Job ID = 11171216 sra ファイルのダウンロード中... Completed: 296477K bytes transferred in 14 seconds (172197K 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 14084117 spots for /home/okishinya/chipatlas/results/dm3/SRX2618525/SRR5319079.sra Written 14084117 spots for /home/okishinya/chipatlas/results/dm3/SRX2618525/SRR5319079.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 rm: cannot remove `[DSE]RR*.fastq': 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: 00:05:58 14084117 reads; of these: 14084117 (100.00%) were unpaired; of these: 614184 (4.36%) aligned 0 times 9153153 (64.99%) aligned exactly 1 time 4316780 (30.65%) aligned >1 times 95.64% overall alignment rate Time searching: 00:05:58 Overall time: 00:05:58 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] 1322940 / 13469933 = 0.0982 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 13:10:36: # Command line: callpeak -t SRX2618525.bam -f BAM -g dm -n SRX2618525.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2618525.20 # format = BAM # ChIP-seq file = ['SRX2618525.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 13:10:36: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:10:36: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:10:36: # Command line: callpeak -t SRX2618525.bam -f BAM -g dm -n SRX2618525.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2618525.05 # format = BAM # ChIP-seq file = ['SRX2618525.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 13:10:36: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:10:36: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:10:36: # Command line: callpeak -t SRX2618525.bam -f BAM -g dm -n SRX2618525.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2618525.10 # format = BAM # ChIP-seq file = ['SRX2618525.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 13:10:36: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:10:36: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:10:42: 1000000 INFO @ Sat, 08 Sep 2018 13:10:42: 1000000 INFO @ Sat, 08 Sep 2018 13:10:42: 1000000 INFO @ Sat, 08 Sep 2018 13:10:47: 2000000 INFO @ Sat, 08 Sep 2018 13:10:48: 2000000 INFO @ Sat, 08 Sep 2018 13:10:48: 2000000 INFO @ Sat, 08 Sep 2018 13:10:53: 3000000 INFO @ Sat, 08 Sep 2018 13:10:54: 3000000 INFO @ Sat, 08 Sep 2018 13:10:54: 3000000 INFO @ Sat, 08 Sep 2018 13:10:59: 4000000 INFO @ Sat, 08 Sep 2018 13:11:00: 4000000 INFO @ Sat, 08 Sep 2018 13:11:00: 4000000 INFO @ Sat, 08 Sep 2018 13:11:05: 5000000 INFO @ Sat, 08 Sep 2018 13:11:06: 5000000 INFO @ Sat, 08 Sep 2018 13:11:06: 5000000 INFO @ Sat, 08 Sep 2018 13:11:11: 6000000 INFO @ Sat, 08 Sep 2018 13:11:12: 6000000 INFO @ Sat, 08 Sep 2018 13:11:13: 6000000 INFO @ Sat, 08 Sep 2018 13:11:17: 7000000 INFO @ Sat, 08 Sep 2018 13:11:17: 7000000 INFO @ Sat, 08 Sep 2018 13:11:19: 7000000 INFO @ Sat, 08 Sep 2018 13:11:23: 8000000 INFO @ Sat, 08 Sep 2018 13:11:23: 8000000 INFO @ Sat, 08 Sep 2018 13:11:25: 8000000 INFO @ Sat, 08 Sep 2018 13:11:29: 9000000 INFO @ Sat, 08 Sep 2018 13:11:29: 9000000 INFO @ Sat, 08 Sep 2018 13:11:31: 9000000 INFO @ Sat, 08 Sep 2018 13:11:35: 10000000 INFO @ Sat, 08 Sep 2018 13:11:35: 10000000 INFO @ Sat, 08 Sep 2018 13:11:37: 10000000 INFO @ Sat, 08 Sep 2018 13:11:41: 11000000 INFO @ Sat, 08 Sep 2018 13:11:41: 11000000 INFO @ Sat, 08 Sep 2018 13:11:43: 11000000 INFO @ Sat, 08 Sep 2018 13:11:47: 12000000 INFO @ Sat, 08 Sep 2018 13:11:47: 12000000 INFO @ Sat, 08 Sep 2018 13:11:48: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 13:11:48: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 13:11:48: #1 total tags in treatment: 12146993 INFO @ Sat, 08 Sep 2018 13:11:48: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:11:48: #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 13:11:48: #1 tags after filtering in treatment: 12146993 INFO @ Sat, 08 Sep 2018 13:11:48: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:11:48: #1 finished! INFO @ Sat, 08 Sep 2018 13:11:48: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:11:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:11:48: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 13:11:48: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 13:11:48: #1 total tags in treatment: 12146993 INFO @ Sat, 08 Sep 2018 13:11:48: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:11:48: #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 13:11:48: #1 tags after filtering in treatment: 12146993 INFO @ Sat, 08 Sep 2018 13:11:48: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:11:48: #1 finished! INFO @ Sat, 08 Sep 2018 13:11:48: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:11:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:11:49: #2 number of paired peaks: 101 WARNING @ Sat, 08 Sep 2018 13:11:49: Fewer paired peaks (101) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 101 pairs to build model! INFO @ Sat, 08 Sep 2018 13:11:49: start model_add_line... INFO @ Sat, 08 Sep 2018 13:11:49: start X-correlation... INFO @ Sat, 08 Sep 2018 13:11:49: end of X-cor INFO @ Sat, 08 Sep 2018 13:11:49: #2 finished! INFO @ Sat, 08 Sep 2018 13:11:49: #2 predicted fragment length is 50 bps INFO @ Sat, 08 Sep 2018 13:11:49: #2 alternative fragment length(s) may be 4,50 bps INFO @ Sat, 08 Sep 2018 13:11:49: #2.2 Generate R script for model : SRX2618525.05_model.r WARNING @ Sat, 08 Sep 2018 13:11:49: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 13:11:49: #2 You may need to consider one of the other alternative d(s): 4,50 WARNING @ Sat, 08 Sep 2018 13:11:49: #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 13:11:49: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:11:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:11:49: #2 number of paired peaks: 101 WARNING @ Sat, 08 Sep 2018 13:11:49: Fewer paired peaks (101) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 101 pairs to build model! INFO @ Sat, 08 Sep 2018 13:11:49: start model_add_line... INFO @ Sat, 08 Sep 2018 13:11:49: start X-correlation... INFO @ Sat, 08 Sep 2018 13:11:49: end of X-cor INFO @ Sat, 08 Sep 2018 13:11:49: #2 finished! INFO @ Sat, 08 Sep 2018 13:11:49: #2 predicted fragment length is 50 bps INFO @ Sat, 08 Sep 2018 13:11:49: #2 alternative fragment length(s) may be 4,50 bps INFO @ Sat, 08 Sep 2018 13:11:49: #2.2 Generate R script for model : SRX2618525.10_model.r WARNING @ Sat, 08 Sep 2018 13:11:49: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 13:11:49: #2 You may need to consider one of the other alternative d(s): 4,50 WARNING @ Sat, 08 Sep 2018 13:11:49: #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 13:11:49: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:11:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:11:49: 12000000 INFO @ Sat, 08 Sep 2018 13:11:50: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 13:11:50: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 13:11:50: #1 total tags in treatment: 12146993 INFO @ Sat, 08 Sep 2018 13:11:50: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:11:50: #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 13:11:51: #1 tags after filtering in treatment: 12146993 INFO @ Sat, 08 Sep 2018 13:11:51: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:11:51: #1 finished! INFO @ Sat, 08 Sep 2018 13:11:51: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:11:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:11:51: #2 number of paired peaks: 101 WARNING @ Sat, 08 Sep 2018 13:11:51: Fewer paired peaks (101) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 101 pairs to build model! INFO @ Sat, 08 Sep 2018 13:11:51: start model_add_line... INFO @ Sat, 08 Sep 2018 13:11:52: start X-correlation... INFO @ Sat, 08 Sep 2018 13:11:52: end of X-cor INFO @ Sat, 08 Sep 2018 13:11:52: #2 finished! INFO @ Sat, 08 Sep 2018 13:11:52: #2 predicted fragment length is 50 bps INFO @ Sat, 08 Sep 2018 13:11:52: #2 alternative fragment length(s) may be 4,50 bps INFO @ Sat, 08 Sep 2018 13:11:52: #2.2 Generate R script for model : SRX2618525.20_model.r WARNING @ Sat, 08 Sep 2018 13:11:52: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 13:11:52: #2 You may need to consider one of the other alternative d(s): 4,50 WARNING @ Sat, 08 Sep 2018 13:11:52: #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 13:11:52: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:11:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:12:13: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:12:16: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:12:17: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:12:28: #4 Write output xls file... SRX2618525.10_peaks.xls INFO @ Sat, 08 Sep 2018 13:12:28: #4 Write peak in narrowPeak format file... SRX2618525.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:12:28: #4 Write summits bed file... SRX2618525.10_summits.bed INFO @ Sat, 08 Sep 2018 13:12:28: Done! pass1 - making usageList (9 chroms): 6 millis pass2 - checking and writing primary data (732 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 13:12:30: #4 Write output xls file... SRX2618525.20_peaks.xls INFO @ Sat, 08 Sep 2018 13:12:30: #4 Write peak in narrowPeak format file... SRX2618525.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:12:30: #4 Write summits bed file... SRX2618525.20_summits.bed INFO @ Sat, 08 Sep 2018 13:12:30: Done! pass1 - making usageList (5 chroms): 0 millis pass2 - checking and writing primary data (248 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 13:12:32: #4 Write output xls file... SRX2618525.05_peaks.xls INFO @ Sat, 08 Sep 2018 13:12:32: #4 Write peak in narrowPeak format file... SRX2618525.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:12:32: #4 Write summits bed file... SRX2618525.05_summits.bed INFO @ Sat, 08 Sep 2018 13:12:32: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1350 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。