Job ID = 11171273 sra ファイルのダウンロード中... Completed: 127449K bytes transferred in 7 seconds (147293K bits/sec), in 1 file. Completed: 126852K bytes transferred in 4 seconds (215563K bits/sec), in 1 file. Completed: 127379K bytes transferred in 10 seconds (101497K bits/sec), in 1 file. Completed: 126272K bytes transferred in 6 seconds (151446K 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 6676304 spots for /home/okishinya/chipatlas/results/dm3/SRX3020540/SRR5850423.sra Written 6676304 spots for /home/okishinya/chipatlas/results/dm3/SRX3020540/SRR5850423.sra Read 6712216 spots for /home/okishinya/chipatlas/results/dm3/SRX3020540/SRR5850421.sra Written 6712216 spots for /home/okishinya/chipatlas/results/dm3/SRX3020540/SRR5850421.sra Read 6762446 spots for /home/okishinya/chipatlas/results/dm3/SRX3020540/SRR5850420.sra Written 6762446 spots for /home/okishinya/chipatlas/results/dm3/SRX3020540/SRR5850420.sra Read 6753547 spots for /home/okishinya/chipatlas/results/dm3/SRX3020540/SRR5850422.sra Written 6753547 spots for /home/okishinya/chipatlas/results/dm3/SRX3020540/SRR5850422.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: 00:00:01 Multiseed full-index search: 00:09:25 26904513 reads; of these: 26904513 (100.00%) were unpaired; of these: 4346944 (16.16%) aligned 0 times 17089222 (63.52%) aligned exactly 1 time 5468347 (20.33%) aligned >1 times 83.84% overall alignment rate Time searching: 00:09:26 Overall time: 00:09:26 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] 3570710 / 22557569 = 0.1583 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 13:38:58: # Command line: callpeak -t SRX3020540.bam -f BAM -g dm -n SRX3020540.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3020540.20 # format = BAM # ChIP-seq file = ['SRX3020540.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 13:38:58: # Command line: callpeak -t SRX3020540.bam -f BAM -g dm -n SRX3020540.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3020540.10 # format = BAM # ChIP-seq file = ['SRX3020540.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 13:38:58: # Command line: callpeak -t SRX3020540.bam -f BAM -g dm -n SRX3020540.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3020540.05 # format = BAM # ChIP-seq file = ['SRX3020540.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 13:38:58: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:38:58: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:38:58: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:38:58: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:38:58: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:38:58: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:39:05: 1000000 INFO @ Sat, 08 Sep 2018 13:39:06: 1000000 INFO @ Sat, 08 Sep 2018 13:39:06: 1000000 INFO @ Sat, 08 Sep 2018 13:39:12: 2000000 INFO @ Sat, 08 Sep 2018 13:39:14: 2000000 INFO @ Sat, 08 Sep 2018 13:39:14: 2000000 INFO @ Sat, 08 Sep 2018 13:39:19: 3000000 INFO @ Sat, 08 Sep 2018 13:39:22: 3000000 INFO @ Sat, 08 Sep 2018 13:39:22: 3000000 INFO @ Sat, 08 Sep 2018 13:39:25: 4000000 INFO @ Sat, 08 Sep 2018 13:39:30: 4000000 INFO @ Sat, 08 Sep 2018 13:39:31: 4000000 INFO @ Sat, 08 Sep 2018 13:39:32: 5000000 INFO @ Sat, 08 Sep 2018 13:39:38: 5000000 INFO @ Sat, 08 Sep 2018 13:39:39: 6000000 INFO @ Sat, 08 Sep 2018 13:39:39: 5000000 INFO @ Sat, 08 Sep 2018 13:39:46: 7000000 INFO @ Sat, 08 Sep 2018 13:39:47: 6000000 INFO @ Sat, 08 Sep 2018 13:39:48: 6000000 INFO @ Sat, 08 Sep 2018 13:39:52: 8000000 INFO @ Sat, 08 Sep 2018 13:39:55: 7000000 INFO @ Sat, 08 Sep 2018 13:39:57: 7000000 INFO @ Sat, 08 Sep 2018 13:39:59: 9000000 INFO @ Sat, 08 Sep 2018 13:40:03: 8000000 INFO @ Sat, 08 Sep 2018 13:40:06: 10000000 INFO @ Sat, 08 Sep 2018 13:40:06: 8000000 INFO @ Sat, 08 Sep 2018 13:40:11: 9000000 INFO @ Sat, 08 Sep 2018 13:40:13: 11000000 INFO @ Sat, 08 Sep 2018 13:40:15: 9000000 INFO @ Sat, 08 Sep 2018 13:40:19: 12000000 INFO @ Sat, 08 Sep 2018 13:40:20: 10000000 INFO @ Sat, 08 Sep 2018 13:40:24: 10000000 INFO @ Sat, 08 Sep 2018 13:40:26: 13000000 INFO @ Sat, 08 Sep 2018 13:40:28: 11000000 INFO @ Sat, 08 Sep 2018 13:40:32: 11000000 INFO @ Sat, 08 Sep 2018 13:40:33: 14000000 INFO @ Sat, 08 Sep 2018 13:40:36: 12000000 INFO @ Sat, 08 Sep 2018 13:40:40: 15000000 INFO @ Sat, 08 Sep 2018 13:40:41: 12000000 INFO @ Sat, 08 Sep 2018 13:40:44: 13000000 INFO @ Sat, 08 Sep 2018 13:40:46: 16000000 INFO @ Sat, 08 Sep 2018 13:40:50: 13000000 INFO @ Sat, 08 Sep 2018 13:40:53: 14000000 INFO @ Sat, 08 Sep 2018 13:40:53: 17000000 INFO @ Sat, 08 Sep 2018 13:40:59: 14000000 INFO @ Sat, 08 Sep 2018 13:41:00: 18000000 INFO @ Sat, 08 Sep 2018 13:41:01: 15000000 INFO @ Sat, 08 Sep 2018 13:41:07: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 13:41:07: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 13:41:07: #1 total tags in treatment: 18986859 INFO @ Sat, 08 Sep 2018 13:41:07: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:41:07: #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 13:41:07: #1 tags after filtering in treatment: 18986859 INFO @ Sat, 08 Sep 2018 13:41:07: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:41:07: #1 finished! INFO @ Sat, 08 Sep 2018 13:41:07: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:41:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:41:07: 15000000 INFO @ Sat, 08 Sep 2018 13:41:08: #2 number of paired peaks: 823 WARNING @ Sat, 08 Sep 2018 13:41:08: Fewer paired peaks (823) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 823 pairs to build model! INFO @ Sat, 08 Sep 2018 13:41:08: start model_add_line... INFO @ Sat, 08 Sep 2018 13:41:09: start X-correlation... INFO @ Sat, 08 Sep 2018 13:41:09: end of X-cor INFO @ Sat, 08 Sep 2018 13:41:09: #2 finished! INFO @ Sat, 08 Sep 2018 13:41:09: #2 predicted fragment length is 90 bps INFO @ Sat, 08 Sep 2018 13:41:09: #2 alternative fragment length(s) may be 2,56,90 bps INFO @ Sat, 08 Sep 2018 13:41:09: #2.2 Generate R script for model : SRX3020540.10_model.r INFO @ Sat, 08 Sep 2018 13:41:09: 16000000 WARNING @ Sat, 08 Sep 2018 13:41:09: #2 Since the d (90) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 13:41:09: #2 You may need to consider one of the other alternative d(s): 2,56,90 WARNING @ Sat, 08 Sep 2018 13:41:09: #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 13:41:09: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:41:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:41:15: 16000000 INFO @ Sat, 08 Sep 2018 13:41:16: 17000000 INFO @ Sat, 08 Sep 2018 13:41:23: 17000000 INFO @ Sat, 08 Sep 2018 13:41:23: 18000000 INFO @ Sat, 08 Sep 2018 13:41:30: 18000000 INFO @ Sat, 08 Sep 2018 13:41:30: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 13:41:30: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 13:41:30: #1 total tags in treatment: 18986859 INFO @ Sat, 08 Sep 2018 13:41:30: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:41:30: #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 13:41:31: #1 tags after filtering in treatment: 18986859 INFO @ Sat, 08 Sep 2018 13:41:31: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:41:31: #1 finished! INFO @ Sat, 08 Sep 2018 13:41:31: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:41:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:41:32: #2 number of paired peaks: 823 WARNING @ Sat, 08 Sep 2018 13:41:32: Fewer paired peaks (823) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 823 pairs to build model! INFO @ Sat, 08 Sep 2018 13:41:32: start model_add_line... INFO @ Sat, 08 Sep 2018 13:41:32: start X-correlation... INFO @ Sat, 08 Sep 2018 13:41:32: end of X-cor INFO @ Sat, 08 Sep 2018 13:41:32: #2 finished! INFO @ Sat, 08 Sep 2018 13:41:32: #2 predicted fragment length is 90 bps INFO @ Sat, 08 Sep 2018 13:41:32: #2 alternative fragment length(s) may be 2,56,90 bps INFO @ Sat, 08 Sep 2018 13:41:32: #2.2 Generate R script for model : SRX3020540.05_model.r WARNING @ Sat, 08 Sep 2018 13:41:32: #2 Since the d (90) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 13:41:32: #2 You may need to consider one of the other alternative d(s): 2,56,90 WARNING @ Sat, 08 Sep 2018 13:41:32: #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 13:41:32: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:41:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:41:37: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 13:41:37: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 13:41:37: #1 total tags in treatment: 18986859 INFO @ Sat, 08 Sep 2018 13:41:37: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:41:37: #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 13:41:38: #1 tags after filtering in treatment: 18986859 INFO @ Sat, 08 Sep 2018 13:41:38: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:41:38: #1 finished! INFO @ Sat, 08 Sep 2018 13:41:38: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:41:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:41:39: #2 number of paired peaks: 823 WARNING @ Sat, 08 Sep 2018 13:41:39: Fewer paired peaks (823) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 823 pairs to build model! INFO @ Sat, 08 Sep 2018 13:41:39: start model_add_line... INFO @ Sat, 08 Sep 2018 13:41:39: start X-correlation... INFO @ Sat, 08 Sep 2018 13:41:39: end of X-cor INFO @ Sat, 08 Sep 2018 13:41:39: #2 finished! INFO @ Sat, 08 Sep 2018 13:41:39: #2 predicted fragment length is 90 bps INFO @ Sat, 08 Sep 2018 13:41:39: #2 alternative fragment length(s) may be 2,56,90 bps INFO @ Sat, 08 Sep 2018 13:41:39: #2.2 Generate R script for model : SRX3020540.20_model.r WARNING @ Sat, 08 Sep 2018 13:41:39: #2 Since the d (90) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 13:41:39: #2 You may need to consider one of the other alternative d(s): 2,56,90 WARNING @ Sat, 08 Sep 2018 13:41:39: #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 13:41:39: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:41:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:41:50: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:42:11: #4 Write output xls file... SRX3020540.10_peaks.xls INFO @ Sat, 08 Sep 2018 13:42:11: #4 Write peak in narrowPeak format file... SRX3020540.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:42:11: #4 Write summits bed file... SRX3020540.10_summits.bed INFO @ Sat, 08 Sep 2018 13:42:11: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1753 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 13:42:15: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:42:21: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:42:36: #4 Write output xls file... SRX3020540.05_peaks.xls INFO @ Sat, 08 Sep 2018 13:42:36: #4 Write peak in narrowPeak format file... SRX3020540.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:42:36: #4 Write summits bed file... SRX3020540.05_summits.bed INFO @ Sat, 08 Sep 2018 13:42:36: Done! pass1 - making usageList (15 chroms): 5 millis pass2 - checking and writing primary data (4379 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 13:42:43: #4 Write output xls file... SRX3020540.20_peaks.xls INFO @ Sat, 08 Sep 2018 13:42:43: #4 Write peak in narrowPeak format file... SRX3020540.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:42:43: #4 Write summits bed file... SRX3020540.20_summits.bed INFO @ Sat, 08 Sep 2018 13:42:43: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (749 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。