Job ID = 11597770 sra ファイルのダウンロード中... Completed: 412768K bytes transferred in 13 seconds (247512K bits/sec), in 1 file. Completed: 404330K bytes transferred in 13 seconds (240586K 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 14291311 spots for /home/okishinya/chipatlas/results/dm3/ERX1266825/ERR1193507.sra Written 14291311 spots for /home/okishinya/chipatlas/results/dm3/ERX1266825/ERR1193507.sra Read 14543494 spots for /home/okishinya/chipatlas/results/dm3/ERX1266825/ERR1193514.sra Written 14543494 spots for /home/okishinya/chipatlas/results/dm3/ERX1266825/ERR1193514.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: 00:08:20 28834805 reads; of these: 28834805 (100.00%) were unpaired; of these: 12865175 (44.62%) aligned 0 times 10246287 (35.53%) aligned exactly 1 time 5723343 (19.85%) aligned >1 times 55.38% overall alignment rate Time searching: 00:08:20 Overall time: 00:08:20 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] 2110546 / 15969630 = 0.1322 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 @ Wed, 30 Jan 2019 14:50:38: # Command line: callpeak -t ERX1266825.bam -f BAM -g dm -n ERX1266825.20 -q 1e-20 # ARGUMENTS LIST: # name = ERX1266825.20 # format = BAM # ChIP-seq file = ['ERX1266825.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 @ Wed, 30 Jan 2019 14:50:38: #1 read tag files... INFO @ Wed, 30 Jan 2019 14:50:38: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 14:50:38: # Command line: callpeak -t ERX1266825.bam -f BAM -g dm -n ERX1266825.05 -q 1e-05 # ARGUMENTS LIST: # name = ERX1266825.05 # format = BAM # ChIP-seq file = ['ERX1266825.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 @ Wed, 30 Jan 2019 14:50:38: #1 read tag files... INFO @ Wed, 30 Jan 2019 14:50:38: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 14:50:38: # Command line: callpeak -t ERX1266825.bam -f BAM -g dm -n ERX1266825.10 -q 1e-10 # ARGUMENTS LIST: # name = ERX1266825.10 # format = BAM # ChIP-seq file = ['ERX1266825.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 @ Wed, 30 Jan 2019 14:50:38: #1 read tag files... INFO @ Wed, 30 Jan 2019 14:50:38: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 14:50:45: 1000000 INFO @ Wed, 30 Jan 2019 14:50:45: 1000000 INFO @ Wed, 30 Jan 2019 14:50:45: 1000000 INFO @ Wed, 30 Jan 2019 14:50:52: 2000000 INFO @ Wed, 30 Jan 2019 14:50:52: 2000000 INFO @ Wed, 30 Jan 2019 14:50:52: 2000000 INFO @ Wed, 30 Jan 2019 14:50:59: 3000000 INFO @ Wed, 30 Jan 2019 14:50:59: 3000000 INFO @ Wed, 30 Jan 2019 14:50:59: 3000000 INFO @ Wed, 30 Jan 2019 14:51:06: 4000000 INFO @ Wed, 30 Jan 2019 14:51:06: 4000000 INFO @ Wed, 30 Jan 2019 14:51:06: 4000000 INFO @ Wed, 30 Jan 2019 14:51:13: 5000000 INFO @ Wed, 30 Jan 2019 14:51:13: 5000000 INFO @ Wed, 30 Jan 2019 14:51:13: 5000000 INFO @ Wed, 30 Jan 2019 14:51:19: 6000000 INFO @ Wed, 30 Jan 2019 14:51:20: 6000000 INFO @ Wed, 30 Jan 2019 14:51:20: 6000000 INFO @ Wed, 30 Jan 2019 14:51:26: 7000000 INFO @ Wed, 30 Jan 2019 14:51:26: 7000000 INFO @ Wed, 30 Jan 2019 14:51:27: 7000000 INFO @ Wed, 30 Jan 2019 14:51:33: 8000000 INFO @ Wed, 30 Jan 2019 14:51:33: 8000000 INFO @ Wed, 30 Jan 2019 14:51:34: 8000000 INFO @ Wed, 30 Jan 2019 14:51:40: 9000000 INFO @ Wed, 30 Jan 2019 14:51:41: 9000000 INFO @ Wed, 30 Jan 2019 14:51:41: 9000000 INFO @ Wed, 30 Jan 2019 14:51:47: 10000000 INFO @ Wed, 30 Jan 2019 14:51:49: 10000000 INFO @ Wed, 30 Jan 2019 14:51:49: 10000000 INFO @ Wed, 30 Jan 2019 14:51:54: 11000000 INFO @ Wed, 30 Jan 2019 14:51:56: 11000000 INFO @ Wed, 30 Jan 2019 14:51:57: 11000000 INFO @ Wed, 30 Jan 2019 14:52:01: 12000000 INFO @ Wed, 30 Jan 2019 14:52:03: 12000000 INFO @ Wed, 30 Jan 2019 14:52:04: 12000000 INFO @ Wed, 30 Jan 2019 14:52:08: 13000000 INFO @ Wed, 30 Jan 2019 14:52:10: 13000000 INFO @ Wed, 30 Jan 2019 14:52:11: 13000000 INFO @ Wed, 30 Jan 2019 14:52:14: #1 tag size is determined as 44 bps INFO @ Wed, 30 Jan 2019 14:52:14: #1 tag size = 44 INFO @ Wed, 30 Jan 2019 14:52:14: #1 total tags in treatment: 13859084 INFO @ Wed, 30 Jan 2019 14:52:14: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 14:52:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 30 Jan 2019 14:52:14: #1 tags after filtering in treatment: 13859084 INFO @ Wed, 30 Jan 2019 14:52:14: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 14:52:14: #1 finished! INFO @ Wed, 30 Jan 2019 14:52:14: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 14:52:14: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 14:52:15: #2 number of paired peaks: 182 WARNING @ Wed, 30 Jan 2019 14:52:15: Fewer paired peaks (182) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 182 pairs to build model! INFO @ Wed, 30 Jan 2019 14:52:15: start model_add_line... INFO @ Wed, 30 Jan 2019 14:52:15: start X-correlation... INFO @ Wed, 30 Jan 2019 14:52:15: end of X-cor INFO @ Wed, 30 Jan 2019 14:52:15: #2 finished! INFO @ Wed, 30 Jan 2019 14:52:15: #2 predicted fragment length is 49 bps INFO @ Wed, 30 Jan 2019 14:52:15: #2 alternative fragment length(s) may be 49 bps INFO @ Wed, 30 Jan 2019 14:52:15: #2.2 Generate R script for model : ERX1266825.05_model.r WARNING @ Wed, 30 Jan 2019 14:52:15: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 30 Jan 2019 14:52:15: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Wed, 30 Jan 2019 14:52:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 30 Jan 2019 14:52:15: #3 Call peaks... INFO @ Wed, 30 Jan 2019 14:52:15: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 14:52:16: #1 tag size is determined as 44 bps INFO @ Wed, 30 Jan 2019 14:52:16: #1 tag size = 44 INFO @ Wed, 30 Jan 2019 14:52:16: #1 total tags in treatment: 13859084 INFO @ Wed, 30 Jan 2019 14:52:16: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 14:52:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 30 Jan 2019 14:52:17: #1 tags after filtering in treatment: 13859084 INFO @ Wed, 30 Jan 2019 14:52:17: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 14:52:17: #1 finished! INFO @ Wed, 30 Jan 2019 14:52:17: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 14:52:17: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 14:52:17: #1 tag size is determined as 44 bps INFO @ Wed, 30 Jan 2019 14:52:17: #1 tag size = 44 INFO @ Wed, 30 Jan 2019 14:52:17: #1 total tags in treatment: 13859084 INFO @ Wed, 30 Jan 2019 14:52:17: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 14:52:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 30 Jan 2019 14:52:17: #1 tags after filtering in treatment: 13859084 INFO @ Wed, 30 Jan 2019 14:52:17: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 14:52:17: #1 finished! INFO @ Wed, 30 Jan 2019 14:52:17: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 14:52:17: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 14:52:18: #2 number of paired peaks: 182 WARNING @ Wed, 30 Jan 2019 14:52:18: Fewer paired peaks (182) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 182 pairs to build model! INFO @ Wed, 30 Jan 2019 14:52:18: start model_add_line... INFO @ Wed, 30 Jan 2019 14:52:18: start X-correlation... INFO @ Wed, 30 Jan 2019 14:52:18: end of X-cor INFO @ Wed, 30 Jan 2019 14:52:18: #2 finished! INFO @ Wed, 30 Jan 2019 14:52:18: #2 predicted fragment length is 49 bps INFO @ Wed, 30 Jan 2019 14:52:18: #2 alternative fragment length(s) may be 49 bps INFO @ Wed, 30 Jan 2019 14:52:18: #2.2 Generate R script for model : ERX1266825.20_model.r WARNING @ Wed, 30 Jan 2019 14:52:18: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 30 Jan 2019 14:52:18: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Wed, 30 Jan 2019 14:52:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 30 Jan 2019 14:52:18: #3 Call peaks... INFO @ Wed, 30 Jan 2019 14:52:18: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 14:52:18: #2 number of paired peaks: 182 WARNING @ Wed, 30 Jan 2019 14:52:18: Fewer paired peaks (182) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 182 pairs to build model! INFO @ Wed, 30 Jan 2019 14:52:18: start model_add_line... INFO @ Wed, 30 Jan 2019 14:52:18: start X-correlation... INFO @ Wed, 30 Jan 2019 14:52:18: end of X-cor INFO @ Wed, 30 Jan 2019 14:52:18: #2 finished! INFO @ Wed, 30 Jan 2019 14:52:18: #2 predicted fragment length is 49 bps INFO @ Wed, 30 Jan 2019 14:52:18: #2 alternative fragment length(s) may be 49 bps INFO @ Wed, 30 Jan 2019 14:52:18: #2.2 Generate R script for model : ERX1266825.10_model.r WARNING @ Wed, 30 Jan 2019 14:52:18: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 30 Jan 2019 14:52:18: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Wed, 30 Jan 2019 14:52:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 30 Jan 2019 14:52:18: #3 Call peaks... INFO @ Wed, 30 Jan 2019 14:52:18: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 14:52:45: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 14:52:46: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 14:52:47: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 14:53:00: #4 Write output xls file... ERX1266825.05_peaks.xls INFO @ Wed, 30 Jan 2019 14:53:00: #4 Write peak in narrowPeak format file... ERX1266825.05_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 14:53:00: #4 Write summits bed file... ERX1266825.05_summits.bed INFO @ Wed, 30 Jan 2019 14:53:00: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1693 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 30 Jan 2019 14:53:01: #4 Write output xls file... ERX1266825.10_peaks.xls INFO @ Wed, 30 Jan 2019 14:53:01: #4 Write peak in narrowPeak format file... ERX1266825.10_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 14:53:01: #4 Write summits bed file... ERX1266825.10_summits.bed INFO @ Wed, 30 Jan 2019 14:53:01: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1437 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 30 Jan 2019 14:53:02: #4 Write output xls file... ERX1266825.20_peaks.xls INFO @ Wed, 30 Jan 2019 14:53:02: #4 Write peak in narrowPeak format file... ERX1266825.20_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 14:53:02: #4 Write summits bed file... ERX1266825.20_summits.bed INFO @ Wed, 30 Jan 2019 14:53:02: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1050 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。