Job ID = 9037684 sra ファイルのダウンロード中... Completed: 144340K bytes transferred in 5 seconds (231958K 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 14324 0 14324 0 0 1699 0 --:--:-- 0:00:08 --:--:-- 7140 100 44954 0 44954 0 0 4854 0 --:--:-- 0:00:09 --:--:-- 15851 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 7440588 spots for /home/okishinya/chipatlas/results/sacCer3/SRX977475/SRR1951321.sra Written 7440588 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: 00:01:04 7440588 reads; of these: 7440588 (100.00%) were unpaired; of these: 648102 (8.71%) aligned 0 times 5913357 (79.47%) aligned exactly 1 time 879129 (11.82%) aligned >1 times 91.29% overall alignment rate Time searching: 00:01:04 Overall time: 00:01:04 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] 6659773 / 6792486 = 0.9805 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 05:11:21: # Command line: callpeak -t SRX977475.bam -f BAM -g 12100000 -n SRX977475.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX977475.05 # format = BAM # ChIP-seq file = ['SRX977475.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 05:11:21: #1 read tag files... INFO @ Sun, 04 Jun 2017 05:11:21: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 05:11:21: # Command line: callpeak -t SRX977475.bam -f BAM -g 12100000 -n SRX977475.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX977475.10 # format = BAM # ChIP-seq file = ['SRX977475.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 05:11:21: #1 read tag files... INFO @ Sun, 04 Jun 2017 05:11:21: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 05:11:21: # Command line: callpeak -t SRX977475.bam -f BAM -g 12100000 -n SRX977475.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX977475.20 # format = BAM # ChIP-seq file = ['SRX977475.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 05:11:21: #1 read tag files... INFO @ Sun, 04 Jun 2017 05:11:21: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 05:11:22: #1 tag size is determined as 40 bps INFO @ Sun, 04 Jun 2017 05:11:22: #1 tag size = 40 INFO @ Sun, 04 Jun 2017 05:11:22: #1 total tags in treatment: 132713 INFO @ Sun, 04 Jun 2017 05:11:22: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 05:11:22: #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 05:11:22: #1 tag size is determined as 40 bps INFO @ Sun, 04 Jun 2017 05:11:22: #1 tag size = 40 INFO @ Sun, 04 Jun 2017 05:11:22: #1 total tags in treatment: 132713 INFO @ Sun, 04 Jun 2017 05:11:22: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 05:11:22: #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 05:11:22: #1 tag size is determined as 40 bps INFO @ Sun, 04 Jun 2017 05:11:22: #1 tag size = 40 INFO @ Sun, 04 Jun 2017 05:11:22: #1 total tags in treatment: 132713 INFO @ Sun, 04 Jun 2017 05:11:22: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 05:11:22: #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 05:11:22: #1 tags after filtering in treatment: 132574 INFO @ Sun, 04 Jun 2017 05:11:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 05:11:22: #1 finished! INFO @ Sun, 04 Jun 2017 05:11:22: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 05:11:22: #1 tags after filtering in treatment: 132574 INFO @ Sun, 04 Jun 2017 05:11:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 05:11:22: #1 finished! INFO @ Sun, 04 Jun 2017 05:11:22: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 05:11:22: #1 tags after filtering in treatment: 132574 INFO @ Sun, 04 Jun 2017 05:11:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 05:11:22: #1 finished! INFO @ Sun, 04 Jun 2017 05:11:22: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 05:11:22: #2 number of paired peaks: 564 WARNING @ Sun, 04 Jun 2017 05:11:22: Fewer paired peaks (564) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 564 pairs to build model! INFO @ Sun, 04 Jun 2017 05:11:22: start model_add_line... INFO @ Sun, 04 Jun 2017 05:11:22: #2 number of paired peaks: 564 WARNING @ Sun, 04 Jun 2017 05:11:22: Fewer paired peaks (564) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 564 pairs to build model! INFO @ Sun, 04 Jun 2017 05:11:22: start model_add_line... INFO @ Sun, 04 Jun 2017 05:11:22: #2 number of paired peaks: 564 WARNING @ Sun, 04 Jun 2017 05:11:22: Fewer paired peaks (564) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 564 pairs to build model! INFO @ Sun, 04 Jun 2017 05:11:22: start model_add_line... INFO @ Sun, 04 Jun 2017 05:11:23: start X-correlation... INFO @ Sun, 04 Jun 2017 05:11:23: end of X-cor INFO @ Sun, 04 Jun 2017 05:11:23: #2 finished! INFO @ Sun, 04 Jun 2017 05:11:23: #2 predicted fragment length is 37 bps INFO @ Sun, 04 Jun 2017 05:11:23: #2 alternative fragment length(s) may be 1,37,58,107,140,173,207,250,288,394,490,513,529,559,590 bps INFO @ Sun, 04 Jun 2017 05:11:23: #2.2 Generate R script for model : SRX977475.05_model.r WARNING @ Sun, 04 Jun 2017 05:11:23: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Jun 2017 05:11:23: #2 You may need to consider one of the other alternative d(s): 1,37,58,107,140,173,207,250,288,394,490,513,529,559,590 WARNING @ Sun, 04 Jun 2017 05:11:23: #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 05:11:23: #3 Call peaks... INFO @ Sun, 04 Jun 2017 05:11:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 05:11:23: start X-correlation... INFO @ Sun, 04 Jun 2017 05:11:23: end of X-cor INFO @ Sun, 04 Jun 2017 05:11:23: #2 finished! INFO @ Sun, 04 Jun 2017 05:11:23: #2 predicted fragment length is 37 bps INFO @ Sun, 04 Jun 2017 05:11:23: #2 alternative fragment length(s) may be 1,37,58,107,140,173,207,250,288,394,490,513,529,559,590 bps INFO @ Sun, 04 Jun 2017 05:11:23: #2.2 Generate R script for model : SRX977475.20_model.r INFO @ Sun, 04 Jun 2017 05:11:23: start X-correlation... INFO @ Sun, 04 Jun 2017 05:11:23: end of X-cor INFO @ Sun, 04 Jun 2017 05:11:23: #2 finished! INFO @ Sun, 04 Jun 2017 05:11:23: #2 predicted fragment length is 37 bps INFO @ Sun, 04 Jun 2017 05:11:23: #2 alternative fragment length(s) may be 1,37,58,107,140,173,207,250,288,394,490,513,529,559,590 bps INFO @ Sun, 04 Jun 2017 05:11:23: #2.2 Generate R script for model : SRX977475.10_model.r WARNING @ Sun, 04 Jun 2017 05:11:23: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Jun 2017 05:11:23: #2 You may need to consider one of the other alternative d(s): 1,37,58,107,140,173,207,250,288,394,490,513,529,559,590 WARNING @ Sun, 04 Jun 2017 05:11:23: #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 05:11:23: #3 Call peaks... INFO @ Sun, 04 Jun 2017 05:11:23: #3 Pre-compute pvalue-qvalue table... WARNING @ Sun, 04 Jun 2017 05:11:23: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Jun 2017 05:11:23: #2 You may need to consider one of the other alternative d(s): 1,37,58,107,140,173,207,250,288,394,490,513,529,559,590 WARNING @ Sun, 04 Jun 2017 05:11:23: #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 05:11:23: #3 Call peaks... INFO @ Sun, 04 Jun 2017 05:11:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 05:11:23: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 05:11:24: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 05:11:24: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 04 Jun 2017 05:11:24: #4 Write output xls file... SRX977475.05_peaks.xls INFO @ Sun, 04 Jun 2017 05:11:24: #4 Write peak in narrowPeak format file... SRX977475.05_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 05:11:24: #4 Write summits bed file... SRX977475.05_summits.bed INFO @ Sun, 04 Jun 2017 05:11:24: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (136 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 05:11:24: #4 Write output xls file... SRX977475.10_peaks.xls INFO @ Sun, 04 Jun 2017 05:11:24: #4 Write peak in narrowPeak format file... SRX977475.10_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 05:11:24: #4 Write summits bed file... SRX977475.10_summits.bed INFO @ Sun, 04 Jun 2017 05:11:24: Done! INFO @ Sun, 04 Jun 2017 05:11:24: #4 Write output xls file... SRX977475.20_peaks.xls INFO @ Sun, 04 Jun 2017 05:11:24: #4 Write peak in narrowPeak format file... SRX977475.20_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 05:11:24: #4 Write summits bed file... SRX977475.20_summits.bed INFO @ Sun, 04 Jun 2017 05:11:24: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (35 records, 4 fields): 2 millis CompletedMACS2peakCalling pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (16 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。