Job ID = 11244856 sra ファイルのダウンロード中... Completed: 79884K bytes transferred in 4 seconds (159560K bits/sec), in 1 file. Completed: 224177K bytes transferred in 5 seconds (323263K 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... Read 2703452 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3732412/SRR6759924.sra Written 2703452 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3732412/SRR6759924.sra Read 7499118 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3732412/SRR6759925.sra Written 7499118 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3732412/SRR6759925.sra 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 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: 00:01:44 10202570 reads; of these: 10202570 (100.00%) were unpaired; of these: 3540971 (34.71%) aligned 0 times 5495050 (53.86%) aligned exactly 1 time 1166549 (11.43%) aligned >1 times 65.29% overall alignment rate Time searching: 00:01:44 Overall time: 00:01:44 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_rmdupse_core] 3399609 / 6661599 = 0.5103 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 @ Tue, 09 Oct 2018 22:11:09: # Command line: callpeak -t SRX3732412.bam -f BAM -g 12100000 -n SRX3732412.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3732412.20 # format = BAM # ChIP-seq file = ['SRX3732412.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 @ Tue, 09 Oct 2018 22:11:09: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:11:09: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:11:09: # Command line: callpeak -t SRX3732412.bam -f BAM -g 12100000 -n SRX3732412.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3732412.10 # format = BAM # ChIP-seq file = ['SRX3732412.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 @ Tue, 09 Oct 2018 22:11:09: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:11:09: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:11:09: # Command line: callpeak -t SRX3732412.bam -f BAM -g 12100000 -n SRX3732412.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3732412.05 # format = BAM # ChIP-seq file = ['SRX3732412.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 @ Tue, 09 Oct 2018 22:11:09: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:11:09: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:11:15: 1000000 INFO @ Tue, 09 Oct 2018 22:11:16: 1000000 INFO @ Tue, 09 Oct 2018 22:11:16: 1000000 INFO @ Tue, 09 Oct 2018 22:11:22: 2000000 INFO @ Tue, 09 Oct 2018 22:11:23: 2000000 INFO @ Tue, 09 Oct 2018 22:11:23: 2000000 INFO @ Tue, 09 Oct 2018 22:11:29: 3000000 INFO @ Tue, 09 Oct 2018 22:11:30: 3000000 INFO @ Tue, 09 Oct 2018 22:11:30: 3000000 INFO @ Tue, 09 Oct 2018 22:11:31: #1 tag size is determined as 50 bps INFO @ Tue, 09 Oct 2018 22:11:31: #1 tag size = 50 INFO @ Tue, 09 Oct 2018 22:11:31: #1 total tags in treatment: 3261990 INFO @ Tue, 09 Oct 2018 22:11:31: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:11:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 22:11:31: #1 tags after filtering in treatment: 3261990 INFO @ Tue, 09 Oct 2018 22:11:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 09 Oct 2018 22:11:31: #1 finished! INFO @ Tue, 09 Oct 2018 22:11:31: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:11:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:11:31: #2 number of paired peaks: 163 WARNING @ Tue, 09 Oct 2018 22:11:31: Fewer paired peaks (163) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 163 pairs to build model! INFO @ Tue, 09 Oct 2018 22:11:31: start model_add_line... INFO @ Tue, 09 Oct 2018 22:11:31: start X-correlation... INFO @ Tue, 09 Oct 2018 22:11:31: end of X-cor INFO @ Tue, 09 Oct 2018 22:11:31: #2 finished! INFO @ Tue, 09 Oct 2018 22:11:31: #2 predicted fragment length is 36 bps INFO @ Tue, 09 Oct 2018 22:11:31: #2 alternative fragment length(s) may be 1,36,154,205,225,254,414,482,517,592 bps INFO @ Tue, 09 Oct 2018 22:11:31: #2.2 Generate R script for model : SRX3732412.05_model.r WARNING @ Tue, 09 Oct 2018 22:11:31: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 09 Oct 2018 22:11:31: #2 You may need to consider one of the other alternative d(s): 1,36,154,205,225,254,414,482,517,592 WARNING @ Tue, 09 Oct 2018 22:11:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 09 Oct 2018 22:11:31: #3 Call peaks... INFO @ Tue, 09 Oct 2018 22:11:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 22:11:32: #1 tag size is determined as 50 bps INFO @ Tue, 09 Oct 2018 22:11:32: #1 tag size = 50 INFO @ Tue, 09 Oct 2018 22:11:32: #1 total tags in treatment: 3261990 INFO @ Tue, 09 Oct 2018 22:11:32: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:11:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 22:11:32: #1 tag size is determined as 50 bps INFO @ Tue, 09 Oct 2018 22:11:32: #1 tag size = 50 INFO @ Tue, 09 Oct 2018 22:11:32: #1 total tags in treatment: 3261990 INFO @ Tue, 09 Oct 2018 22:11:32: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:11:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 22:11:32: #1 tags after filtering in treatment: 3261990 INFO @ Tue, 09 Oct 2018 22:11:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 09 Oct 2018 22:11:32: #1 finished! INFO @ Tue, 09 Oct 2018 22:11:32: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:11:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:11:32: #1 tags after filtering in treatment: 3261990 INFO @ Tue, 09 Oct 2018 22:11:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 09 Oct 2018 22:11:32: #1 finished! INFO @ Tue, 09 Oct 2018 22:11:32: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:11:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:11:32: #2 number of paired peaks: 163 WARNING @ Tue, 09 Oct 2018 22:11:32: Fewer paired peaks (163) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 163 pairs to build model! INFO @ Tue, 09 Oct 2018 22:11:32: start model_add_line... INFO @ Tue, 09 Oct 2018 22:11:32: #2 number of paired peaks: 163 WARNING @ Tue, 09 Oct 2018 22:11:32: Fewer paired peaks (163) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 163 pairs to build model! INFO @ Tue, 09 Oct 2018 22:11:32: start model_add_line... INFO @ Tue, 09 Oct 2018 22:11:32: start X-correlation... INFO @ Tue, 09 Oct 2018 22:11:32: start X-correlation... INFO @ Tue, 09 Oct 2018 22:11:32: end of X-cor INFO @ Tue, 09 Oct 2018 22:11:32: end of X-cor INFO @ Tue, 09 Oct 2018 22:11:32: #2 finished! INFO @ Tue, 09 Oct 2018 22:11:32: #2 finished! INFO @ Tue, 09 Oct 2018 22:11:32: #2 predicted fragment length is 36 bps INFO @ Tue, 09 Oct 2018 22:11:32: #2 predicted fragment length is 36 bps INFO @ Tue, 09 Oct 2018 22:11:32: #2 alternative fragment length(s) may be 1,36,154,205,225,254,414,482,517,592 bps INFO @ Tue, 09 Oct 2018 22:11:32: #2 alternative fragment length(s) may be 1,36,154,205,225,254,414,482,517,592 bps INFO @ Tue, 09 Oct 2018 22:11:32: #2.2 Generate R script for model : SRX3732412.10_model.r INFO @ Tue, 09 Oct 2018 22:11:32: #2.2 Generate R script for model : SRX3732412.20_model.r WARNING @ Tue, 09 Oct 2018 22:11:32: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 09 Oct 2018 22:11:32: #2 You may need to consider one of the other alternative d(s): 1,36,154,205,225,254,414,482,517,592 WARNING @ Tue, 09 Oct 2018 22:11:32: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 09 Oct 2018 22:11:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. WARNING @ Tue, 09 Oct 2018 22:11:32: #2 You may need to consider one of the other alternative d(s): 1,36,154,205,225,254,414,482,517,592 INFO @ Tue, 09 Oct 2018 22:11:32: #3 Call peaks... WARNING @ Tue, 09 Oct 2018 22:11:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 09 Oct 2018 22:11:32: #3 Call peaks... INFO @ Tue, 09 Oct 2018 22:11:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 22:11:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 22:11:37: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 22:11:38: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 22:11:38: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 22:11:39: #4 Write output xls file... SRX3732412.05_peaks.xls INFO @ Tue, 09 Oct 2018 22:11:39: #4 Write peak in narrowPeak format file... SRX3732412.05_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 22:11:39: #4 Write summits bed file... SRX3732412.05_summits.bed INFO @ Tue, 09 Oct 2018 22:11:39: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (217 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 09 Oct 2018 22:11:41: #4 Write output xls file... SRX3732412.20_peaks.xls INFO @ Tue, 09 Oct 2018 22:11:41: #4 Write peak in narrowPeak format file... SRX3732412.20_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 22:11:41: #4 Write summits bed file... SRX3732412.20_summits.bed INFO @ Tue, 09 Oct 2018 22:11:41: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (10 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 09 Oct 2018 22:11:41: #4 Write output xls file... SRX3732412.10_peaks.xls INFO @ Tue, 09 Oct 2018 22:11:41: #4 Write peak in narrowPeak format file... SRX3732412.10_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 22:11:41: #4 Write summits bed file... SRX3732412.10_summits.bed INFO @ Tue, 09 Oct 2018 22:11:41: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (34 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。