Job ID = 10320324 sra ファイルのダウンロード中... Completed: 263105K bytes transferred in 37 seconds (57215K 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 9168017 spots for /home/okishinya/chipatlas/results/ce10/SRX3043415/SRR5875899.sra Written 9168017 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: 00:02:50 9168017 reads; of these: 9168017 (100.00%) were unpaired; of these: 3427533 (37.39%) aligned 0 times 4948869 (53.98%) aligned exactly 1 time 791615 (8.63%) aligned >1 times 62.61% overall alignment rate Time searching: 00:02:50 Overall time: 00:02:50 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 346504 / 5740484 = 0.0604 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, 11 Jan 2018 02:09:54: # Command line: callpeak -t SRX3043415.bam -f BAM -g ce -n SRX3043415.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3043415.10 # format = BAM # ChIP-seq file = ['SRX3043415.bam'] # control file = None # effective genome size = 9.00e+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, 11 Jan 2018 02:09:54: #1 read tag files... INFO @ Thu, 11 Jan 2018 02:09:54: #1 read treatment tags... INFO @ Thu, 11 Jan 2018 02:09:54: # Command line: callpeak -t SRX3043415.bam -f BAM -g ce -n SRX3043415.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3043415.20 # format = BAM # ChIP-seq file = ['SRX3043415.bam'] # control file = None # effective genome size = 9.00e+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, 11 Jan 2018 02:09:54: #1 read tag files... INFO @ Thu, 11 Jan 2018 02:09:54: #1 read treatment tags... INFO @ Thu, 11 Jan 2018 02:09:54: # Command line: callpeak -t SRX3043415.bam -f BAM -g ce -n SRX3043415.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3043415.05 # format = BAM # ChIP-seq file = ['SRX3043415.bam'] # control file = None # effective genome size = 9.00e+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, 11 Jan 2018 02:09:54: #1 read tag files... INFO @ Thu, 11 Jan 2018 02:09:54: #1 read treatment tags... INFO @ Thu, 11 Jan 2018 02:10:00: 1000000 INFO @ Thu, 11 Jan 2018 02:10:00: 1000000 INFO @ Thu, 11 Jan 2018 02:10:00: 1000000 INFO @ Thu, 11 Jan 2018 02:10:07: 2000000 INFO @ Thu, 11 Jan 2018 02:10:07: 2000000 INFO @ Thu, 11 Jan 2018 02:10:07: 2000000 INFO @ Thu, 11 Jan 2018 02:10:14: 3000000 INFO @ Thu, 11 Jan 2018 02:10:14: 3000000 INFO @ Thu, 11 Jan 2018 02:10:14: 3000000 INFO @ Thu, 11 Jan 2018 02:10:21: 4000000 INFO @ Thu, 11 Jan 2018 02:10:21: 4000000 INFO @ Thu, 11 Jan 2018 02:10:21: 4000000 INFO @ Thu, 11 Jan 2018 02:10:27: 5000000 INFO @ Thu, 11 Jan 2018 02:10:28: 5000000 INFO @ Thu, 11 Jan 2018 02:10:28: 5000000 INFO @ Thu, 11 Jan 2018 02:10:30: #1 tag size is determined as 50 bps INFO @ Thu, 11 Jan 2018 02:10:30: #1 tag size = 50 INFO @ Thu, 11 Jan 2018 02:10:30: #1 total tags in treatment: 5393980 INFO @ Thu, 11 Jan 2018 02:10:30: #1 user defined the maximum tags... INFO @ Thu, 11 Jan 2018 02:10:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 11 Jan 2018 02:10:30: #1 tags after filtering in treatment: 5393980 INFO @ Thu, 11 Jan 2018 02:10:30: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 11 Jan 2018 02:10:30: #1 finished! INFO @ Thu, 11 Jan 2018 02:10:30: #2 Build Peak Model... INFO @ Thu, 11 Jan 2018 02:10:30: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 11 Jan 2018 02:10:30: #1 tag size is determined as 50 bps INFO @ Thu, 11 Jan 2018 02:10:30: #1 tag size = 50 INFO @ Thu, 11 Jan 2018 02:10:30: #1 total tags in treatment: 5393980 INFO @ Thu, 11 Jan 2018 02:10:30: #1 user defined the maximum tags... INFO @ Thu, 11 Jan 2018 02:10:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 11 Jan 2018 02:10:30: #1 tag size is determined as 50 bps INFO @ Thu, 11 Jan 2018 02:10:30: #1 tag size = 50 INFO @ Thu, 11 Jan 2018 02:10:30: #1 total tags in treatment: 5393980 INFO @ Thu, 11 Jan 2018 02:10:30: #1 user defined the maximum tags... INFO @ Thu, 11 Jan 2018 02:10:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 11 Jan 2018 02:10:30: #1 tags after filtering in treatment: 5393980 INFO @ Thu, 11 Jan 2018 02:10:30: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 11 Jan 2018 02:10:30: #1 finished! INFO @ Thu, 11 Jan 2018 02:10:30: #2 Build Peak Model... INFO @ Thu, 11 Jan 2018 02:10:30: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 11 Jan 2018 02:10:30: #1 tags after filtering in treatment: 5393980 INFO @ Thu, 11 Jan 2018 02:10:30: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 11 Jan 2018 02:10:30: #1 finished! INFO @ Thu, 11 Jan 2018 02:10:30: #2 Build Peak Model... INFO @ Thu, 11 Jan 2018 02:10:30: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 11 Jan 2018 02:10:31: #2 number of paired peaks: 237 WARNING @ Thu, 11 Jan 2018 02:10:31: Fewer paired peaks (237) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 237 pairs to build model! INFO @ Thu, 11 Jan 2018 02:10:31: start model_add_line... INFO @ Thu, 11 Jan 2018 02:10:31: start X-correlation... INFO @ Thu, 11 Jan 2018 02:10:31: end of X-cor INFO @ Thu, 11 Jan 2018 02:10:31: #2 finished! INFO @ Thu, 11 Jan 2018 02:10:31: #2 predicted fragment length is 50 bps INFO @ Thu, 11 Jan 2018 02:10:31: #2 alternative fragment length(s) may be 4,50,193 bps INFO @ Thu, 11 Jan 2018 02:10:31: #2.2 Generate R script for model : SRX3043415.10_model.r WARNING @ Thu, 11 Jan 2018 02:10:31: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 11 Jan 2018 02:10:31: #2 You may need to consider one of the other alternative d(s): 4,50,193 WARNING @ Thu, 11 Jan 2018 02:10:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 11 Jan 2018 02:10:31: #3 Call peaks... INFO @ Thu, 11 Jan 2018 02:10:31: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 11 Jan 2018 02:10:31: #2 number of paired peaks: 237 WARNING @ Thu, 11 Jan 2018 02:10:31: Fewer paired peaks (237) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 237 pairs to build model! INFO @ Thu, 11 Jan 2018 02:10:31: start model_add_line... INFO @ Thu, 11 Jan 2018 02:10:31: #2 number of paired peaks: 237 WARNING @ Thu, 11 Jan 2018 02:10:31: Fewer paired peaks (237) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 237 pairs to build model! INFO @ Thu, 11 Jan 2018 02:10:31: start model_add_line... INFO @ Thu, 11 Jan 2018 02:10:31: start X-correlation... INFO @ Thu, 11 Jan 2018 02:10:31: end of X-cor INFO @ Thu, 11 Jan 2018 02:10:31: #2 finished! INFO @ Thu, 11 Jan 2018 02:10:31: #2 predicted fragment length is 50 bps INFO @ Thu, 11 Jan 2018 02:10:31: #2 alternative fragment length(s) may be 4,50,193 bps INFO @ Thu, 11 Jan 2018 02:10:31: #2.2 Generate R script for model : SRX3043415.20_model.r WARNING @ Thu, 11 Jan 2018 02:10:31: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 11 Jan 2018 02:10:31: #2 You may need to consider one of the other alternative d(s): 4,50,193 WARNING @ Thu, 11 Jan 2018 02:10:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 11 Jan 2018 02:10:31: #3 Call peaks... INFO @ Thu, 11 Jan 2018 02:10:31: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 11 Jan 2018 02:10:31: start X-correlation... INFO @ Thu, 11 Jan 2018 02:10:31: end of X-cor INFO @ Thu, 11 Jan 2018 02:10:31: #2 finished! INFO @ Thu, 11 Jan 2018 02:10:31: #2 predicted fragment length is 50 bps INFO @ Thu, 11 Jan 2018 02:10:31: #2 alternative fragment length(s) may be 4,50,193 bps INFO @ Thu, 11 Jan 2018 02:10:31: #2.2 Generate R script for model : SRX3043415.05_model.r WARNING @ Thu, 11 Jan 2018 02:10:31: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 11 Jan 2018 02:10:31: #2 You may need to consider one of the other alternative d(s): 4,50,193 WARNING @ Thu, 11 Jan 2018 02:10:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 11 Jan 2018 02:10:31: #3 Call peaks... INFO @ Thu, 11 Jan 2018 02:10:31: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 11 Jan 2018 02:10:42: #3 Call peaks for each chromosome... INFO @ Thu, 11 Jan 2018 02:10:43: #3 Call peaks for each chromosome... INFO @ Thu, 11 Jan 2018 02:10:43: #3 Call peaks for each chromosome... INFO @ Thu, 11 Jan 2018 02:10:49: #4 Write output xls file... SRX3043415.10_peaks.xls INFO @ Thu, 11 Jan 2018 02:10:49: #4 Write peak in narrowPeak format file... SRX3043415.10_peaks.narrowPeak INFO @ Thu, 11 Jan 2018 02:10:49: #4 Write summits bed file... SRX3043415.10_summits.bed INFO @ Thu, 11 Jan 2018 02:10:49: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (215 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 11 Jan 2018 02:10:49: #4 Write output xls file... SRX3043415.05_peaks.xls INFO @ Thu, 11 Jan 2018 02:10:49: #4 Write peak in narrowPeak format file... SRX3043415.05_peaks.narrowPeak INFO @ Thu, 11 Jan 2018 02:10:49: #4 Write summits bed file... SRX3043415.05_summits.bed INFO @ Thu, 11 Jan 2018 02:10:49: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (386 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Thu, 11 Jan 2018 02:10:50: #4 Write output xls file... SRX3043415.20_peaks.xls INFO @ Thu, 11 Jan 2018 02:10:50: #4 Write peak in narrowPeak format file... SRX3043415.20_peaks.narrowPeak INFO @ Thu, 11 Jan 2018 02:10:50: #4 Write summits bed file... SRX3043415.20_summits.bed INFO @ Thu, 11 Jan 2018 02:10:50: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (62 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。