Job ID = 9037680 sra ファイルのダウンロード中... Completed: 224163K bytes transferred in 4 seconds (368937K 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 6903 0 6903 0 0 869 0 --:--:-- 0:00:07 --:--:-- 4371 100 44191 0 44191 0 0 4926 0 --:--:-- 0:00:08 --:--:-- 16905 100 46062 0 46062 0 0 5063 0 --:--:-- 0:00:09 --:--:-- 16810 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 9985557 spots for /home/okishinya/chipatlas/results/sacCer3/SRX977471/SRR1951317.sra Written 9985557 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: 00:00:57 9985557 reads; of these: 9985557 (100.00%) were unpaired; of these: 5511402 (55.19%) aligned 0 times 3535434 (35.41%) aligned exactly 1 time 938721 (9.40%) aligned >1 times 44.81% overall alignment rate Time searching: 00:00:57 Overall time: 00:00:57 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] 4375886 / 4474155 = 0.9780 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 05:10:37: # Command line: callpeak -t SRX977471.bam -f BAM -g 12100000 -n SRX977471.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX977471.05 # format = BAM # ChIP-seq file = ['SRX977471.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 05:10:37: #1 read tag files... INFO @ Sun, 04 Jun 2017 05:10:37: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 05:10:37: # Command line: callpeak -t SRX977471.bam -f BAM -g 12100000 -n SRX977471.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX977471.10 # format = BAM # ChIP-seq file = ['SRX977471.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 05:10:37: #1 read tag files... INFO @ Sun, 04 Jun 2017 05:10:37: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 05:10:37: # Command line: callpeak -t SRX977471.bam -f BAM -g 12100000 -n SRX977471.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX977471.20 # format = BAM # ChIP-seq file = ['SRX977471.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 05:10:37: #1 read tag files... INFO @ Sun, 04 Jun 2017 05:10:37: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 05:10:38: #1 tag size is determined as 40 bps INFO @ Sun, 04 Jun 2017 05:10:38: #1 tag size = 40 INFO @ Sun, 04 Jun 2017 05:10:38: #1 total tags in treatment: 98269 INFO @ Sun, 04 Jun 2017 05:10:38: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 05:10:38: #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 05:10:38: #1 tag size is determined as 40 bps INFO @ Sun, 04 Jun 2017 05:10:38: #1 tag size = 40 INFO @ Sun, 04 Jun 2017 05:10:38: #1 total tags in treatment: 98269 INFO @ Sun, 04 Jun 2017 05:10:38: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 05:10:38: #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 05:10:38: #1 tags after filtering in treatment: 97972 INFO @ Sun, 04 Jun 2017 05:10:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 05:10:38: #1 finished! INFO @ Sun, 04 Jun 2017 05:10:38: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 05:10:38: #1 tag size is determined as 40 bps INFO @ Sun, 04 Jun 2017 05:10:38: #1 tag size = 40 INFO @ Sun, 04 Jun 2017 05:10:38: #1 total tags in treatment: 98269 INFO @ Sun, 04 Jun 2017 05:10:38: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 05:10:38: #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 05:10:38: #1 tags after filtering in treatment: 97972 INFO @ Sun, 04 Jun 2017 05:10:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 05:10:38: #1 finished! INFO @ Sun, 04 Jun 2017 05:10:38: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 05:10:38: #1 tags after filtering in treatment: 97972 INFO @ Sun, 04 Jun 2017 05:10:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 05:10:38: #1 finished! INFO @ Sun, 04 Jun 2017 05:10:38: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 05:10:38: #2 number of paired peaks: 422 WARNING @ Sun, 04 Jun 2017 05:10:38: Fewer paired peaks (422) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 422 pairs to build model! INFO @ Sun, 04 Jun 2017 05:10:38: start model_add_line... INFO @ Sun, 04 Jun 2017 05:10:38: #2 number of paired peaks: 422 WARNING @ Sun, 04 Jun 2017 05:10:38: Fewer paired peaks (422) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 422 pairs to build model! INFO @ Sun, 04 Jun 2017 05:10:38: start model_add_line... INFO @ Sun, 04 Jun 2017 05:10:38: #2 number of paired peaks: 422 WARNING @ Sun, 04 Jun 2017 05:10:38: Fewer paired peaks (422) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 422 pairs to build model! INFO @ Sun, 04 Jun 2017 05:10:38: start model_add_line... INFO @ Sun, 04 Jun 2017 05:10:38: start X-correlation... INFO @ Sun, 04 Jun 2017 05:10:38: end of X-cor INFO @ Sun, 04 Jun 2017 05:10:38: #2 finished! INFO @ Sun, 04 Jun 2017 05:10:38: #2 predicted fragment length is 39 bps INFO @ Sun, 04 Jun 2017 05:10:38: #2 alternative fragment length(s) may be 23,39,76,133,174,231,269,289,309,355,423,498,517,571 bps INFO @ Sun, 04 Jun 2017 05:10:38: #2.2 Generate R script for model : SRX977471.20_model.r WARNING @ Sun, 04 Jun 2017 05:10:38: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Jun 2017 05:10:38: #2 You may need to consider one of the other alternative d(s): 23,39,76,133,174,231,269,289,309,355,423,498,517,571 WARNING @ Sun, 04 Jun 2017 05:10:38: #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 05:10:38: #3 Call peaks... INFO @ Sun, 04 Jun 2017 05:10:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 05:10:38: start X-correlation... INFO @ Sun, 04 Jun 2017 05:10:38: start X-correlation... INFO @ Sun, 04 Jun 2017 05:10:38: end of X-cor INFO @ Sun, 04 Jun 2017 05:10:38: #2 finished! INFO @ Sun, 04 Jun 2017 05:10:38: #2 predicted fragment length is 39 bps INFO @ Sun, 04 Jun 2017 05:10:38: #2 alternative fragment length(s) may be 23,39,76,133,174,231,269,289,309,355,423,498,517,571 bps INFO @ Sun, 04 Jun 2017 05:10:38: #2.2 Generate R script for model : SRX977471.05_model.r INFO @ Sun, 04 Jun 2017 05:10:38: end of X-cor INFO @ Sun, 04 Jun 2017 05:10:38: #2 finished! INFO @ Sun, 04 Jun 2017 05:10:38: #2 predicted fragment length is 39 bps INFO @ Sun, 04 Jun 2017 05:10:38: #2 alternative fragment length(s) may be 23,39,76,133,174,231,269,289,309,355,423,498,517,571 bps INFO @ Sun, 04 Jun 2017 05:10:38: #2.2 Generate R script for model : SRX977471.10_model.r WARNING @ Sun, 04 Jun 2017 05:10:38: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Jun 2017 05:10:38: #2 You may need to consider one of the other alternative d(s): 23,39,76,133,174,231,269,289,309,355,423,498,517,571 WARNING @ Sun, 04 Jun 2017 05:10:38: #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 05:10:38: #3 Call peaks... INFO @ Sun, 04 Jun 2017 05:10:38: #3 Pre-compute pvalue-qvalue table... WARNING @ Sun, 04 Jun 2017 05:10:38: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Jun 2017 05:10:38: #2 You may need to consider one of the other alternative d(s): 23,39,76,133,174,231,269,289,309,355,423,498,517,571 WARNING @ Sun, 04 Jun 2017 05:10:38: #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 05:10:38: #3 Call peaks... INFO @ Sun, 04 Jun 2017 05:10:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 05:10:39: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 05:10:39: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 05:10:39: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 04 Jun 2017 05:10:39: #4 Write output xls file... SRX977471.20_peaks.xls INFO @ Sun, 04 Jun 2017 05:10:39: #4 Write peak in narrowPeak format file... SRX977471.20_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 05:10:39: #4 Write summits bed file... SRX977471.20_summits.bed INFO @ Sun, 04 Jun 2017 05:10:39: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (18 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 05:10:39: #4 Write output xls file... SRX977471.05_peaks.xls INFO @ Sun, 04 Jun 2017 05:10:39: #4 Write output xls file... SRX977471.10_peaks.xls INFO @ Sun, 04 Jun 2017 05:10:39: #4 Write peak in narrowPeak format file... SRX977471.05_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 05:10:39: #4 Write peak in narrowPeak format file... SRX977471.10_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 05:10:39: #4 Write summits bed file... SRX977471.05_summits.bed INFO @ Sun, 04 Jun 2017 05:10:39: #4 Write summits bed file... SRX977471.10_summits.bed INFO @ Sun, 04 Jun 2017 05:10:40: Done! INFO @ Sun, 04 Jun 2017 05:10:40: Done! pass1 - making usageList (15 chroms): 0 millis pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (35 records, 4 fields)pass2 - checking and writing primary data (56 records, 4 fields): 2 millis : 2 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BigWig に変換しました。