Job ID = 9036158 sra ファイルのダウンロード中... Completed: 3993806K bytes transferred in 35 seconds (922016K bits/sec), in 1 file, 2 directories. % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- 0:00:06 --:--:-- 0 100 14324 0 14324 0 0 1923 0 --:--:-- 0:00:07 --:--:-- 13312 100 62318 0 62318 0 0 7381 0 --:--:-- 0:00:08 --:--:-- 30061 100 67043 0 67043 0 0 7940 0 --:--:-- 0:00:08 --:--:-- 32325 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 84650572 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1631846/SRR3225782.sra Written 84650572 spots total 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: 00:40:29 84650572 reads; of these: 84650572 (100.00%) were unpaired; of these: 84639882 (99.99%) aligned 0 times 9689 (0.01%) aligned exactly 1 time 1001 (0.00%) aligned >1 times 0.01% overall alignment rate Time searching: 00:40:29 Overall time: 00:40:29 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_rmdupse_core] 3434 / 10690 = 0.3212 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Sun, 04 Jun 2017 03:12:29: # Command line: callpeak -t SRX1631846.bam -f BAM -g 12100000 -n SRX1631846.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1631846.10 # format = BAM # ChIP-seq file = ['SRX1631846.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 INFO @ Sun, 04 Jun 2017 03:12:29: #1 read tag files... INFO @ Sun, 04 Jun 2017 03:12:29: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 03:12:29: # Command line: callpeak -t SRX1631846.bam -f BAM -g 12100000 -n SRX1631846.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1631846.05 # format = BAM # ChIP-seq file = ['SRX1631846.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 INFO @ Sun, 04 Jun 2017 03:12:29: #1 read tag files... INFO @ Sun, 04 Jun 2017 03:12:29: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 03:12:29: # Command line: callpeak -t SRX1631846.bam -f BAM -g 12100000 -n SRX1631846.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1631846.20 # format = BAM # ChIP-seq file = ['SRX1631846.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 INFO @ Sun, 04 Jun 2017 03:12:29: #1 read tag files... INFO @ Sun, 04 Jun 2017 03:12:29: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 03:12:29: #1 tag size is determined as 100 bps INFO @ Sun, 04 Jun 2017 03:12:29: #1 tag size = 100 INFO @ Sun, 04 Jun 2017 03:12:29: #1 total tags in treatment: 7256 INFO @ Sun, 04 Jun 2017 03:12:29: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 03:12:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Jun 2017 03:12:29: #1 tag size is determined as 100 bps INFO @ Sun, 04 Jun 2017 03:12:29: #1 tag size = 100 INFO @ Sun, 04 Jun 2017 03:12:29: #1 total tags in treatment: 7256 INFO @ Sun, 04 Jun 2017 03:12:29: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 03:12:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Jun 2017 03:12:29: #1 tags after filtering in treatment: 7021 INFO @ Sun, 04 Jun 2017 03:12:29: #1 Redundant rate of treatment: 0.03 INFO @ Sun, 04 Jun 2017 03:12:29: #1 finished! INFO @ Sun, 04 Jun 2017 03:12:29: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 03:12:29: #1 tag size is determined as 100 bps INFO @ Sun, 04 Jun 2017 03:12:29: #1 tag size = 100 INFO @ Sun, 04 Jun 2017 03:12:29: #1 total tags in treatment: 7256 INFO @ Sun, 04 Jun 2017 03:12:29: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 03:12:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Jun 2017 03:12:29: #1 tags after filtering in treatment: 7021 INFO @ Sun, 04 Jun 2017 03:12:29: #1 Redundant rate of treatment: 0.03 INFO @ Sun, 04 Jun 2017 03:12:29: #1 finished! INFO @ Sun, 04 Jun 2017 03:12:29: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 03:12:29: #1 tags after filtering in treatment: 7021 INFO @ Sun, 04 Jun 2017 03:12:29: #1 Redundant rate of treatment: 0.03 INFO @ Sun, 04 Jun 2017 03:12:29: #1 finished! INFO @ Sun, 04 Jun 2017 03:12:29: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 03:12:29: #2 number of paired peaks: 130 WARNING @ Sun, 04 Jun 2017 03:12:29: Fewer paired peaks (130) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 130 pairs to build model! INFO @ Sun, 04 Jun 2017 03:12:29: start model_add_line... INFO @ Sun, 04 Jun 2017 03:12:29: #2 number of paired peaks: 130 WARNING @ Sun, 04 Jun 2017 03:12:29: Fewer paired peaks (130) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 130 pairs to build model! INFO @ Sun, 04 Jun 2017 03:12:29: start model_add_line... INFO @ Sun, 04 Jun 2017 03:12:29: #2 number of paired peaks: 130 WARNING @ Sun, 04 Jun 2017 03:12:29: Fewer paired peaks (130) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 130 pairs to build model! INFO @ Sun, 04 Jun 2017 03:12:29: start model_add_line... INFO @ Sun, 04 Jun 2017 03:12:29: start X-correlation... INFO @ Sun, 04 Jun 2017 03:12:29: start X-correlation... INFO @ Sun, 04 Jun 2017 03:12:29: end of X-cor INFO @ Sun, 04 Jun 2017 03:12:29: #2 finished! INFO @ Sun, 04 Jun 2017 03:12:29: #2 predicted fragment length is 156 bps INFO @ Sun, 04 Jun 2017 03:12:29: #2 alternative fragment length(s) may be 0,22,43,156,198,222,252,289,339,381,409,470,543,593 bps INFO @ Sun, 04 Jun 2017 03:12:29: #2.2 Generate R script for model : SRX1631846.10_model.r INFO @ Sun, 04 Jun 2017 03:12:29: end of X-cor INFO @ Sun, 04 Jun 2017 03:12:29: #2 finished! INFO @ Sun, 04 Jun 2017 03:12:29: #2 predicted fragment length is 156 bps INFO @ Sun, 04 Jun 2017 03:12:29: #2 alternative fragment length(s) may be 0,22,43,156,198,222,252,289,339,381,409,470,543,593 bps INFO @ Sun, 04 Jun 2017 03:12:29: #2.2 Generate R script for model : SRX1631846.05_model.r INFO @ Sun, 04 Jun 2017 03:12:29: start X-correlation... WARNING @ Sun, 04 Jun 2017 03:12:29: #2 Since the d (156) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Jun 2017 03:12:29: #2 You may need to consider one of the other alternative d(s): 0,22,43,156,198,222,252,289,339,381,409,470,543,593 WARNING @ Sun, 04 Jun 2017 03:12:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 04 Jun 2017 03:12:29: #3 Call peaks... INFO @ Sun, 04 Jun 2017 03:12:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 03:12:29: end of X-cor INFO @ Sun, 04 Jun 2017 03:12:29: #2 finished! INFO @ Sun, 04 Jun 2017 03:12:29: #2 predicted fragment length is 156 bps INFO @ Sun, 04 Jun 2017 03:12:29: #2 alternative fragment length(s) may be 0,22,43,156,198,222,252,289,339,381,409,470,543,593 bps INFO @ Sun, 04 Jun 2017 03:12:29: #2.2 Generate R script for model : SRX1631846.20_model.r WARNING @ Sun, 04 Jun 2017 03:12:29: #2 Since the d (156) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Jun 2017 03:12:29: #2 You may need to consider one of the other alternative d(s): 0,22,43,156,198,222,252,289,339,381,409,470,543,593 WARNING @ Sun, 04 Jun 2017 03:12:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 04 Jun 2017 03:12:29: #3 Call peaks... INFO @ Sun, 04 Jun 2017 03:12:29: #3 Pre-compute pvalue-qvalue table... WARNING @ Sun, 04 Jun 2017 03:12:29: #2 Since the d (156) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Jun 2017 03:12:29: #2 You may need to consider one of the other alternative d(s): 0,22,43,156,198,222,252,289,339,381,409,470,543,593 WARNING @ Sun, 04 Jun 2017 03:12:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 04 Jun 2017 03:12:29: #3 Call peaks... INFO @ Sun, 04 Jun 2017 03:12:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 03:12:30: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 03:12:30: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 03:12:30: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 03:12:30: #4 Write output xls file... SRX1631846.20_peaks.xls INFO @ Sun, 04 Jun 2017 03:12:30: #4 Write peak in narrowPeak format file... SRX1631846.20_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 03:12:30: #4 Write output xls file... SRX1631846.05_peaks.xls INFO @ Sun, 04 Jun 2017 03:12:30: #4 Write summits bed file... SRX1631846.20_summits.bed INFO @ Sun, 04 Jun 2017 03:12:30: #4 Write output xls file... SRX1631846.10_peaks.xls INFO @ Sun, 04 Jun 2017 03:12:30: Done! INFO @ Sun, 04 Jun 2017 03:12:30: #4 Write peak in narrowPeak format file... SRX1631846.05_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 03:12:30: #4 Write peak in narrowPeak format file... SRX1631846.10_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 03:12:30: #4 Write summits bed file... SRX1631846.10_summits.bed INFO @ Sun, 04 Jun 2017 03:12:30: #4 Write summits bed file... SRX1631846.05_summits.bed INFO @ Sun, 04 Jun 2017 03:12:30: Done! INFO @ Sun, 04 Jun 2017 03:12:30: Done! pass1 - making usageList (3 chroms): 0 millis pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (4 records, 4 fields): 2 millis pass2 - checking and writing primary data (14 records, 4 fields): 2 millis pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (32 records, 4 fields): 2 millis CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling