Job ID = 10608866 sra ファイルのダウンロード中... Completed: 639461K bytes transferred in 41 seconds (126953K 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 14067291 spots for /home/okishinya/chipatlas/results/rn6/SRX2727600/SRR5437663.sra Written 14067291 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: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:24:50 14067291 reads; of these: 14067291 (100.00%) were unpaired; of these: 454414 (3.23%) aligned 0 times 10404183 (73.96%) aligned exactly 1 time 3208694 (22.81%) aligned >1 times 96.77% overall alignment rate Time searching: 00:24:53 Overall time: 00:24:53 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] 483703 / 13612877 = 0.0355 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 @ Thu, 03 May 2018 22:44:48: # Command line: callpeak -t SRX2727600.bam -f BAM -g 2.15e9 -n SRX2727600.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2727600.10 # format = BAM # ChIP-seq file = ['SRX2727600.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 @ Thu, 03 May 2018 22:44:48: #1 read tag files... INFO @ Thu, 03 May 2018 22:44:48: # Command line: callpeak -t SRX2727600.bam -f BAM -g 2.15e9 -n SRX2727600.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2727600.20 # format = BAM # ChIP-seq file = ['SRX2727600.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 @ Thu, 03 May 2018 22:44:48: #1 read treatment tags... INFO @ Thu, 03 May 2018 22:44:48: #1 read tag files... INFO @ Thu, 03 May 2018 22:44:48: #1 read treatment tags... INFO @ Thu, 03 May 2018 22:44:48: # Command line: callpeak -t SRX2727600.bam -f BAM -g 2.15e9 -n SRX2727600.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2727600.05 # format = BAM # ChIP-seq file = ['SRX2727600.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 @ Thu, 03 May 2018 22:44:48: #1 read tag files... INFO @ Thu, 03 May 2018 22:44:48: #1 read treatment tags... INFO @ Thu, 03 May 2018 22:44:56: 1000000 INFO @ Thu, 03 May 2018 22:44:56: 1000000 INFO @ Thu, 03 May 2018 22:44:56: 1000000 INFO @ Thu, 03 May 2018 22:45:04: 2000000 INFO @ Thu, 03 May 2018 22:45:04: 2000000 INFO @ Thu, 03 May 2018 22:45:04: 2000000 INFO @ Thu, 03 May 2018 22:45:12: 3000000 INFO @ Thu, 03 May 2018 22:45:12: 3000000 INFO @ Thu, 03 May 2018 22:45:12: 3000000 INFO @ Thu, 03 May 2018 22:45:20: 4000000 INFO @ Thu, 03 May 2018 22:45:20: 4000000 INFO @ Thu, 03 May 2018 22:45:20: 4000000 INFO @ Thu, 03 May 2018 22:45:27: 5000000 INFO @ Thu, 03 May 2018 22:45:27: 5000000 INFO @ Thu, 03 May 2018 22:45:28: 5000000 INFO @ Thu, 03 May 2018 22:45:35: 6000000 INFO @ Thu, 03 May 2018 22:45:35: 6000000 INFO @ Thu, 03 May 2018 22:45:35: 6000000 INFO @ Thu, 03 May 2018 22:45:43: 7000000 INFO @ Thu, 03 May 2018 22:45:43: 7000000 INFO @ Thu, 03 May 2018 22:45:43: 7000000 INFO @ Thu, 03 May 2018 22:45:51: 8000000 INFO @ Thu, 03 May 2018 22:45:51: 8000000 INFO @ Thu, 03 May 2018 22:45:51: 8000000 INFO @ Thu, 03 May 2018 22:45:59: 9000000 INFO @ Thu, 03 May 2018 22:45:59: 9000000 INFO @ Thu, 03 May 2018 22:45:59: 9000000 INFO @ Thu, 03 May 2018 22:46:06: 10000000 INFO @ Thu, 03 May 2018 22:46:07: 10000000 INFO @ Thu, 03 May 2018 22:46:07: 10000000 INFO @ Thu, 03 May 2018 22:46:14: 11000000 INFO @ Thu, 03 May 2018 22:46:14: 11000000 INFO @ Thu, 03 May 2018 22:46:15: 11000000 INFO @ Thu, 03 May 2018 22:46:22: 12000000 INFO @ Thu, 03 May 2018 22:46:22: 12000000 INFO @ Thu, 03 May 2018 22:46:22: 12000000 INFO @ Thu, 03 May 2018 22:46:30: 13000000 INFO @ Thu, 03 May 2018 22:46:30: 13000000 INFO @ Thu, 03 May 2018 22:46:31: 13000000 INFO @ Thu, 03 May 2018 22:46:31: #1 tag size is determined as 100 bps INFO @ Thu, 03 May 2018 22:46:31: #1 tag size = 100 INFO @ Thu, 03 May 2018 22:46:31: #1 total tags in treatment: 13129174 INFO @ Thu, 03 May 2018 22:46:31: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 22:46:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 03 May 2018 22:46:32: #1 tag size is determined as 100 bps INFO @ Thu, 03 May 2018 22:46:32: #1 tag size = 100 INFO @ Thu, 03 May 2018 22:46:32: #1 total tags in treatment: 13129174 INFO @ Thu, 03 May 2018 22:46:32: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 22:46:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 03 May 2018 22:46:32: #1 tag size is determined as 100 bps INFO @ Thu, 03 May 2018 22:46:32: #1 tag size = 100 INFO @ Thu, 03 May 2018 22:46:32: #1 total tags in treatment: 13129174 INFO @ Thu, 03 May 2018 22:46:32: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 22:46:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 03 May 2018 22:46:32: #1 tags after filtering in treatment: 13128989 INFO @ Thu, 03 May 2018 22:46:32: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 03 May 2018 22:46:32: #1 finished! INFO @ Thu, 03 May 2018 22:46:32: #2 Build Peak Model... INFO @ Thu, 03 May 2018 22:46:32: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 22:46:32: #1 tags after filtering in treatment: 13128989 INFO @ Thu, 03 May 2018 22:46:32: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 03 May 2018 22:46:32: #1 finished! INFO @ Thu, 03 May 2018 22:46:32: #2 Build Peak Model... INFO @ Thu, 03 May 2018 22:46:32: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 22:46:32: #1 tags after filtering in treatment: 13128989 INFO @ Thu, 03 May 2018 22:46:32: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 03 May 2018 22:46:32: #1 finished! INFO @ Thu, 03 May 2018 22:46:32: #2 Build Peak Model... INFO @ Thu, 03 May 2018 22:46:32: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 22:46:34: #2 number of paired peaks: 5254 INFO @ Thu, 03 May 2018 22:46:34: start model_add_line... INFO @ Thu, 03 May 2018 22:46:34: #2 number of paired peaks: 5254 INFO @ Thu, 03 May 2018 22:46:34: start model_add_line... INFO @ Thu, 03 May 2018 22:46:34: #2 number of paired peaks: 5254 INFO @ Thu, 03 May 2018 22:46:34: start model_add_line... INFO @ Thu, 03 May 2018 22:46:34: start X-correlation... INFO @ Thu, 03 May 2018 22:46:34: start X-correlation... INFO @ Thu, 03 May 2018 22:46:34: end of X-cor INFO @ Thu, 03 May 2018 22:46:34: #2 finished! INFO @ Thu, 03 May 2018 22:46:34: #2 predicted fragment length is 100 bps INFO @ Thu, 03 May 2018 22:46:34: #2 alternative fragment length(s) may be 100 bps INFO @ Thu, 03 May 2018 22:46:34: #2.2 Generate R script for model : SRX2727600.05_model.r INFO @ Thu, 03 May 2018 22:46:34: end of X-cor INFO @ Thu, 03 May 2018 22:46:34: #2 finished! INFO @ Thu, 03 May 2018 22:46:34: #2 predicted fragment length is 100 bps INFO @ Thu, 03 May 2018 22:46:34: #2 alternative fragment length(s) may be 100 bps INFO @ Thu, 03 May 2018 22:46:34: #2.2 Generate R script for model : SRX2727600.20_model.r WARNING @ Thu, 03 May 2018 22:46:34: #2 Since the d (100) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 03 May 2018 22:46:34: #2 You may need to consider one of the other alternative d(s): 100 WARNING @ Thu, 03 May 2018 22:46:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 03 May 2018 22:46:34: #3 Call peaks... WARNING @ Thu, 03 May 2018 22:46:34: #2 Since the d (100) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 03 May 2018 22:46:34: #2 You may need to consider one of the other alternative d(s): 100 WARNING @ Thu, 03 May 2018 22:46:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 03 May 2018 22:46:34: #3 Call peaks... INFO @ Thu, 03 May 2018 22:46:34: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 03 May 2018 22:46:34: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 03 May 2018 22:46:34: start X-correlation... INFO @ Thu, 03 May 2018 22:46:34: end of X-cor INFO @ Thu, 03 May 2018 22:46:34: #2 finished! INFO @ Thu, 03 May 2018 22:46:34: #2 predicted fragment length is 100 bps INFO @ Thu, 03 May 2018 22:46:34: #2 alternative fragment length(s) may be 100 bps INFO @ Thu, 03 May 2018 22:46:34: #2.2 Generate R script for model : SRX2727600.10_model.r WARNING @ Thu, 03 May 2018 22:46:34: #2 Since the d (100) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 03 May 2018 22:46:34: #2 You may need to consider one of the other alternative d(s): 100 WARNING @ Thu, 03 May 2018 22:46:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 03 May 2018 22:46:34: #3 Call peaks... INFO @ Thu, 03 May 2018 22:46:34: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 03 May 2018 22:47:07: #3 Call peaks for each chromosome... INFO @ Thu, 03 May 2018 22:47:07: #3 Call peaks for each chromosome... INFO @ Thu, 03 May 2018 22:47:07: #3 Call peaks for each chromosome... INFO @ Thu, 03 May 2018 22:47:24: #4 Write output xls file... SRX2727600.10_peaks.xls INFO @ Thu, 03 May 2018 22:47:24: #4 Write peak in narrowPeak format file... SRX2727600.10_peaks.narrowPeak INFO @ Thu, 03 May 2018 22:47:24: #4 Write summits bed file... SRX2727600.10_summits.bed INFO @ Thu, 03 May 2018 22:47:24: Done! pass1 - making usageList (28 chroms): 0 millis pass2 - checking and writing primary data (467 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 03 May 2018 22:47:25: #4 Write output xls file... SRX2727600.05_peaks.xls INFO @ Thu, 03 May 2018 22:47:25: #4 Write peak in narrowPeak format file... SRX2727600.05_peaks.narrowPeak INFO @ Thu, 03 May 2018 22:47:25: #4 Write summits bed file... SRX2727600.05_summits.bed INFO @ Thu, 03 May 2018 22:47:25: Done! pass1 - making usageList (35 chroms): 1 millis pass2 - checking and writing primary data (788 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 03 May 2018 22:47:27: #4 Write output xls file... SRX2727600.20_peaks.xls INFO @ Thu, 03 May 2018 22:47:27: #4 Write peak in narrowPeak format file... SRX2727600.20_peaks.narrowPeak INFO @ Thu, 03 May 2018 22:47:27: #4 Write summits bed file... SRX2727600.20_summits.bed INFO @ Thu, 03 May 2018 22:47:27: Done! pass1 - making usageList (22 chroms): 1 millis pass2 - checking and writing primary data (260 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。