Job ID = 11598010 sra ファイルのダウンロード中... Completed: 415573K bytes transferred in 7 seconds (446055K 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 17496131 spots for /home/okishinya/chipatlas/results/dm3/SRX4664665/SRR7813092.sra Written 17496131 spots for /home/okishinya/chipatlas/results/dm3/SRX4664665/SRR7813092.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: 00:07:15 17496131 reads; of these: 17496131 (100.00%) were unpaired; of these: 457019 (2.61%) aligned 0 times 11832523 (67.63%) aligned exactly 1 time 5206589 (29.76%) aligned >1 times 97.39% overall alignment rate Time searching: 00:07:15 Overall time: 00:07:15 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] 1991678 / 17039112 = 0.1169 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 17:07:16: # Command line: callpeak -t SRX4664665.bam -f BAM -g dm -n SRX4664665.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4664665.10 # format = BAM # ChIP-seq file = ['SRX4664665.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 17:07:16: #1 read tag files... INFO @ Wed, 30 Jan 2019 17:07:16: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 17:07:16: # Command line: callpeak -t SRX4664665.bam -f BAM -g dm -n SRX4664665.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4664665.05 # format = BAM # ChIP-seq file = ['SRX4664665.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 17:07:16: #1 read tag files... INFO @ Wed, 30 Jan 2019 17:07:16: # Command line: callpeak -t SRX4664665.bam -f BAM -g dm -n SRX4664665.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4664665.20 # format = BAM # ChIP-seq file = ['SRX4664665.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 17:07:16: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 17:07:16: #1 read tag files... INFO @ Wed, 30 Jan 2019 17:07:16: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 17:07:22: 1000000 INFO @ Wed, 30 Jan 2019 17:07:22: 1000000 INFO @ Wed, 30 Jan 2019 17:07:22: 1000000 INFO @ Wed, 30 Jan 2019 17:07:28: 2000000 INFO @ Wed, 30 Jan 2019 17:07:29: 2000000 INFO @ Wed, 30 Jan 2019 17:07:29: 2000000 INFO @ Wed, 30 Jan 2019 17:07:35: 3000000 INFO @ Wed, 30 Jan 2019 17:07:35: 3000000 INFO @ Wed, 30 Jan 2019 17:07:35: 3000000 INFO @ Wed, 30 Jan 2019 17:07:41: 4000000 INFO @ Wed, 30 Jan 2019 17:07:41: 4000000 INFO @ Wed, 30 Jan 2019 17:07:42: 4000000 INFO @ Wed, 30 Jan 2019 17:07:47: 5000000 INFO @ Wed, 30 Jan 2019 17:07:47: 5000000 INFO @ Wed, 30 Jan 2019 17:07:48: 5000000 INFO @ Wed, 30 Jan 2019 17:07:54: 6000000 INFO @ Wed, 30 Jan 2019 17:07:54: 6000000 INFO @ Wed, 30 Jan 2019 17:07:55: 6000000 INFO @ Wed, 30 Jan 2019 17:08:00: 7000000 INFO @ Wed, 30 Jan 2019 17:08:00: 7000000 INFO @ Wed, 30 Jan 2019 17:08:01: 7000000 INFO @ Wed, 30 Jan 2019 17:08:06: 8000000 INFO @ Wed, 30 Jan 2019 17:08:07: 8000000 INFO @ Wed, 30 Jan 2019 17:08:08: 8000000 INFO @ Wed, 30 Jan 2019 17:08:13: 9000000 INFO @ Wed, 30 Jan 2019 17:08:13: 9000000 INFO @ Wed, 30 Jan 2019 17:08:15: 9000000 INFO @ Wed, 30 Jan 2019 17:08:19: 10000000 INFO @ Wed, 30 Jan 2019 17:08:20: 10000000 INFO @ Wed, 30 Jan 2019 17:08:21: 10000000 INFO @ Wed, 30 Jan 2019 17:08:25: 11000000 INFO @ Wed, 30 Jan 2019 17:08:27: 11000000 INFO @ Wed, 30 Jan 2019 17:08:28: 11000000 INFO @ Wed, 30 Jan 2019 17:08:31: 12000000 INFO @ Wed, 30 Jan 2019 17:08:33: 12000000 INFO @ Wed, 30 Jan 2019 17:08:35: 12000000 INFO @ Wed, 30 Jan 2019 17:08:38: 13000000 INFO @ Wed, 30 Jan 2019 17:08:40: 13000000 INFO @ Wed, 30 Jan 2019 17:08:41: 13000000 INFO @ Wed, 30 Jan 2019 17:08:44: 14000000 INFO @ Wed, 30 Jan 2019 17:08:46: 14000000 INFO @ Wed, 30 Jan 2019 17:08:48: 14000000 INFO @ Wed, 30 Jan 2019 17:08:50: 15000000 INFO @ Wed, 30 Jan 2019 17:08:51: #1 tag size is determined as 50 bps INFO @ Wed, 30 Jan 2019 17:08:51: #1 tag size = 50 INFO @ Wed, 30 Jan 2019 17:08:51: #1 total tags in treatment: 15047434 INFO @ Wed, 30 Jan 2019 17:08:51: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 17:08:51: #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 17:08:51: #1 tags after filtering in treatment: 15047434 INFO @ Wed, 30 Jan 2019 17:08:51: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 17:08:51: #1 finished! INFO @ Wed, 30 Jan 2019 17:08:51: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 17:08:51: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 17:08:52: #2 number of paired peaks: 846 WARNING @ Wed, 30 Jan 2019 17:08:52: Fewer paired peaks (846) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 846 pairs to build model! INFO @ Wed, 30 Jan 2019 17:08:52: start model_add_line... INFO @ Wed, 30 Jan 2019 17:08:52: start X-correlation... INFO @ Wed, 30 Jan 2019 17:08:52: end of X-cor INFO @ Wed, 30 Jan 2019 17:08:52: #2 finished! INFO @ Wed, 30 Jan 2019 17:08:52: #2 predicted fragment length is 86 bps INFO @ Wed, 30 Jan 2019 17:08:52: #2 alternative fragment length(s) may be 86 bps INFO @ Wed, 30 Jan 2019 17:08:52: #2.2 Generate R script for model : SRX4664665.10_model.r WARNING @ Wed, 30 Jan 2019 17:08:52: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 30 Jan 2019 17:08:52: #2 You may need to consider one of the other alternative d(s): 86 WARNING @ Wed, 30 Jan 2019 17:08:52: #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 17:08:52: #3 Call peaks... INFO @ Wed, 30 Jan 2019 17:08:52: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 17:08:53: 15000000 INFO @ Wed, 30 Jan 2019 17:08:53: #1 tag size is determined as 50 bps INFO @ Wed, 30 Jan 2019 17:08:53: #1 tag size = 50 INFO @ Wed, 30 Jan 2019 17:08:53: #1 total tags in treatment: 15047434 INFO @ Wed, 30 Jan 2019 17:08:53: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 17:08:53: #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 17:08:53: #1 tags after filtering in treatment: 15047434 INFO @ Wed, 30 Jan 2019 17:08:53: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 17:08:53: #1 finished! INFO @ Wed, 30 Jan 2019 17:08:53: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 17:08:53: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 17:08:55: #2 number of paired peaks: 846 WARNING @ Wed, 30 Jan 2019 17:08:55: Fewer paired peaks (846) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 846 pairs to build model! INFO @ Wed, 30 Jan 2019 17:08:55: start model_add_line... INFO @ Wed, 30 Jan 2019 17:08:55: 15000000 INFO @ Wed, 30 Jan 2019 17:08:55: start X-correlation... INFO @ Wed, 30 Jan 2019 17:08:55: end of X-cor INFO @ Wed, 30 Jan 2019 17:08:55: #2 finished! INFO @ Wed, 30 Jan 2019 17:08:55: #2 predicted fragment length is 86 bps INFO @ Wed, 30 Jan 2019 17:08:55: #2 alternative fragment length(s) may be 86 bps INFO @ Wed, 30 Jan 2019 17:08:55: #2.2 Generate R script for model : SRX4664665.05_model.r WARNING @ Wed, 30 Jan 2019 17:08:55: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 30 Jan 2019 17:08:55: #2 You may need to consider one of the other alternative d(s): 86 WARNING @ Wed, 30 Jan 2019 17:08:55: #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 17:08:55: #3 Call peaks... INFO @ Wed, 30 Jan 2019 17:08:55: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 17:08:55: #1 tag size is determined as 50 bps INFO @ Wed, 30 Jan 2019 17:08:55: #1 tag size = 50 INFO @ Wed, 30 Jan 2019 17:08:55: #1 total tags in treatment: 15047434 INFO @ Wed, 30 Jan 2019 17:08:55: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 17:08:55: #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 17:08:55: #1 tags after filtering in treatment: 15047434 INFO @ Wed, 30 Jan 2019 17:08:55: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 17:08:55: #1 finished! INFO @ Wed, 30 Jan 2019 17:08:55: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 17:08:55: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 17:08:57: #2 number of paired peaks: 846 WARNING @ Wed, 30 Jan 2019 17:08:57: Fewer paired peaks (846) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 846 pairs to build model! INFO @ Wed, 30 Jan 2019 17:08:57: start model_add_line... INFO @ Wed, 30 Jan 2019 17:08:57: start X-correlation... INFO @ Wed, 30 Jan 2019 17:08:57: end of X-cor INFO @ Wed, 30 Jan 2019 17:08:57: #2 finished! INFO @ Wed, 30 Jan 2019 17:08:57: #2 predicted fragment length is 86 bps INFO @ Wed, 30 Jan 2019 17:08:57: #2 alternative fragment length(s) may be 86 bps INFO @ Wed, 30 Jan 2019 17:08:57: #2.2 Generate R script for model : SRX4664665.20_model.r WARNING @ Wed, 30 Jan 2019 17:08:57: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 30 Jan 2019 17:08:57: #2 You may need to consider one of the other alternative d(s): 86 WARNING @ Wed, 30 Jan 2019 17:08:57: #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 17:08:57: #3 Call peaks... INFO @ Wed, 30 Jan 2019 17:08:57: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 17:09:28: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 17:09:28: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 17:09:30: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 17:09:45: #4 Write output xls file... SRX4664665.05_peaks.xls INFO @ Wed, 30 Jan 2019 17:09:45: #4 Write peak in narrowPeak format file... SRX4664665.05_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 17:09:45: #4 Write summits bed file... SRX4664665.05_summits.bed INFO @ Wed, 30 Jan 2019 17:09:45: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4864 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Wed, 30 Jan 2019 17:09:48: #4 Write output xls file... SRX4664665.20_peaks.xls INFO @ Wed, 30 Jan 2019 17:09:48: #4 Write peak in narrowPeak format file... SRX4664665.20_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 17:09:48: #4 Write summits bed file... SRX4664665.20_summits.bed INFO @ Wed, 30 Jan 2019 17:09:48: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1942 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 30 Jan 2019 17:09:49: #4 Write output xls file... SRX4664665.10_peaks.xls INFO @ Wed, 30 Jan 2019 17:09:49: #4 Write peak in narrowPeak format file... SRX4664665.10_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 17:09:49: #4 Write summits bed file... SRX4664665.10_summits.bed INFO @ Wed, 30 Jan 2019 17:09:49: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3125 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。