Job ID = 10194762 sra ファイルのダウンロード中... Completed: 814618K bytes transferred in 7 seconds (940436K 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 16065708 spots for /home/okishinya/chipatlas/results/rn6/SRX1184182/SRR2243267.sra Written 16065708 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: 00:00:01 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:21:42 16065708 reads; of these: 16065708 (100.00%) were unpaired; of these: 913323 (5.68%) aligned 0 times 11408608 (71.01%) aligned exactly 1 time 3743777 (23.30%) aligned >1 times 94.32% overall alignment rate Time searching: 00:21:46 Overall time: 00:21:46 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 428910 / 15152385 = 0.0283 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 @ Fri, 10 Nov 2017 16:47:06: # Command line: callpeak -t SRX1184182.bam -f BAM -g 2.15e9 -n SRX1184182.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1184182.05 # format = BAM # ChIP-seq file = ['SRX1184182.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Fri, 10 Nov 2017 16:47:06: #1 read tag files... INFO @ Fri, 10 Nov 2017 16:47:06: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 16:47:06: # Command line: callpeak -t SRX1184182.bam -f BAM -g 2.15e9 -n SRX1184182.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1184182.20 # format = BAM # ChIP-seq file = ['SRX1184182.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Fri, 10 Nov 2017 16:47:06: #1 read tag files... INFO @ Fri, 10 Nov 2017 16:47:06: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 16:47:06: # Command line: callpeak -t SRX1184182.bam -f BAM -g 2.15e9 -n SRX1184182.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1184182.10 # format = BAM # ChIP-seq file = ['SRX1184182.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Fri, 10 Nov 2017 16:47:06: #1 read tag files... INFO @ Fri, 10 Nov 2017 16:47:06: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 16:47:13: 1000000 INFO @ Fri, 10 Nov 2017 16:47:14: 1000000 INFO @ Fri, 10 Nov 2017 16:47:14: 1000000 INFO @ Fri, 10 Nov 2017 16:47:21: 2000000 INFO @ Fri, 10 Nov 2017 16:47:21: 2000000 INFO @ Fri, 10 Nov 2017 16:47:22: 2000000 INFO @ Fri, 10 Nov 2017 16:47:29: 3000000 INFO @ Fri, 10 Nov 2017 16:47:29: 3000000 INFO @ Fri, 10 Nov 2017 16:47:30: 3000000 INFO @ Fri, 10 Nov 2017 16:47:36: 4000000 INFO @ Fri, 10 Nov 2017 16:47:36: 4000000 INFO @ Fri, 10 Nov 2017 16:47:38: 4000000 INFO @ Fri, 10 Nov 2017 16:47:43: 5000000 INFO @ Fri, 10 Nov 2017 16:47:44: 5000000 INFO @ Fri, 10 Nov 2017 16:47:46: 5000000 INFO @ Fri, 10 Nov 2017 16:47:50: 6000000 INFO @ Fri, 10 Nov 2017 16:47:51: 6000000 INFO @ Fri, 10 Nov 2017 16:47:54: 6000000 INFO @ Fri, 10 Nov 2017 16:47:57: 7000000 INFO @ Fri, 10 Nov 2017 16:47:59: 7000000 INFO @ Fri, 10 Nov 2017 16:48:02: 7000000 INFO @ Fri, 10 Nov 2017 16:48:04: 8000000 INFO @ Fri, 10 Nov 2017 16:48:07: 8000000 INFO @ Fri, 10 Nov 2017 16:48:10: 8000000 INFO @ Fri, 10 Nov 2017 16:48:12: 9000000 INFO @ Fri, 10 Nov 2017 16:48:15: 9000000 INFO @ Fri, 10 Nov 2017 16:48:19: 9000000 INFO @ Fri, 10 Nov 2017 16:48:19: 10000000 INFO @ Fri, 10 Nov 2017 16:48:22: 10000000 INFO @ Fri, 10 Nov 2017 16:48:26: 11000000 INFO @ Fri, 10 Nov 2017 16:48:27: 10000000 INFO @ Fri, 10 Nov 2017 16:48:30: 11000000 INFO @ Fri, 10 Nov 2017 16:48:33: 12000000 INFO @ Fri, 10 Nov 2017 16:48:35: 11000000 INFO @ Fri, 10 Nov 2017 16:48:38: 12000000 INFO @ Fri, 10 Nov 2017 16:48:40: 13000000 INFO @ Fri, 10 Nov 2017 16:48:43: 12000000 INFO @ Fri, 10 Nov 2017 16:48:46: 13000000 INFO @ Fri, 10 Nov 2017 16:48:48: 14000000 INFO @ Fri, 10 Nov 2017 16:48:51: 13000000 INFO @ Fri, 10 Nov 2017 16:48:53: #1 tag size is determined as 75 bps INFO @ Fri, 10 Nov 2017 16:48:53: #1 tag size = 75 INFO @ Fri, 10 Nov 2017 16:48:53: #1 total tags in treatment: 14723475 INFO @ Fri, 10 Nov 2017 16:48:53: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 16:48:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 16:48:53: 14000000 INFO @ Fri, 10 Nov 2017 16:48:54: #1 tags after filtering in treatment: 14723306 INFO @ Fri, 10 Nov 2017 16:48:54: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 16:48:54: #1 finished! INFO @ Fri, 10 Nov 2017 16:48:54: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 16:48:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 16:48:55: #2 number of paired peaks: 6802 INFO @ Fri, 10 Nov 2017 16:48:55: start model_add_line... INFO @ Fri, 10 Nov 2017 16:48:56: start X-correlation... INFO @ Fri, 10 Nov 2017 16:48:56: end of X-cor INFO @ Fri, 10 Nov 2017 16:48:56: #2 finished! INFO @ Fri, 10 Nov 2017 16:48:56: #2 predicted fragment length is 79 bps INFO @ Fri, 10 Nov 2017 16:48:56: #2 alternative fragment length(s) may be 79 bps INFO @ Fri, 10 Nov 2017 16:48:56: #2.2 Generate R script for model : SRX1184182.10_model.r WARNING @ Fri, 10 Nov 2017 16:48:56: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 16:48:56: #2 You may need to consider one of the other alternative d(s): 79 WARNING @ Fri, 10 Nov 2017 16:48:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Nov 2017 16:48:56: #3 Call peaks... INFO @ Fri, 10 Nov 2017 16:48:56: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 16:48:59: #1 tag size is determined as 75 bps INFO @ Fri, 10 Nov 2017 16:48:59: #1 tag size = 75 INFO @ Fri, 10 Nov 2017 16:48:59: #1 total tags in treatment: 14723475 INFO @ Fri, 10 Nov 2017 16:48:59: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 16:48:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 16:48:59: 14000000 INFO @ Fri, 10 Nov 2017 16:49:00: #1 tags after filtering in treatment: 14723306 INFO @ Fri, 10 Nov 2017 16:49:00: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 16:49:00: #1 finished! INFO @ Fri, 10 Nov 2017 16:49:00: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 16:49:00: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 16:49:01: #2 number of paired peaks: 6802 INFO @ Fri, 10 Nov 2017 16:49:01: start model_add_line... INFO @ Fri, 10 Nov 2017 16:49:02: start X-correlation... INFO @ Fri, 10 Nov 2017 16:49:02: end of X-cor INFO @ Fri, 10 Nov 2017 16:49:02: #2 finished! INFO @ Fri, 10 Nov 2017 16:49:02: #2 predicted fragment length is 79 bps INFO @ Fri, 10 Nov 2017 16:49:02: #2 alternative fragment length(s) may be 79 bps INFO @ Fri, 10 Nov 2017 16:49:02: #2.2 Generate R script for model : SRX1184182.20_model.r WARNING @ Fri, 10 Nov 2017 16:49:02: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 16:49:02: #2 You may need to consider one of the other alternative d(s): 79 WARNING @ Fri, 10 Nov 2017 16:49:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Nov 2017 16:49:02: #3 Call peaks... INFO @ Fri, 10 Nov 2017 16:49:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 16:49:05: #1 tag size is determined as 75 bps INFO @ Fri, 10 Nov 2017 16:49:05: #1 tag size = 75 INFO @ Fri, 10 Nov 2017 16:49:05: #1 total tags in treatment: 14723475 INFO @ Fri, 10 Nov 2017 16:49:05: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 16:49:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 16:49:06: #1 tags after filtering in treatment: 14723306 INFO @ Fri, 10 Nov 2017 16:49:06: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 16:49:06: #1 finished! INFO @ Fri, 10 Nov 2017 16:49:06: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 16:49:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 16:49:07: #2 number of paired peaks: 6802 INFO @ Fri, 10 Nov 2017 16:49:07: start model_add_line... INFO @ Fri, 10 Nov 2017 16:49:07: start X-correlation... INFO @ Fri, 10 Nov 2017 16:49:07: end of X-cor INFO @ Fri, 10 Nov 2017 16:49:07: #2 finished! INFO @ Fri, 10 Nov 2017 16:49:07: #2 predicted fragment length is 79 bps INFO @ Fri, 10 Nov 2017 16:49:07: #2 alternative fragment length(s) may be 79 bps INFO @ Fri, 10 Nov 2017 16:49:07: #2.2 Generate R script for model : SRX1184182.05_model.r WARNING @ Fri, 10 Nov 2017 16:49:07: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 16:49:07: #2 You may need to consider one of the other alternative d(s): 79 WARNING @ Fri, 10 Nov 2017 16:49:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Nov 2017 16:49:07: #3 Call peaks... INFO @ Fri, 10 Nov 2017 16:49:07: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 16:49:31: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 16:49:37: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 16:49:45: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 16:49:50: #4 Write output xls file... SRX1184182.10_peaks.xls INFO @ Fri, 10 Nov 2017 16:49:50: #4 Write peak in narrowPeak format file... SRX1184182.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 16:49:50: #4 Write summits bed file... SRX1184182.10_summits.bed INFO @ Fri, 10 Nov 2017 16:49:50: Done! pass1 - making usageList (39 chroms): 0 millis pass2 - checking and writing primary data (574 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 16:49:59: #4 Write output xls file... SRX1184182.20_peaks.xls INFO @ Fri, 10 Nov 2017 16:49:59: #4 Write peak in narrowPeak format file... SRX1184182.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 16:49:59: #4 Write summits bed file... SRX1184182.20_summits.bed INFO @ Fri, 10 Nov 2017 16:49:59: Done! pass1 - making usageList (32 chroms): 0 millis pass2 - checking and writing primary data (275 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 16:50:06: #4 Write output xls file... SRX1184182.05_peaks.xls INFO @ Fri, 10 Nov 2017 16:50:06: #4 Write peak in narrowPeak format file... SRX1184182.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 16:50:06: #4 Write summits bed file... SRX1184182.05_summits.bed INFO @ Fri, 10 Nov 2017 16:50:06: Done! pass1 - making usageList (47 chroms): 1 millis pass2 - checking and writing primary data (1284 records, 4 fields): 29 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。