Job ID = 10194742 sra ファイルのダウンロード中... Completed: 395517K bytes transferred in 6 seconds (517217K 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 15593158 spots for /home/okishinya/chipatlas/results/rn6/SRX1068231/SRR2073190.sra Written 15593158 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: 00:00:01 Multiseed full-index search: 00:17:19 15593158 reads; of these: 15593158 (100.00%) were unpaired; of these: 333902 (2.14%) aligned 0 times 11169037 (71.63%) aligned exactly 1 time 4090219 (26.23%) aligned >1 times 97.86% overall alignment rate Time searching: 00:17:23 Overall time: 00:17:23 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] 600168 / 15259256 = 0.0393 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 23:46:09: # Command line: callpeak -t SRX1068231.bam -f BAM -g 2.15e9 -n SRX1068231.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1068231.05 # format = BAM # ChIP-seq file = ['SRX1068231.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 23:46:09: # Command line: callpeak -t SRX1068231.bam -f BAM -g 2.15e9 -n SRX1068231.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1068231.20 # format = BAM # ChIP-seq file = ['SRX1068231.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 23:46:09: # Command line: callpeak -t SRX1068231.bam -f BAM -g 2.15e9 -n SRX1068231.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1068231.10 # format = BAM # ChIP-seq file = ['SRX1068231.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 23:46:09: #1 read tag files... INFO @ Fri, 10 Nov 2017 23:46:09: #1 read tag files... INFO @ Fri, 10 Nov 2017 23:46:09: #1 read tag files... INFO @ Fri, 10 Nov 2017 23:46:09: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 23:46:09: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 23:46:09: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 23:46:16: 1000000 INFO @ Fri, 10 Nov 2017 23:46:16: 1000000 INFO @ Fri, 10 Nov 2017 23:46:16: 1000000 INFO @ Fri, 10 Nov 2017 23:46:23: 2000000 INFO @ Fri, 10 Nov 2017 23:46:23: 2000000 INFO @ Fri, 10 Nov 2017 23:46:23: 2000000 INFO @ Fri, 10 Nov 2017 23:46:29: 3000000 INFO @ Fri, 10 Nov 2017 23:46:29: 3000000 INFO @ Fri, 10 Nov 2017 23:46:30: 3000000 INFO @ Fri, 10 Nov 2017 23:46:36: 4000000 INFO @ Fri, 10 Nov 2017 23:46:36: 4000000 INFO @ Fri, 10 Nov 2017 23:46:36: 4000000 INFO @ Fri, 10 Nov 2017 23:46:43: 5000000 INFO @ Fri, 10 Nov 2017 23:46:43: 5000000 INFO @ Fri, 10 Nov 2017 23:46:43: 5000000 INFO @ Fri, 10 Nov 2017 23:46:50: 6000000 INFO @ Fri, 10 Nov 2017 23:46:50: 6000000 INFO @ Fri, 10 Nov 2017 23:46:50: 6000000 INFO @ Fri, 10 Nov 2017 23:46:56: 7000000 INFO @ Fri, 10 Nov 2017 23:46:56: 7000000 INFO @ Fri, 10 Nov 2017 23:46:57: 7000000 INFO @ Fri, 10 Nov 2017 23:47:03: 8000000 INFO @ Fri, 10 Nov 2017 23:47:03: 8000000 INFO @ Fri, 10 Nov 2017 23:47:04: 8000000 INFO @ Fri, 10 Nov 2017 23:47:10: 9000000 INFO @ Fri, 10 Nov 2017 23:47:10: 9000000 INFO @ Fri, 10 Nov 2017 23:47:10: 9000000 INFO @ Fri, 10 Nov 2017 23:47:17: 10000000 INFO @ Fri, 10 Nov 2017 23:47:17: 10000000 INFO @ Fri, 10 Nov 2017 23:47:17: 10000000 INFO @ Fri, 10 Nov 2017 23:47:24: 11000000 INFO @ Fri, 10 Nov 2017 23:47:24: 11000000 INFO @ Fri, 10 Nov 2017 23:47:24: 11000000 INFO @ Fri, 10 Nov 2017 23:47:31: 12000000 INFO @ Fri, 10 Nov 2017 23:47:31: 12000000 INFO @ Fri, 10 Nov 2017 23:47:31: 12000000 INFO @ Fri, 10 Nov 2017 23:47:37: 13000000 INFO @ Fri, 10 Nov 2017 23:47:37: 13000000 INFO @ Fri, 10 Nov 2017 23:47:38: 13000000 INFO @ Fri, 10 Nov 2017 23:47:44: 14000000 INFO @ Fri, 10 Nov 2017 23:47:44: 14000000 INFO @ Fri, 10 Nov 2017 23:47:44: 14000000 INFO @ Fri, 10 Nov 2017 23:47:49: #1 tag size is determined as 64 bps INFO @ Fri, 10 Nov 2017 23:47:49: #1 tag size = 64 INFO @ Fri, 10 Nov 2017 23:47:49: #1 total tags in treatment: 14659088 INFO @ Fri, 10 Nov 2017 23:47:49: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 23:47:49: #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 23:47:49: #1 tag size is determined as 64 bps INFO @ Fri, 10 Nov 2017 23:47:49: #1 tag size = 64 INFO @ Fri, 10 Nov 2017 23:47:49: #1 total tags in treatment: 14659088 INFO @ Fri, 10 Nov 2017 23:47:49: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 23:47:49: #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 23:47:49: #1 tag size is determined as 64 bps INFO @ Fri, 10 Nov 2017 23:47:49: #1 tag size = 64 INFO @ Fri, 10 Nov 2017 23:47:49: #1 total tags in treatment: 14659088 INFO @ Fri, 10 Nov 2017 23:47:49: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 23:47:49: #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 23:47:49: #1 tags after filtering in treatment: 14658920 INFO @ Fri, 10 Nov 2017 23:47:49: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 23:47:49: #1 finished! INFO @ Fri, 10 Nov 2017 23:47:49: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 23:47:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 23:47:50: #1 tags after filtering in treatment: 14658920 INFO @ Fri, 10 Nov 2017 23:47:50: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 23:47:50: #1 finished! INFO @ Fri, 10 Nov 2017 23:47:50: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 23:47:50: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 23:47:50: #1 tags after filtering in treatment: 14658920 INFO @ Fri, 10 Nov 2017 23:47:50: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 23:47:50: #1 finished! INFO @ Fri, 10 Nov 2017 23:47:50: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 23:47:50: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 23:47:51: #2 number of paired peaks: 5877 INFO @ Fri, 10 Nov 2017 23:47:51: start model_add_line... INFO @ Fri, 10 Nov 2017 23:47:51: #2 number of paired peaks: 5877 INFO @ Fri, 10 Nov 2017 23:47:51: start model_add_line... INFO @ Fri, 10 Nov 2017 23:47:51: #2 number of paired peaks: 5877 INFO @ Fri, 10 Nov 2017 23:47:51: start model_add_line... INFO @ Fri, 10 Nov 2017 23:47:51: start X-correlation... INFO @ Fri, 10 Nov 2017 23:47:51: end of X-cor INFO @ Fri, 10 Nov 2017 23:47:51: #2 finished! INFO @ Fri, 10 Nov 2017 23:47:51: #2 predicted fragment length is 64 bps INFO @ Fri, 10 Nov 2017 23:47:51: #2 alternative fragment length(s) may be 64,231,411,531 bps INFO @ Fri, 10 Nov 2017 23:47:51: #2.2 Generate R script for model : SRX1068231.20_model.r WARNING @ Fri, 10 Nov 2017 23:47:51: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 23:47:51: #2 You may need to consider one of the other alternative d(s): 64,231,411,531 WARNING @ Fri, 10 Nov 2017 23:47:51: #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 23:47:51: #3 Call peaks... INFO @ Fri, 10 Nov 2017 23:47:51: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 23:47:51: start X-correlation... INFO @ Fri, 10 Nov 2017 23:47:51: end of X-cor INFO @ Fri, 10 Nov 2017 23:47:51: #2 finished! INFO @ Fri, 10 Nov 2017 23:47:51: #2 predicted fragment length is 64 bps INFO @ Fri, 10 Nov 2017 23:47:51: #2 alternative fragment length(s) may be 64,231,411,531 bps INFO @ Fri, 10 Nov 2017 23:47:51: #2.2 Generate R script for model : SRX1068231.10_model.r WARNING @ Fri, 10 Nov 2017 23:47:51: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 23:47:51: #2 You may need to consider one of the other alternative d(s): 64,231,411,531 WARNING @ Fri, 10 Nov 2017 23:47:51: #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 23:47:51: #3 Call peaks... INFO @ Fri, 10 Nov 2017 23:47:51: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 23:47:51: start X-correlation... INFO @ Fri, 10 Nov 2017 23:47:51: end of X-cor INFO @ Fri, 10 Nov 2017 23:47:51: #2 finished! INFO @ Fri, 10 Nov 2017 23:47:51: #2 predicted fragment length is 64 bps INFO @ Fri, 10 Nov 2017 23:47:51: #2 alternative fragment length(s) may be 64,231,411,531 bps INFO @ Fri, 10 Nov 2017 23:47:51: #2.2 Generate R script for model : SRX1068231.05_model.r WARNING @ Fri, 10 Nov 2017 23:47:51: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 23:47:51: #2 You may need to consider one of the other alternative d(s): 64,231,411,531 WARNING @ Fri, 10 Nov 2017 23:47:51: #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 23:47:51: #3 Call peaks... INFO @ Fri, 10 Nov 2017 23:47:51: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 23:48:26: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 23:48:27: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 23:48:29: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 23:48:46: #4 Write output xls file... SRX1068231.05_peaks.xls INFO @ Fri, 10 Nov 2017 23:48:46: #4 Write peak in narrowPeak format file... SRX1068231.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 23:48:46: #4 Write summits bed file... SRX1068231.05_summits.bed INFO @ Fri, 10 Nov 2017 23:48:46: Done! pass1 - making usageList (36 chroms): 1 millis pass2 - checking and writing primary data (1094 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 23:48:46: #4 Write output xls file... SRX1068231.20_peaks.xls INFO @ Fri, 10 Nov 2017 23:48:46: #4 Write peak in narrowPeak format file... SRX1068231.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 23:48:46: #4 Write summits bed file... SRX1068231.20_summits.bed INFO @ Fri, 10 Nov 2017 23:48:46: Done! pass1 - making usageList (26 chroms): 1 millis pass2 - checking and writing primary data (344 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 23:48:48: #4 Write output xls file... SRX1068231.10_peaks.xls INFO @ Fri, 10 Nov 2017 23:48:48: #4 Write peak in narrowPeak format file... SRX1068231.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 23:48:48: #4 Write summits bed file... SRX1068231.10_summits.bed INFO @ Fri, 10 Nov 2017 23:48:48: Done! pass1 - making usageList (33 chroms): 1 millis pass2 - checking and writing primary data (667 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。