Job ID = 10175301 sra ファイルのダウンロード中... Completed: 851248K bytes transferred in 65 seconds (105671K 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 37125274 spots for /home/okishinya/chipatlas/results/dm3/SRX3170974/SRR6019821.sra Written 37125274 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:18:13 37125274 reads; of these: 37125274 (100.00%) were unpaired; of these: 2823965 (7.61%) aligned 0 times 20094282 (54.13%) aligned exactly 1 time 14207027 (38.27%) aligned >1 times 92.39% overall alignment rate Time searching: 00:18:13 Overall time: 00:18:13 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 16 files... [bam_rmdupse_core] 12416397 / 34301309 = 0.3620 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 12:52:03: # Command line: callpeak -t SRX3170974.bam -f BAM -g dm -n SRX3170974.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3170974.10 # format = BAM # ChIP-seq file = ['SRX3170974.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 12:52:03: # Command line: callpeak -t SRX3170974.bam -f BAM -g dm -n SRX3170974.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3170974.20 # format = BAM # ChIP-seq file = ['SRX3170974.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 12:52:03: #1 read tag files... INFO @ Mon, 06 Nov 2017 12:52:03: #1 read tag files... INFO @ Mon, 06 Nov 2017 12:52:03: #1 read treatment tags... INFO @ Mon, 06 Nov 2017 12:52:03: #1 read treatment tags... INFO @ Mon, 06 Nov 2017 12:52:03: # Command line: callpeak -t SRX3170974.bam -f BAM -g dm -n SRX3170974.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3170974.05 # format = BAM # ChIP-seq file = ['SRX3170974.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 12:52:03: #1 read tag files... INFO @ Mon, 06 Nov 2017 12:52:03: #1 read treatment tags... INFO @ Mon, 06 Nov 2017 12:52:11: 1000000 INFO @ Mon, 06 Nov 2017 12:52:11: 1000000 INFO @ Mon, 06 Nov 2017 12:52:11: 1000000 INFO @ Mon, 06 Nov 2017 12:52:20: 2000000 INFO @ Mon, 06 Nov 2017 12:52:20: 2000000 INFO @ Mon, 06 Nov 2017 12:52:20: 2000000 INFO @ Mon, 06 Nov 2017 12:52:28: 3000000 INFO @ Mon, 06 Nov 2017 12:52:28: 3000000 INFO @ Mon, 06 Nov 2017 12:52:28: 3000000 INFO @ Mon, 06 Nov 2017 12:52:35: 4000000 INFO @ Mon, 06 Nov 2017 12:52:36: 4000000 INFO @ Mon, 06 Nov 2017 12:52:36: 4000000 INFO @ Mon, 06 Nov 2017 12:52:43: 5000000 INFO @ Mon, 06 Nov 2017 12:52:43: 5000000 INFO @ Mon, 06 Nov 2017 12:52:44: 5000000 INFO @ Mon, 06 Nov 2017 12:52:51: 6000000 INFO @ Mon, 06 Nov 2017 12:52:51: 6000000 INFO @ Mon, 06 Nov 2017 12:52:52: 6000000 INFO @ Mon, 06 Nov 2017 12:52:59: 7000000 INFO @ Mon, 06 Nov 2017 12:52:59: 7000000 INFO @ Mon, 06 Nov 2017 12:53:00: 7000000 INFO @ Mon, 06 Nov 2017 12:53:07: 8000000 INFO @ Mon, 06 Nov 2017 12:53:07: 8000000 INFO @ Mon, 06 Nov 2017 12:53:08: 8000000 INFO @ Mon, 06 Nov 2017 12:53:15: 9000000 INFO @ Mon, 06 Nov 2017 12:53:15: 9000000 INFO @ Mon, 06 Nov 2017 12:53:17: 9000000 INFO @ Mon, 06 Nov 2017 12:53:22: 10000000 INFO @ Mon, 06 Nov 2017 12:53:23: 10000000 INFO @ Mon, 06 Nov 2017 12:53:25: 10000000 INFO @ Mon, 06 Nov 2017 12:53:31: 11000000 INFO @ Mon, 06 Nov 2017 12:53:31: 11000000 INFO @ Mon, 06 Nov 2017 12:53:34: 11000000 INFO @ Mon, 06 Nov 2017 12:53:39: 12000000 INFO @ Mon, 06 Nov 2017 12:53:39: 12000000 INFO @ Mon, 06 Nov 2017 12:53:42: 12000000 INFO @ Mon, 06 Nov 2017 12:53:47: 13000000 INFO @ Mon, 06 Nov 2017 12:53:47: 13000000 INFO @ Mon, 06 Nov 2017 12:53:50: 13000000 INFO @ Mon, 06 Nov 2017 12:53:55: 14000000 INFO @ Mon, 06 Nov 2017 12:53:55: 14000000 INFO @ Mon, 06 Nov 2017 12:53:59: 14000000 INFO @ Mon, 06 Nov 2017 12:54:03: 15000000 INFO @ Mon, 06 Nov 2017 12:54:03: 15000000 INFO @ Mon, 06 Nov 2017 12:54:07: 15000000 INFO @ Mon, 06 Nov 2017 12:54:10: 16000000 INFO @ Mon, 06 Nov 2017 12:54:11: 16000000 INFO @ Mon, 06 Nov 2017 12:54:15: 16000000 INFO @ Mon, 06 Nov 2017 12:54:18: 17000000 INFO @ Mon, 06 Nov 2017 12:54:19: 17000000 INFO @ Mon, 06 Nov 2017 12:54:23: 17000000 INFO @ Mon, 06 Nov 2017 12:54:26: 18000000 INFO @ Mon, 06 Nov 2017 12:54:27: 18000000 INFO @ Mon, 06 Nov 2017 12:54:31: 18000000 INFO @ Mon, 06 Nov 2017 12:54:34: 19000000 INFO @ Mon, 06 Nov 2017 12:54:35: 19000000 INFO @ Mon, 06 Nov 2017 12:54:40: 19000000 INFO @ Mon, 06 Nov 2017 12:54:42: 20000000 INFO @ Mon, 06 Nov 2017 12:54:43: 20000000 INFO @ Mon, 06 Nov 2017 12:54:48: 20000000 INFO @ Mon, 06 Nov 2017 12:54:50: 21000000 INFO @ Mon, 06 Nov 2017 12:54:51: 21000000 INFO @ Mon, 06 Nov 2017 12:54:56: 21000000 INFO @ Mon, 06 Nov 2017 12:54:58: #1 tag size is determined as 49 bps INFO @ Mon, 06 Nov 2017 12:54:58: #1 tag size = 49 INFO @ Mon, 06 Nov 2017 12:54:58: #1 total tags in treatment: 21884912 INFO @ Mon, 06 Nov 2017 12:54:58: #1 user defined the maximum tags... INFO @ Mon, 06 Nov 2017 12:54:58: #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 12:54:58: #1 tags after filtering in treatment: 21884912 INFO @ Mon, 06 Nov 2017 12:54:58: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Nov 2017 12:54:58: #1 finished! INFO @ Mon, 06 Nov 2017 12:54:58: #2 Build Peak Model... INFO @ Mon, 06 Nov 2017 12:54:58: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Nov 2017 12:54:59: #1 tag size is determined as 49 bps INFO @ Mon, 06 Nov 2017 12:54:59: #1 tag size = 49 INFO @ Mon, 06 Nov 2017 12:54:59: #1 total tags in treatment: 21884912 INFO @ Mon, 06 Nov 2017 12:54:59: #1 user defined the maximum tags... INFO @ Mon, 06 Nov 2017 12:54:59: #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 12:54:59: #1 tags after filtering in treatment: 21884912 INFO @ Mon, 06 Nov 2017 12:54:59: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Nov 2017 12:54:59: #1 finished! INFO @ Mon, 06 Nov 2017 12:54:59: #2 Build Peak Model... INFO @ Mon, 06 Nov 2017 12:54:59: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Nov 2017 12:55:00: #2 number of paired peaks: 172 WARNING @ Mon, 06 Nov 2017 12:55:00: Fewer paired peaks (172) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 172 pairs to build model! INFO @ Mon, 06 Nov 2017 12:55:00: start model_add_line... INFO @ Mon, 06 Nov 2017 12:55:00: start X-correlation... INFO @ Mon, 06 Nov 2017 12:55:00: end of X-cor INFO @ Mon, 06 Nov 2017 12:55:00: #2 finished! INFO @ Mon, 06 Nov 2017 12:55:00: #2 predicted fragment length is 40 bps INFO @ Mon, 06 Nov 2017 12:55:00: #2 alternative fragment length(s) may be 4,40 bps INFO @ Mon, 06 Nov 2017 12:55:00: #2.2 Generate R script for model : SRX3170974.10_model.r WARNING @ Mon, 06 Nov 2017 12:55:00: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 06 Nov 2017 12:55:00: #2 You may need to consider one of the other alternative d(s): 4,40 WARNING @ Mon, 06 Nov 2017 12:55:00: #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 12:55:00: #3 Call peaks... INFO @ Mon, 06 Nov 2017 12:55:00: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Nov 2017 12:55:01: #2 number of paired peaks: 172 WARNING @ Mon, 06 Nov 2017 12:55:01: Fewer paired peaks (172) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 172 pairs to build model! INFO @ Mon, 06 Nov 2017 12:55:01: start model_add_line... INFO @ Mon, 06 Nov 2017 12:55:01: start X-correlation... INFO @ Mon, 06 Nov 2017 12:55:01: end of X-cor INFO @ Mon, 06 Nov 2017 12:55:01: #2 finished! INFO @ Mon, 06 Nov 2017 12:55:01: #2 predicted fragment length is 40 bps INFO @ Mon, 06 Nov 2017 12:55:01: #2 alternative fragment length(s) may be 4,40 bps INFO @ Mon, 06 Nov 2017 12:55:01: #2.2 Generate R script for model : SRX3170974.20_model.r WARNING @ Mon, 06 Nov 2017 12:55:01: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 06 Nov 2017 12:55:01: #2 You may need to consider one of the other alternative d(s): 4,40 WARNING @ Mon, 06 Nov 2017 12:55:01: #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 12:55:01: #3 Call peaks... INFO @ Mon, 06 Nov 2017 12:55:01: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Nov 2017 12:55:03: #1 tag size is determined as 49 bps INFO @ Mon, 06 Nov 2017 12:55:03: #1 tag size = 49 INFO @ Mon, 06 Nov 2017 12:55:03: #1 total tags in treatment: 21884912 INFO @ Mon, 06 Nov 2017 12:55:03: #1 user defined the maximum tags... INFO @ Mon, 06 Nov 2017 12:55:03: #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 12:55:04: #1 tags after filtering in treatment: 21884912 INFO @ Mon, 06 Nov 2017 12:55:04: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Nov 2017 12:55:04: #1 finished! INFO @ Mon, 06 Nov 2017 12:55:04: #2 Build Peak Model... INFO @ Mon, 06 Nov 2017 12:55:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Nov 2017 12:55:05: #2 number of paired peaks: 172 WARNING @ Mon, 06 Nov 2017 12:55:05: Fewer paired peaks (172) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 172 pairs to build model! INFO @ Mon, 06 Nov 2017 12:55:05: start model_add_line... INFO @ Mon, 06 Nov 2017 12:55:05: start X-correlation... INFO @ Mon, 06 Nov 2017 12:55:05: end of X-cor INFO @ Mon, 06 Nov 2017 12:55:05: #2 finished! INFO @ Mon, 06 Nov 2017 12:55:05: #2 predicted fragment length is 40 bps INFO @ Mon, 06 Nov 2017 12:55:05: #2 alternative fragment length(s) may be 4,40 bps INFO @ Mon, 06 Nov 2017 12:55:05: #2.2 Generate R script for model : SRX3170974.05_model.r WARNING @ Mon, 06 Nov 2017 12:55:05: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 06 Nov 2017 12:55:05: #2 You may need to consider one of the other alternative d(s): 4,40 WARNING @ Mon, 06 Nov 2017 12:55:05: #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 12:55:05: #3 Call peaks... INFO @ Mon, 06 Nov 2017 12:55:05: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Nov 2017 12:55:40: #3 Call peaks for each chromosome... INFO @ Mon, 06 Nov 2017 12:55:45: #3 Call peaks for each chromosome... INFO @ Mon, 06 Nov 2017 12:55:50: #3 Call peaks for each chromosome... INFO @ Mon, 06 Nov 2017 12:56:03: #4 Write output xls file... SRX3170974.10_peaks.xls INFO @ Mon, 06 Nov 2017 12:56:03: #4 Write peak in narrowPeak format file... SRX3170974.10_peaks.narrowPeak INFO @ Mon, 06 Nov 2017 12:56:04: #4 Write summits bed file... SRX3170974.10_summits.bed INFO @ Mon, 06 Nov 2017 12:56:04: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (4375 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 06 Nov 2017 12:56:11: #4 Write output xls file... SRX3170974.20_peaks.xls INFO @ Mon, 06 Nov 2017 12:56:11: #4 Write peak in narrowPeak format file... SRX3170974.20_peaks.narrowPeak INFO @ Mon, 06 Nov 2017 12:56:11: #4 Write summits bed file... SRX3170974.20_summits.bed INFO @ Mon, 06 Nov 2017 12:56:11: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1346 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 06 Nov 2017 12:56:17: #4 Write output xls file... SRX3170974.05_peaks.xls INFO @ Mon, 06 Nov 2017 12:56:17: #4 Write peak in narrowPeak format file... SRX3170974.05_peaks.narrowPeak INFO @ Mon, 06 Nov 2017 12:56:17: #4 Write summits bed file... SRX3170974.05_summits.bed INFO @ Mon, 06 Nov 2017 12:56:18: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (14089 records, 4 fields): 17 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。