 9000000 INFO @ Sat, 08 Sep 2018 13:37:36: 9000000 INFO @ Sat, 08 Sep 2018 13:37:36: 10000000 INFO @ Sat, 08 Sep 2018 13:37:42: 11000000 INFO @ Sat, 08 Sep 2018 13:37:42: 10000000 INFO @ Sat, 08 Sep 2018 13:37:42: 10000000 INFO @ Sat, 08 Sep 2018 13:37:48: 12000000 INFO @ Sat, 08 Sep 2018 13:37:49: 11000000 INFO @ Sat, 08 Sep 2018 13:37:49: 11000000 INFO @ Sat, 08 Sep 2018 13:37:54: 13000000 INFO @ Sat, 08 Sep 2018 13:37:56: 12000000 INFO @ Sat, 08 Sep 2018 13:37:56: 12000000 INFO @ Sat, 08 Sep 2018 13:38:00: 14000000 INFO @ Sat, 08 Sep 2018 13:38:03: 13000000 INFO @ Sat, 08 Sep 2018 13:38:03: 13000000 INFO @ Sat, 08 Sep 2018 13:38:06: 15000000 INFO @ Sat, 08 Sep 2018 13:38:10: 14000000 INFO @ Sat, 08 Sep 2018 13:38:10: 14000000 INFO @ Sat, 08 Sep 2018 13:38:13: 16000000 INFO @ Sat, 08 Sep 2018 13:38:16: 15000000 INFO @ Sat, 08 Sep 2018 13:38:16: 15000000 INFO @ Sat, 08 Sep 2018 13:38:19: 17000000 INFO @ Sat, 08 Sep 2018 13:38:23: 16000000 INFO @ Sat, 08 Sep 2018 13:38:23: 16000000 INFO @ Sat, 08 Sep 2018 13:38:25: 18000000 INFO @ Sat, 08 Sep 2018 13:38:30: 17000000 INFO @ Sat, 08 Sep 2018 13:38:30: 17000000 INFO @ Sat, 08 Sep 2018 13:38:31: 19000000 INFO @ Sat, 08 Sep 2018 13:38:33: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 13:38:33: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 13:38:33: #1 total tags in treatment: 19327656 INFO @ Sat, 08 Sep 2018 13:38:33: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:38:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 13:38:34: #1 tags after filtering in treatment: 19327656 INFO @ Sat, 08 Sep 2018 13:38:34: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:38:34: #1 finished! INFO @ Sat, 08 Sep 2018 13:38:34: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:38:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:38:35: #2 number of paired peaks: 194 WARNING @ Sat, 08 Sep 2018 13:38:35: Fewer paired peaks (194) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 194 pairs to build model! INFO @ Sat, 08 Sep 2018 13:38:35: start model_add_line... INFO @ Sat, 08 Sep 2018 13:38:35: start X-correlation... INFO @ Sat, 08 Sep 2018 13:38:35: end of X-cor INFO @ Sat, 08 Sep 2018 13:38:35: #2 finished! INFO @ Sat, 08 Sep 2018 13:38:35: #2 predicted fragment length is 38 bps INFO @ Sat, 08 Sep 2018 13:38:35: #2 alternative fragment length(s) may be 2,38,539,598 bps INFO @ Sat, 08 Sep 2018 13:38:35: #2.2 Generate R script for model : SRX3020532.10_model.r WARNING @ Sat, 08 Sep 2018 13:38:35: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 13:38:35: #2 You may need to consider one of the other alternative d(s): 2,38,539,598 WARNING @ Sat, 08 Sep 2018 13:38:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 13:38:35: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:38:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:38:37: 18000000 INFO @ Sat, 08 Sep 2018 13:38:37: 18000000 INFO @ Sat, 08 Sep 2018 13:38:43: 19000000 INFO @ Sat, 08 Sep 2018 13:38:43: 19000000 INFO @ Sat, 08 Sep 2018 13:38:46: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 13:38:46: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 13:38:46: #1 total tags in treatment: 19327656 INFO @ Sat, 08 Sep 2018 13:38:46: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:38:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 13:38:46: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 13:38:46: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 13:38:46: #1 total tags in treatment: 19327656 INFO @ Sat, 08 Sep 2018 13:38:46: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:38:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 13:38:46: #1 tags after filtering in treatment: 19327656 INFO @ Sat, 08 Sep 2018 13:38:46: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:38:46: #1 finished! INFO @ Sat, 08 Sep 2018 13:38:46: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:38:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:38:46: #1 tags after filtering in treatment: 19327656 INFO @ Sat, 08 Sep 2018 13:38:46: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:38:46: #1 finished! INFO @ Sat, 08 Sep 2018 13:38:46: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:38:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:38:47: #2 number of paired peaks: 194 WARNING @ Sat, 08 Sep 2018 13:38:47: Fewer paired peaks (194) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 194 pairs to build model! INFO @ Sat, 08 Sep 2018 13:38:47: start model_add_line... INFO @ Sat, 08 Sep 2018 13:38:47: #2 number of paired peaks: 194 WARNING @ Sat, 08 Sep 2018 13:38:47: Fewer paired peaks (194) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 194 pairs to build model! INFO @ Sat, 08 Sep 2018 13:38:47: start model_add_line... INFO @ Sat, 08 Sep 2018 13:38:48: start X-correlation... INFO @ Sat, 08 Sep 2018 13:38:48: start X-correlation... INFO @ Sat, 08 Sep 2018 13:38:48: end of X-cor INFO @ Sat, 08 Sep 2018 13:38:48: #2 finished! INFO @ Sat, 08 Sep 2018 13:38:48: #2 predicted fragment length is 38 bps INFO @ Sat, 08 Sep 2018 13:38:48: #2 alternative fragment length(s) may be 2,38,539,598 bps INFO @ Sat, 08 Sep 2018 13:38:48: #2.2 Generate R script for model : SRX3020532.05_model.r INFO @ Sat, 08 Sep 2018 13:38:48: end of X-cor INFO @ Sat, 08 Sep 2018 13:38:48: #2 finished! INFO @ Sat, 08 Sep 2018 13:38:48: #2 predicted fragment length is 38 bps INFO @ Sat, 08 Sep 2018 13:38:48: #2 alternative fragment length(s) may be 2,38,539,598 bps INFO @ Sat, 08 Sep 2018 13:38:48: #2.2 Generate R script for model : SRX3020532.20_model.r WARNING @ Sat, 08 Sep 2018 13:38:48: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 13:38:48: #2 You may need to consider one of the other alternative d(s): 2,38,539,598 WARNING @ Sat, 08 Sep 2018 13:38:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 13:38:48: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:38:48: #3 Pre-compute pvalue-qvalue table... WARNING @ Sat, 08 Sep 2018 13:38:48: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 13:38:48: #2 You may need to consider one of the other alternative d(s): 2,38,539,598 WARNING @ Sat, 08 Sep 2018 13:38:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 13:38:48: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:38:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:39:12: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:39:27: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:39:29: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:39:34: #4 Write output xls file... SRX3020532.10_peaks.xls INFO @ Sat, 08 Sep 2018 13:39:34: #4 Write peak in narrowPeak format file... SRX3020532.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:39:34: #4 Write summits bed file... SRX3020532.10_summits.bed INFO @ Sat, 08 Sep 2018 13:39:34: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1775 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 13:39:48: #4 Write output xls file... SRX3020532.20_peaks.xls INFO @ Sat, 08 Sep 2018 13:39:48: #4 Write peak in narrowPeak format file... SRX3020532.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:39:48: #4 Write summits bed file... SRX3020532.20_summits.bed INFO @ Sat, 08 Sep 2018 13:39:48: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (397 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 13:39:48: #4 Write output xls file... SRX3020532.05_peaks.xls INFO @ Sat, 08 Sep 2018 13:39:48: #4 Write peak in narrowPeak format file... SRX3020532.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:39:48: #4 Write summits bed file... SRX3020532.05_summits.bed INFO @ Sat, 08 Sep 2018 13:39:48: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3228 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。