Job ID = 9036138 sra ファイルのダウンロード中... Completed: 3925681K bytes transferred in 43 seconds (747461K 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 0 0 0 0 0 0 0 0 --:--:-- 0:00:07 --:--:-- 0 100 14324 0 14324 0 0 1654 0 --:--:-- 0:00:08 --:--:-- 6440 100 34894 0 34894 0 0 3811 0 --:--:-- 0:00:09 --:--:-- 12814 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 132662696 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1625717/SRR3218452.sra Written 132662696 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: 00:14:44 132662696 reads; of these: 132662696 (100.00%) were unpaired; of these: 132612780 (99.96%) aligned 0 times 36681 (0.03%) aligned exactly 1 time 13235 (0.01%) aligned >1 times 0.04% overall alignment rate Time searching: 00:14:44 Overall time: 00:14:44 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] 8221 / 49916 = 0.1647 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 02:50:18: # Command line: callpeak -t SRX1625717.bam -f BAM -g 12100000 -n SRX1625717.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1625717.10 # format = BAM # ChIP-seq file = ['SRX1625717.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 02:50:18: #1 read tag files... INFO @ Sun, 04 Jun 2017 02:50:18: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 02:50:18: # Command line: callpeak -t SRX1625717.bam -f BAM -g 12100000 -n SRX1625717.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1625717.05 # format = BAM # ChIP-seq file = ['SRX1625717.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 02:50:18: #1 read tag files... INFO @ Sun, 04 Jun 2017 02:50:18: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 02:50:18: # Command line: callpeak -t SRX1625717.bam -f BAM -g 12100000 -n SRX1625717.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1625717.20 # format = BAM # ChIP-seq file = ['SRX1625717.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 02:50:18: #1 read tag files... INFO @ Sun, 04 Jun 2017 02:50:18: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 02:50:18: #1 tag size is determined as 50 bps INFO @ Sun, 04 Jun 2017 02:50:18: #1 tag size = 50 INFO @ Sun, 04 Jun 2017 02:50:18: #1 total tags in treatment: 41695 INFO @ Sun, 04 Jun 2017 02:50:18: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 02:50:18: #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 02:50:18: #1 tags after filtering in treatment: 41500 INFO @ Sun, 04 Jun 2017 02:50:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 02:50:18: #1 finished! INFO @ Sun, 04 Jun 2017 02:50:18: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 02:50:18: #1 tag size is determined as 50 bps INFO @ Sun, 04 Jun 2017 02:50:18: #1 tag size = 50 INFO @ Sun, 04 Jun 2017 02:50:18: #1 total tags in treatment: 41695 INFO @ Sun, 04 Jun 2017 02:50:18: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 02:50:18: #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 02:50:18: #1 tag size is determined as 50 bps INFO @ Sun, 04 Jun 2017 02:50:18: #1 tag size = 50 INFO @ Sun, 04 Jun 2017 02:50:18: #1 total tags in treatment: 41695 INFO @ Sun, 04 Jun 2017 02:50:18: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 02:50:18: #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 02:50:18: #1 tags after filtering in treatment: 41500 INFO @ Sun, 04 Jun 2017 02:50:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 02:50:18: #1 finished! INFO @ Sun, 04 Jun 2017 02:50:18: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 02:50:18: #1 tags after filtering in treatment: 41500 INFO @ Sun, 04 Jun 2017 02:50:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 02:50:18: #1 finished! INFO @ Sun, 04 Jun 2017 02:50:18: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 02:50:18: #2 number of paired peaks: 211 WARNING @ Sun, 04 Jun 2017 02:50:18: Fewer paired peaks (211) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 211 pairs to build model! INFO @ Sun, 04 Jun 2017 02:50:18: start model_add_line... INFO @ Sun, 04 Jun 2017 02:50:18: #2 number of paired peaks: 211 WARNING @ Sun, 04 Jun 2017 02:50:18: Fewer paired peaks (211) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 211 pairs to build model! INFO @ Sun, 04 Jun 2017 02:50:18: start model_add_line... INFO @ Sun, 04 Jun 2017 02:50:18: #2 number of paired peaks: 211 WARNING @ Sun, 04 Jun 2017 02:50:18: Fewer paired peaks (211) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 211 pairs to build model! INFO @ Sun, 04 Jun 2017 02:50:18: start model_add_line... INFO @ Sun, 04 Jun 2017 02:50:18: start X-correlation... INFO @ Sun, 04 Jun 2017 02:50:18: end of X-cor INFO @ Sun, 04 Jun 2017 02:50:18: #2 finished! INFO @ Sun, 04 Jun 2017 02:50:18: #2 predicted fragment length is 51 bps INFO @ Sun, 04 Jun 2017 02:50:18: #2 alternative fragment length(s) may be 51,109,176,217,246,298,393,422,471,519,549,586 bps INFO @ Sun, 04 Jun 2017 02:50:18: #2.2 Generate R script for model : SRX1625717.10_model.r WARNING @ Sun, 04 Jun 2017 02:50:18: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Jun 2017 02:50:18: #2 You may need to consider one of the other alternative d(s): 51,109,176,217,246,298,393,422,471,519,549,586 WARNING @ Sun, 04 Jun 2017 02:50:18: #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 02:50:18: #3 Call peaks... INFO @ Sun, 04 Jun 2017 02:50:18: start X-correlation... INFO @ Sun, 04 Jun 2017 02:50:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 02:50:18: end of X-cor INFO @ Sun, 04 Jun 2017 02:50:18: #2 finished! INFO @ Sun, 04 Jun 2017 02:50:18: #2 predicted fragment length is 51 bps INFO @ Sun, 04 Jun 2017 02:50:18: #2 alternative fragment length(s) may be 51,109,176,217,246,298,393,422,471,519,549,586 bps INFO @ Sun, 04 Jun 2017 02:50:18: #2.2 Generate R script for model : SRX1625717.05_model.r INFO @ Sun, 04 Jun 2017 02:50:18: start X-correlation... INFO @ Sun, 04 Jun 2017 02:50:18: end of X-cor INFO @ Sun, 04 Jun 2017 02:50:18: #2 finished! INFO @ Sun, 04 Jun 2017 02:50:18: #2 predicted fragment length is 51 bps INFO @ Sun, 04 Jun 2017 02:50:18: #2 alternative fragment length(s) may be 51,109,176,217,246,298,393,422,471,519,549,586 bps INFO @ Sun, 04 Jun 2017 02:50:18: #2.2 Generate R script for model : SRX1625717.20_model.r WARNING @ Sun, 04 Jun 2017 02:50:18: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Jun 2017 02:50:18: #2 You may need to consider one of the other alternative d(s): 51,109,176,217,246,298,393,422,471,519,549,586 WARNING @ Sun, 04 Jun 2017 02:50:18: #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 02:50:18: #3 Call peaks... INFO @ Sun, 04 Jun 2017 02:50:18: #3 Pre-compute pvalue-qvalue table... WARNING @ Sun, 04 Jun 2017 02:50:18: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Jun 2017 02:50:18: #2 You may need to consider one of the other alternative d(s): 51,109,176,217,246,298,393,422,471,519,549,586 WARNING @ Sun, 04 Jun 2017 02:50:18: #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 02:50:18: #3 Call peaks... INFO @ Sun, 04 Jun 2017 02:50:18: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 04 Jun 2017 02:50:18: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 02:50:18: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 02:50:18: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 04 Jun 2017 02:50:19: #4 Write output xls file... SRX1625717.10_peaks.xls INFO @ Sun, 04 Jun 2017 02:50:19: #4 Write peak in narrowPeak format file... SRX1625717.10_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 02:50:19: #4 Write summits bed file... SRX1625717.10_summits.bed INFO @ Sun, 04 Jun 2017 02:50:19: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (26 records, 4 fields): 2 millis INFO @ Sun, 04 Jun 2017 02:50:19: #4 Write output xls file... SRX1625717.05_peaks.xls CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 02:50:19: #4 Write peak in narrowPeak format file... SRX1625717.05_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 02:50:19: #4 Write output xls file... SRX1625717.20_peaks.xls INFO @ Sun, 04 Jun 2017 02:50:19: #4 Write summits bed file... SRX1625717.05_summits.bed INFO @ Sun, 04 Jun 2017 02:50:19: #4 Write peak in narrowPeak format file... SRX1625717.20_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 02:50:19: Done! INFO @ Sun, 04 Jun 2017 02:50:19: #4 Write summits bed file... SRX1625717.20_summits.bed INFO @ Sun, 04 Jun 2017 02:50:19: Done! pass1 - making usageList (16 chroms): 1 millis pass1 - making usageList (3 chroms): 0 millis pass2 - checking and writing primary data (52 records, 4 fields): 2 millis pass2 - checking and writing primary data (3 records, 4 fields): 2 millis CompletedMACS2peakCalling CompletedMACS2peakCalling