Job ID = 10175230 sra ファイルのダウンロード中... Completed: 595928K bytes transferred in 10 seconds (457912K 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... Written 19606545 spots for /home/okishinya/chipatlas/results/dm3/SRX2458933/SRR5140282.sra Written 19606545 spots total 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:06 19606545 reads; of these: 19606545 (100.00%) were unpaired; of these: 1138983 (5.81%) aligned 0 times 13652112 (69.63%) aligned exactly 1 time 4815450 (24.56%) aligned >1 times 94.19% overall alignment rate Time searching: 00:07:07 Overall time: 00:07:07 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] 3496850 / 18467562 = 0.1894 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 @ Mon, 06 Nov 2017 11:54:42: # Command line: callpeak -t SRX2458933.bam -f BAM -g dm -n SRX2458933.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2458933.05 # format = BAM # ChIP-seq file = ['SRX2458933.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 @ Mon, 06 Nov 2017 11:54:42: #1 read tag files... INFO @ Mon, 06 Nov 2017 11:54:42: #1 read treatment tags... INFO @ Mon, 06 Nov 2017 11:54:42: # Command line: callpeak -t SRX2458933.bam -f BAM -g dm -n SRX2458933.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2458933.10 # format = BAM # ChIP-seq file = ['SRX2458933.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 @ Mon, 06 Nov 2017 11:54:42: #1 read tag files... INFO @ Mon, 06 Nov 2017 11:54:42: #1 read treatment tags... INFO @ Mon, 06 Nov 2017 11:54:42: # Command line: callpeak -t SRX2458933.bam -f BAM -g dm -n SRX2458933.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2458933.20 # format = BAM # ChIP-seq file = ['SRX2458933.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 @ Mon, 06 Nov 2017 11:54:42: #1 read tag files... INFO @ Mon, 06 Nov 2017 11:54:42: #1 read treatment tags... INFO @ Mon, 06 Nov 2017 11:54:51: 1000000 INFO @ Mon, 06 Nov 2017 11:54:51: 1000000 INFO @ Mon, 06 Nov 2017 11:54:51: 1000000 INFO @ Mon, 06 Nov 2017 11:54:59: 2000000 INFO @ Mon, 06 Nov 2017 11:54:59: 2000000 INFO @ Mon, 06 Nov 2017 11:54:59: 2000000 INFO @ Mon, 06 Nov 2017 11:55:07: 3000000 INFO @ Mon, 06 Nov 2017 11:55:08: 3000000 INFO @ Mon, 06 Nov 2017 11:55:08: 3000000 INFO @ Mon, 06 Nov 2017 11:55:15: 4000000 INFO @ Mon, 06 Nov 2017 11:55:16: 4000000 INFO @ Mon, 06 Nov 2017 11:55:16: 4000000 INFO @ Mon, 06 Nov 2017 11:55:24: 5000000 INFO @ Mon, 06 Nov 2017 11:55:24: 5000000 INFO @ Mon, 06 Nov 2017 11:55:25: 5000000 INFO @ Mon, 06 Nov 2017 11:55:32: 6000000 INFO @ Mon, 06 Nov 2017 11:55:33: 6000000 INFO @ Mon, 06 Nov 2017 11:55:33: 6000000 INFO @ Mon, 06 Nov 2017 11:55:40: 7000000 INFO @ Mon, 06 Nov 2017 11:55:41: 7000000 INFO @ Mon, 06 Nov 2017 11:55:42: 7000000 INFO @ Mon, 06 Nov 2017 11:55:48: 8000000 INFO @ Mon, 06 Nov 2017 11:55:48: 8000000 INFO @ Mon, 06 Nov 2017 11:55:51: 8000000 INFO @ Mon, 06 Nov 2017 11:55:56: 9000000 INFO @ Mon, 06 Nov 2017 11:55:56: 9000000 INFO @ Mon, 06 Nov 2017 11:56:00: 9000000 INFO @ Mon, 06 Nov 2017 11:56:03: 10000000 INFO @ Mon, 06 Nov 2017 11:56:04: 10000000 INFO @ Mon, 06 Nov 2017 11:56:08: 10000000 INFO @ Mon, 06 Nov 2017 11:56:11: 11000000 INFO @ Mon, 06 Nov 2017 11:56:11: 11000000 INFO @ Mon, 06 Nov 2017 11:56:15: 11000000 INFO @ Mon, 06 Nov 2017 11:56:18: 12000000 INFO @ Mon, 06 Nov 2017 11:56:18: 12000000 INFO @ Mon, 06 Nov 2017 11:56:22: 12000000 INFO @ Mon, 06 Nov 2017 11:56:25: 13000000 INFO @ Mon, 06 Nov 2017 11:56:26: 13000000 INFO @ Mon, 06 Nov 2017 11:56:29: 13000000 INFO @ Mon, 06 Nov 2017 11:56:33: 14000000 INFO @ Mon, 06 Nov 2017 11:56:33: 14000000 INFO @ Mon, 06 Nov 2017 11:56:36: 14000000 INFO @ Mon, 06 Nov 2017 11:56:40: #1 tag size is determined as 49 bps INFO @ Mon, 06 Nov 2017 11:56:40: #1 tag size = 49 INFO @ Mon, 06 Nov 2017 11:56:40: #1 total tags in treatment: 14970712 INFO @ Mon, 06 Nov 2017 11:56:40: #1 user defined the maximum tags... INFO @ Mon, 06 Nov 2017 11:56:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Nov 2017 11:56:40: #1 tag size is determined as 49 bps INFO @ Mon, 06 Nov 2017 11:56:40: #1 tag size = 49 INFO @ Mon, 06 Nov 2017 11:56:40: #1 total tags in treatment: 14970712 INFO @ Mon, 06 Nov 2017 11:56:40: #1 user defined the maximum tags... INFO @ Mon, 06 Nov 2017 11:56:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Nov 2017 11:56:40: #1 tags after filtering in treatment: 14970712 INFO @ Mon, 06 Nov 2017 11:56:40: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Nov 2017 11:56:40: #1 finished! INFO @ Mon, 06 Nov 2017 11:56:40: #2 Build Peak Model... INFO @ Mon, 06 Nov 2017 11:56:40: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Nov 2017 11:56:40: #1 tags after filtering in treatment: 14970712 INFO @ Mon, 06 Nov 2017 11:56:40: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Nov 2017 11:56:40: #1 finished! INFO @ Mon, 06 Nov 2017 11:56:40: #2 Build Peak Model... INFO @ Mon, 06 Nov 2017 11:56:40: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Nov 2017 11:56:41: #2 number of paired peaks: 564 WARNING @ Mon, 06 Nov 2017 11:56:41: Fewer paired peaks (564) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 564 pairs to build model! INFO @ Mon, 06 Nov 2017 11:56:41: start model_add_line... INFO @ Mon, 06 Nov 2017 11:56:42: #2 number of paired peaks: 564 WARNING @ Mon, 06 Nov 2017 11:56:42: Fewer paired peaks (564) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 564 pairs to build model! INFO @ Mon, 06 Nov 2017 11:56:42: start model_add_line... INFO @ Mon, 06 Nov 2017 11:56:42: start X-correlation... INFO @ Mon, 06 Nov 2017 11:56:42: end of X-cor INFO @ Mon, 06 Nov 2017 11:56:42: #2 finished! INFO @ Mon, 06 Nov 2017 11:56:42: #2 predicted fragment length is 42 bps INFO @ Mon, 06 Nov 2017 11:56:42: #2 alternative fragment length(s) may be 3,42 bps INFO @ Mon, 06 Nov 2017 11:56:42: #2.2 Generate R script for model : SRX2458933.10_model.r INFO @ Mon, 06 Nov 2017 11:56:42: start X-correlation... INFO @ Mon, 06 Nov 2017 11:56:42: end of X-cor INFO @ Mon, 06 Nov 2017 11:56:42: #2 finished! INFO @ Mon, 06 Nov 2017 11:56:42: #2 predicted fragment length is 42 bps INFO @ Mon, 06 Nov 2017 11:56:42: #2 alternative fragment length(s) may be 3,42 bps INFO @ Mon, 06 Nov 2017 11:56:42: #2.2 Generate R script for model : SRX2458933.05_model.r WARNING @ Mon, 06 Nov 2017 11:56:42: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 06 Nov 2017 11:56:42: #2 You may need to consider one of the other alternative d(s): 3,42 WARNING @ Mon, 06 Nov 2017 11:56:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 06 Nov 2017 11:56:42: #3 Call peaks... WARNING @ Mon, 06 Nov 2017 11:56:42: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 06 Nov 2017 11:56:42: #2 You may need to consider one of the other alternative d(s): 3,42 INFO @ Mon, 06 Nov 2017 11:56:42: #3 Pre-compute pvalue-qvalue table... WARNING @ Mon, 06 Nov 2017 11:56:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 06 Nov 2017 11:56:42: #3 Call peaks... INFO @ Mon, 06 Nov 2017 11:56:42: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Nov 2017 11:56:42: #1 tag size is determined as 49 bps INFO @ Mon, 06 Nov 2017 11:56:42: #1 tag size = 49 INFO @ Mon, 06 Nov 2017 11:56:42: #1 total tags in treatment: 14970712 INFO @ Mon, 06 Nov 2017 11:56:42: #1 user defined the maximum tags... INFO @ Mon, 06 Nov 2017 11:56:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Nov 2017 11:56:43: #1 tags after filtering in treatment: 14970712 INFO @ Mon, 06 Nov 2017 11:56:43: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Nov 2017 11:56:43: #1 finished! INFO @ Mon, 06 Nov 2017 11:56:43: #2 Build Peak Model... INFO @ Mon, 06 Nov 2017 11:56:43: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Nov 2017 11:56:44: #2 number of paired peaks: 564 WARNING @ Mon, 06 Nov 2017 11:56:44: Fewer paired peaks (564) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 564 pairs to build model! INFO @ Mon, 06 Nov 2017 11:56:44: start model_add_line... INFO @ Mon, 06 Nov 2017 11:56:44: start X-correlation... INFO @ Mon, 06 Nov 2017 11:56:44: end of X-cor INFO @ Mon, 06 Nov 2017 11:56:44: #2 finished! INFO @ Mon, 06 Nov 2017 11:56:44: #2 predicted fragment length is 42 bps INFO @ Mon, 06 Nov 2017 11:56:44: #2 alternative fragment length(s) may be 3,42 bps INFO @ Mon, 06 Nov 2017 11:56:44: #2.2 Generate R script for model : SRX2458933.20_model.r WARNING @ Mon, 06 Nov 2017 11:56:44: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 06 Nov 2017 11:56:44: #2 You may need to consider one of the other alternative d(s): 3,42 WARNING @ Mon, 06 Nov 2017 11:56:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 06 Nov 2017 11:56:44: #3 Call peaks... INFO @ Mon, 06 Nov 2017 11:56:44: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Nov 2017 11:57:12: #3 Call peaks for each chromosome... INFO @ Mon, 06 Nov 2017 11:57:16: #3 Call peaks for each chromosome... INFO @ Mon, 06 Nov 2017 11:57:16: #3 Call peaks for each chromosome... INFO @ Mon, 06 Nov 2017 11:57:29: #4 Write output xls file... SRX2458933.10_peaks.xls INFO @ Mon, 06 Nov 2017 11:57:29: #4 Write peak in narrowPeak format file... SRX2458933.10_peaks.narrowPeak INFO @ Mon, 06 Nov 2017 11:57:29: #4 Write summits bed file... SRX2458933.10_summits.bed INFO @ Mon, 06 Nov 2017 11:57:29: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1444 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 06 Nov 2017 11:57:32: #4 Write output xls file... SRX2458933.20_peaks.xls INFO @ Mon, 06 Nov 2017 11:57:32: #4 Write peak in narrowPeak format file... SRX2458933.20_peaks.narrowPeak INFO @ Mon, 06 Nov 2017 11:57:32: #4 Write summits bed file... SRX2458933.20_summits.bed INFO @ Mon, 06 Nov 2017 11:57:32: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (522 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 06 Nov 2017 11:57:34: #4 Write output xls file... SRX2458933.05_peaks.xls INFO @ Mon, 06 Nov 2017 11:57:34: #4 Write peak in narrowPeak format file... SRX2458933.05_peaks.narrowPeak INFO @ Mon, 06 Nov 2017 11:57:34: #4 Write summits bed file... SRX2458933.05_summits.bed INFO @ Mon, 06 Nov 2017 11:57:34: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2644 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。