Job ID = 9035988 sra ファイルのダウンロード中... Completed: 6590904K bytes transferred in 44 seconds (1222349K 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 0 0 0 0 0 0 0 0 --:--:-- 0:00:07 --:--:-- 0 100 22318 0 22318 0 0 2692 0 --:--:-- 0:00:08 --:--:-- 13675 100 31686 0 31686 0 0 3675 0 --:--:-- 0:00:08 --:--:-- 16133 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 196171775 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1301575/SRR2568522.sra Written 196171775 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: 00:33:55 196171775 reads; of these: 196171775 (100.00%) were unpaired; of these: 69937810 (35.65%) aligned 0 times 98615802 (50.27%) aligned exactly 1 time 27618163 (14.08%) aligned >1 times 64.35% overall alignment rate Time searching: 00:33:55 Overall time: 00:33:55 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 52 files... [bam_rmdupse_core] 125895791 / 126233965 = 0.9973 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 @ Sun, 04 Jun 2017 03:06:12: # Command line: callpeak -t SRX1301575.bam -f BAM -g 12100000 -n SRX1301575.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1301575.05 # format = BAM # ChIP-seq file = ['SRX1301575.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 03:06:12: #1 read tag files... INFO @ Sun, 04 Jun 2017 03:06:12: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 03:06:12: # Command line: callpeak -t SRX1301575.bam -f BAM -g 12100000 -n SRX1301575.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1301575.20 # format = BAM # ChIP-seq file = ['SRX1301575.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 03:06:12: #1 read tag files... INFO @ Sun, 04 Jun 2017 03:06:12: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 03:06:12: # Command line: callpeak -t SRX1301575.bam -f BAM -g 12100000 -n SRX1301575.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1301575.10 # format = BAM # ChIP-seq file = ['SRX1301575.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 03:06:12: #1 read tag files... INFO @ Sun, 04 Jun 2017 03:06:12: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 03:06:14: #1 tag size is determined as 50 bps INFO @ Sun, 04 Jun 2017 03:06:14: #1 tag size = 50 INFO @ Sun, 04 Jun 2017 03:06:14: #1 total tags in treatment: 338174 INFO @ Sun, 04 Jun 2017 03:06:14: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 03:06:14: #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 03:06:14: #1 tag size is determined as 50 bps INFO @ Sun, 04 Jun 2017 03:06:14: #1 tag size = 50 INFO @ Sun, 04 Jun 2017 03:06:14: #1 total tags in treatment: 338174 INFO @ Sun, 04 Jun 2017 03:06:14: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 03:06:14: #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 03:06:14: #1 tag size is determined as 50 bps INFO @ Sun, 04 Jun 2017 03:06:14: #1 tag size = 50 INFO @ Sun, 04 Jun 2017 03:06:14: #1 total tags in treatment: 338174 INFO @ Sun, 04 Jun 2017 03:06:14: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 03:06:14: #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 03:06:14: #1 tags after filtering in treatment: 336051 INFO @ Sun, 04 Jun 2017 03:06:14: #1 Redundant rate of treatment: 0.01 INFO @ Sun, 04 Jun 2017 03:06:14: #1 finished! INFO @ Sun, 04 Jun 2017 03:06:14: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 03:06:14: #1 tags after filtering in treatment: 336051 INFO @ Sun, 04 Jun 2017 03:06:14: #1 Redundant rate of treatment: 0.01 INFO @ Sun, 04 Jun 2017 03:06:14: #1 finished! INFO @ Sun, 04 Jun 2017 03:06:14: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 03:06:14: #1 tags after filtering in treatment: 336051 INFO @ Sun, 04 Jun 2017 03:06:14: #1 Redundant rate of treatment: 0.01 INFO @ Sun, 04 Jun 2017 03:06:14: #1 finished! INFO @ Sun, 04 Jun 2017 03:06:14: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 03:06:14: #2 number of paired peaks: 575 WARNING @ Sun, 04 Jun 2017 03:06:14: Fewer paired peaks (575) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 575 pairs to build model! INFO @ Sun, 04 Jun 2017 03:06:14: start model_add_line... INFO @ Sun, 04 Jun 2017 03:06:14: #2 number of paired peaks: 575 WARNING @ Sun, 04 Jun 2017 03:06:14: Fewer paired peaks (575) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 575 pairs to build model! INFO @ Sun, 04 Jun 2017 03:06:14: start model_add_line... INFO @ Sun, 04 Jun 2017 03:06:14: #2 number of paired peaks: 575 WARNING @ Sun, 04 Jun 2017 03:06:14: Fewer paired peaks (575) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 575 pairs to build model! INFO @ Sun, 04 Jun 2017 03:06:14: start model_add_line... INFO @ Sun, 04 Jun 2017 03:06:16: start X-correlation... INFO @ Sun, 04 Jun 2017 03:06:16: end of X-cor INFO @ Sun, 04 Jun 2017 03:06:16: #2 finished! INFO @ Sun, 04 Jun 2017 03:06:16: #2 predicted fragment length is 56 bps INFO @ Sun, 04 Jun 2017 03:06:16: #2 alternative fragment length(s) may be 56,464,518,561 bps INFO @ Sun, 04 Jun 2017 03:06:16: #2.2 Generate R script for model : SRX1301575.10_model.r WARNING @ Sun, 04 Jun 2017 03:06:16: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Jun 2017 03:06:16: #2 You may need to consider one of the other alternative d(s): 56,464,518,561 WARNING @ Sun, 04 Jun 2017 03:06:16: #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 03:06:16: #3 Call peaks... INFO @ Sun, 04 Jun 2017 03:06:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 03:06:16: start X-correlation... INFO @ Sun, 04 Jun 2017 03:06:16: end of X-cor INFO @ Sun, 04 Jun 2017 03:06:16: #2 finished! INFO @ Sun, 04 Jun 2017 03:06:16: #2 predicted fragment length is 56 bps INFO @ Sun, 04 Jun 2017 03:06:16: #2 alternative fragment length(s) may be 56,464,518,561 bps INFO @ Sun, 04 Jun 2017 03:06:16: #2.2 Generate R script for model : SRX1301575.20_model.r WARNING @ Sun, 04 Jun 2017 03:06:16: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Jun 2017 03:06:16: #2 You may need to consider one of the other alternative d(s): 56,464,518,561 WARNING @ Sun, 04 Jun 2017 03:06:16: #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 03:06:16: #3 Call peaks... INFO @ Sun, 04 Jun 2017 03:06:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 03:06:16: start X-correlation... INFO @ Sun, 04 Jun 2017 03:06:16: end of X-cor INFO @ Sun, 04 Jun 2017 03:06:16: #2 finished! INFO @ Sun, 04 Jun 2017 03:06:16: #2 predicted fragment length is 56 bps INFO @ Sun, 04 Jun 2017 03:06:16: #2 alternative fragment length(s) may be 56,464,518,561 bps INFO @ Sun, 04 Jun 2017 03:06:16: #2.2 Generate R script for model : SRX1301575.05_model.r WARNING @ Sun, 04 Jun 2017 03:06:16: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Jun 2017 03:06:16: #2 You may need to consider one of the other alternative d(s): 56,464,518,561 WARNING @ Sun, 04 Jun 2017 03:06:16: #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 03:06:16: #3 Call peaks... INFO @ Sun, 04 Jun 2017 03:06:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 03:06:18: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 03:06:18: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 03:06:18: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 04 Jun 2017 03:06:19: #4 Write output xls file... SRX1301575.20_peaks.xls INFO @ Sun, 04 Jun 2017 03:06:19: #4 Write peak in narrowPeak format file... SRX1301575.20_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 03:06:19: #4 Write summits bed file... SRX1301575.20_summits.bed INFO @ Sun, 04 Jun 2017 03:06:19: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (159 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 03:06:20: #4 Write output xls file... SRX1301575.10_peaks.xls INFO @ Sun, 04 Jun 2017 03:06:20: #4 Write peak in narrowPeak format file... SRX1301575.10_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 03:06:20: #4 Write summits bed file... SRX1301575.10_summits.bed INFO @ Sun, 04 Jun 2017 03:06:20: Done! BigWig に変換しました。 INFO @ Sun, 04 Jun 2017 03:06:20: #4 Write output xls file... SRX1301575.05_peaks.xls pass1 - making usageList (16 chroms): 0 millis INFO @ Sun, 04 Jun 2017 03:06:20: #4 Write peak in narrowPeak format file... SRX1301575.05_peaks.narrowPeak pass2 - checking and writing primary data (352 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 03:06:20: #4 Write summits bed file... SRX1301575.05_summits.bed INFO @ Sun, 04 Jun 2017 03:06:20: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (632 records, 4 fields): 3 millis CompletedMACS2peakCalling