Job ID = 10608979 sra ファイルのダウンロード中... Completed: 825357K bytes transferred in 56 seconds (118676K 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 25833766 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2745373/SRR5457304.sra Written 25833766 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: 00:08:29 25833766 reads; of these: 25833766 (100.00%) were unpaired; of these: 5774712 (22.35%) aligned 0 times 10407687 (40.29%) aligned exactly 1 time 9651367 (37.36%) aligned >1 times 77.65% overall alignment rate Time searching: 00:08:29 Overall time: 00:08:29 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 16113575 / 20059054 = 0.8033 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 23:06:56: # Command line: callpeak -t SRX2745373.bam -f BAM -g 12100000 -n SRX2745373.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2745373.05 # format = BAM # ChIP-seq file = ['SRX2745373.bam'] # control file = None # effective genome size = 1.21e+07 # 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 23:06:56: #1 read tag files... INFO @ Thu, 03 May 2018 23:06:56: #1 read treatment tags... INFO @ Thu, 03 May 2018 23:06:56: # Command line: callpeak -t SRX2745373.bam -f BAM -g 12100000 -n SRX2745373.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2745373.20 # format = BAM # ChIP-seq file = ['SRX2745373.bam'] # control file = None # effective genome size = 1.21e+07 # 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 23:06:56: #1 read tag files... INFO @ Thu, 03 May 2018 23:06:56: #1 read treatment tags... INFO @ Thu, 03 May 2018 23:06:56: # Command line: callpeak -t SRX2745373.bam -f BAM -g 12100000 -n SRX2745373.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2745373.10 # format = BAM # ChIP-seq file = ['SRX2745373.bam'] # control file = None # effective genome size = 1.21e+07 # 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 23:06:56: #1 read tag files... INFO @ Thu, 03 May 2018 23:06:56: #1 read treatment tags... INFO @ Thu, 03 May 2018 23:07:05: 1000000 INFO @ Thu, 03 May 2018 23:07:05: 1000000 INFO @ Thu, 03 May 2018 23:07:05: 1000000 INFO @ Thu, 03 May 2018 23:07:14: 2000000 INFO @ Thu, 03 May 2018 23:07:14: 2000000 INFO @ Thu, 03 May 2018 23:07:14: 2000000 INFO @ Thu, 03 May 2018 23:07:24: 3000000 INFO @ Thu, 03 May 2018 23:07:24: 3000000 INFO @ Thu, 03 May 2018 23:07:24: 3000000 INFO @ Thu, 03 May 2018 23:07:32: #1 tag size is determined as 50 bps INFO @ Thu, 03 May 2018 23:07:32: #1 tag size = 50 INFO @ Thu, 03 May 2018 23:07:32: #1 total tags in treatment: 3945479 INFO @ Thu, 03 May 2018 23:07:32: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 23:07:32: #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 23:07:32: #1 tag size is determined as 50 bps INFO @ Thu, 03 May 2018 23:07:32: #1 tag size = 50 INFO @ Thu, 03 May 2018 23:07:32: #1 total tags in treatment: 3945479 INFO @ Thu, 03 May 2018 23:07:32: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 23:07:32: #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 23:07:32: #1 tag size is determined as 50 bps INFO @ Thu, 03 May 2018 23:07:32: #1 tag size = 50 INFO @ Thu, 03 May 2018 23:07:32: #1 total tags in treatment: 3945479 INFO @ Thu, 03 May 2018 23:07:32: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 23:07:32: #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 23:07:32: #1 tags after filtering in treatment: 3945479 INFO @ Thu, 03 May 2018 23:07:32: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 03 May 2018 23:07:32: #1 finished! INFO @ Thu, 03 May 2018 23:07:32: #2 Build Peak Model... INFO @ Thu, 03 May 2018 23:07:32: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 23:07:32: #1 tags after filtering in treatment: 3945479 INFO @ Thu, 03 May 2018 23:07:32: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 03 May 2018 23:07:32: #1 finished! INFO @ Thu, 03 May 2018 23:07:32: #2 Build Peak Model... INFO @ Thu, 03 May 2018 23:07:32: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 23:07:32: #1 tags after filtering in treatment: 3945479 INFO @ Thu, 03 May 2018 23:07:32: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 03 May 2018 23:07:32: #1 finished! INFO @ Thu, 03 May 2018 23:07:32: #2 Build Peak Model... INFO @ Thu, 03 May 2018 23:07:32: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 23:07:33: #2 number of paired peaks: 171 WARNING @ Thu, 03 May 2018 23:07:33: Fewer paired peaks (171) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 171 pairs to build model! INFO @ Thu, 03 May 2018 23:07:33: start model_add_line... INFO @ Thu, 03 May 2018 23:07:33: #2 number of paired peaks: 171 WARNING @ Thu, 03 May 2018 23:07:33: Fewer paired peaks (171) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 171 pairs to build model! INFO @ Thu, 03 May 2018 23:07:33: start model_add_line... INFO @ Thu, 03 May 2018 23:07:33: start X-correlation... INFO @ Thu, 03 May 2018 23:07:33: start X-correlation... INFO @ Thu, 03 May 2018 23:07:33: end of X-cor INFO @ Thu, 03 May 2018 23:07:33: #2 finished! INFO @ Thu, 03 May 2018 23:07:33: #2 predicted fragment length is 0 bps INFO @ Thu, 03 May 2018 23:07:33: #2 alternative fragment length(s) may be 0,15,39,69,98,140,181,225,270,310,329,345,360,383,429,487,506,587 bps INFO @ Thu, 03 May 2018 23:07:33: #2.2 Generate R script for model : SRX2745373.20_model.r INFO @ Thu, 03 May 2018 23:07:33: end of X-cor INFO @ Thu, 03 May 2018 23:07:33: #2 finished! INFO @ Thu, 03 May 2018 23:07:33: #2 number of paired peaks: 171 INFO @ Thu, 03 May 2018 23:07:33: #2 predicted fragment length is 0 bps WARNING @ Thu, 03 May 2018 23:07:33: Fewer paired peaks (171) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 171 pairs to build model! INFO @ Thu, 03 May 2018 23:07:33: #2 alternative fragment length(s) may be 0,15,39,69,98,140,181,225,270,310,329,345,360,383,429,487,506,587 bps INFO @ Thu, 03 May 2018 23:07:33: start model_add_line... INFO @ Thu, 03 May 2018 23:07:33: #2.2 Generate R script for model : SRX2745373.10_model.r WARNING @ Thu, 03 May 2018 23:07:33: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 03 May 2018 23:07:33: #2 You may need to consider one of the other alternative d(s): 0,15,39,69,98,140,181,225,270,310,329,345,360,383,429,487,506,587 WARNING @ Thu, 03 May 2018 23:07:33: #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 23:07:33: #3 Call peaks... WARNING @ Thu, 03 May 2018 23:07:33: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 03 May 2018 23:07:33: #2 You may need to consider one of the other alternative d(s): 0,15,39,69,98,140,181,225,270,310,329,345,360,383,429,487,506,587 WARNING @ Thu, 03 May 2018 23:07:33: #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 23:07:33: #3 Call peaks... INFO @ Thu, 03 May 2018 23:07:33: start X-correlation... INFO @ Thu, 03 May 2018 23:07:33: end of X-cor INFO @ Thu, 03 May 2018 23:07:33: #2 finished! INFO @ Thu, 03 May 2018 23:07:33: #2 predicted fragment length is 0 bps INFO @ Thu, 03 May 2018 23:07:33: #2 alternative fragment length(s) may be 0,15,39,69,98,140,181,225,270,310,329,345,360,383,429,487,506,587 bps INFO @ Thu, 03 May 2018 23:07:33: #2.2 Generate R script for model : SRX2745373.05_model.r INFO @ Thu, 03 May 2018 23:07:33: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 03 May 2018 23:07:33: #3 Pre-compute pvalue-qvalue table... WARNING @ Thu, 03 May 2018 23:07:33: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 03 May 2018 23:07:33: #2 You may need to consider one of the other alternative d(s): 0,15,39,69,98,140,181,225,270,310,329,345,360,383,429,487,506,587 WARNING @ Thu, 03 May 2018 23:07:33: #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 23:07:33: #3 Call peaks... INFO @ Thu, 03 May 2018 23:07:33: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 03 May 2018 23:07:34: #3 Call peaks for each chromosome... INFO @ Thu, 03 May 2018 23:07:34: #3 Call peaks for each chromosome... INFO @ Thu, 03 May 2018 23:07:34: #4 Write output xls file... SRX2745373.10_peaks.xls INFO @ Thu, 03 May 2018 23:07:34: #4 Write output xls file... SRX2745373.20_peaks.xls INFO @ Thu, 03 May 2018 23:07:34: #4 Write peak in narrowPeak format file... SRX2745373.10_peaks.narrowPeak INFO @ Thu, 03 May 2018 23:07:34: #4 Write peak in narrowPeak format file... SRX2745373.20_peaks.narrowPeak INFO @ Thu, 03 May 2018 23:07:34: #4 Write summits bed file... SRX2745373.10_summits.bed INFO @ Thu, 03 May 2018 23:07:34: #4 Write summits bed file... SRX2745373.20_summits.bed INFO @ Thu, 03 May 2018 23:07:34: Done! INFO @ Thu, 03 May 2018 23:07:34: Done! INFO @ Thu, 03 May 2018 23:07:34: #3 Call peaks for each chromosome... INFO @ Thu, 03 May 2018 23:07:34: #4 Write output xls file... SRX2745373.05_peaks.xls INFO @ Thu, 03 May 2018 23:07:34: #4 Write peak in narrowPeak format file... SRX2745373.05_peaks.narrowPeak INFO @ Thu, 03 May 2018 23:07:34: #4 Write summits bed file... SRX2745373.05_summits.bed INFO @ Thu, 03 May 2018 23:07:34: Done! pass1 - making usageList (0 chroms)pass1 - making usageList (0 chroms): 2 millis : 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling CompletedMACS2peakCalling pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。