Job ID = 9037660 sra ファイルのダウンロード中... Completed: 420445K bytes transferred in 7 seconds (478501K 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 --:--:-- 0:00:08 --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:09 --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:10 --:--:-- 0 100 7663 0 7663 0 0 698 0 --:--:-- 0:00:10 --:--:-- 1698 100 30318 0 30318 0 0 2533 0 --:--:-- 0:00:11 --:--:-- 6726 100 64551 0 64551 0 0 4979 0 --:--:-- 0:00:12 --:--:-- 14335 100 66422 0 66422 0 0 5123 0 --:--:-- 0:00:12 --:--:-- 18961 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 16806250 spots for /home/okishinya/chipatlas/results/sacCer3/SRX977451/SRR1951297.sra Written 16806250 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: 00:01:55 16806250 reads; of these: 16806250 (100.00%) were unpaired; of these: 1571935 (9.35%) aligned 0 times 5925466 (35.26%) aligned exactly 1 time 9308849 (55.39%) aligned >1 times 90.65% overall alignment rate Time searching: 00:01:55 Overall time: 00:01:55 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 8 files... [bam_rmdupse_core] 14813731 / 15234315 = 0.9724 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 05:10:42: # Command line: callpeak -t SRX977451.bam -f BAM -g 12100000 -n SRX977451.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX977451.20 # format = BAM # ChIP-seq file = ['SRX977451.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 05:10:42: #1 read tag files... INFO @ Sun, 04 Jun 2017 05:10:42: # Command line: callpeak -t SRX977451.bam -f BAM -g 12100000 -n SRX977451.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX977451.10 # format = BAM # ChIP-seq file = ['SRX977451.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 05:10:42: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 05:10:42: #1 read tag files... INFO @ Sun, 04 Jun 2017 05:10:42: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 05:10:42: # Command line: callpeak -t SRX977451.bam -f BAM -g 12100000 -n SRX977451.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX977451.05 # format = BAM # ChIP-seq file = ['SRX977451.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 05:10:42: #1 read tag files... INFO @ Sun, 04 Jun 2017 05:10:42: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 05:10:44: #1 tag size is determined as 45 bps INFO @ Sun, 04 Jun 2017 05:10:44: #1 tag size = 45 INFO @ Sun, 04 Jun 2017 05:10:44: #1 total tags in treatment: 420584 INFO @ Sun, 04 Jun 2017 05:10:44: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 05:10:44: #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 05:10:44: #1 tag size is determined as 45 bps INFO @ Sun, 04 Jun 2017 05:10:44: #1 tag size = 45 INFO @ Sun, 04 Jun 2017 05:10:44: #1 total tags in treatment: 420584 INFO @ Sun, 04 Jun 2017 05:10:44: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 05:10:44: #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 05:10:44: #1 tag size is determined as 45 bps INFO @ Sun, 04 Jun 2017 05:10:44: #1 tag size = 45 INFO @ Sun, 04 Jun 2017 05:10:44: #1 total tags in treatment: 420584 INFO @ Sun, 04 Jun 2017 05:10:44: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 05:10:44: #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 05:10:44: #1 tags after filtering in treatment: 419686 INFO @ Sun, 04 Jun 2017 05:10:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 05:10:44: #1 finished! INFO @ Sun, 04 Jun 2017 05:10:44: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 05:10:44: #1 tags after filtering in treatment: 419686 INFO @ Sun, 04 Jun 2017 05:10:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 05:10:44: #1 finished! INFO @ Sun, 04 Jun 2017 05:10:44: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 05:10:44: #1 tags after filtering in treatment: 419686 INFO @ Sun, 04 Jun 2017 05:10:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 05:10:44: #1 finished! INFO @ Sun, 04 Jun 2017 05:10:44: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 05:10:44: #2 number of paired peaks: 312 WARNING @ Sun, 04 Jun 2017 05:10:44: Fewer paired peaks (312) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 312 pairs to build model! INFO @ Sun, 04 Jun 2017 05:10:44: start model_add_line... INFO @ Sun, 04 Jun 2017 05:10:44: #2 number of paired peaks: 312 WARNING @ Sun, 04 Jun 2017 05:10:44: Fewer paired peaks (312) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 312 pairs to build model! INFO @ Sun, 04 Jun 2017 05:10:44: start model_add_line... INFO @ Sun, 04 Jun 2017 05:10:44: #2 number of paired peaks: 312 WARNING @ Sun, 04 Jun 2017 05:10:44: Fewer paired peaks (312) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 312 pairs to build model! INFO @ Sun, 04 Jun 2017 05:10:44: start model_add_line... INFO @ Sun, 04 Jun 2017 05:10:45: start X-correlation... INFO @ Sun, 04 Jun 2017 05:10:45: start X-correlation... INFO @ Sun, 04 Jun 2017 05:10:45: end of X-cor INFO @ Sun, 04 Jun 2017 05:10:45: #2 finished! INFO @ Sun, 04 Jun 2017 05:10:45: #2 predicted fragment length is 52 bps INFO @ Sun, 04 Jun 2017 05:10:45: #2 alternative fragment length(s) may be 52 bps INFO @ Sun, 04 Jun 2017 05:10:45: #2.2 Generate R script for model : SRX977451.10_model.r INFO @ Sun, 04 Jun 2017 05:10:45: end of X-cor INFO @ Sun, 04 Jun 2017 05:10:45: #2 finished! INFO @ Sun, 04 Jun 2017 05:10:45: #2 predicted fragment length is 52 bps INFO @ Sun, 04 Jun 2017 05:10:45: #2 alternative fragment length(s) may be 52 bps INFO @ Sun, 04 Jun 2017 05:10:45: #2.2 Generate R script for model : SRX977451.05_model.r WARNING @ Sun, 04 Jun 2017 05:10:45: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Jun 2017 05:10:45: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Sun, 04 Jun 2017 05:10:45: #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 05:10:45: #3 Call peaks... INFO @ Sun, 04 Jun 2017 05:10:45: #3 Pre-compute pvalue-qvalue table... WARNING @ Sun, 04 Jun 2017 05:10:45: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Jun 2017 05:10:45: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Sun, 04 Jun 2017 05:10:45: #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 05:10:45: #3 Call peaks... INFO @ Sun, 04 Jun 2017 05:10:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 05:10:45: start X-correlation... INFO @ Sun, 04 Jun 2017 05:10:45: end of X-cor INFO @ Sun, 04 Jun 2017 05:10:45: #2 finished! INFO @ Sun, 04 Jun 2017 05:10:45: #2 predicted fragment length is 52 bps INFO @ Sun, 04 Jun 2017 05:10:45: #2 alternative fragment length(s) may be 52 bps INFO @ Sun, 04 Jun 2017 05:10:45: #2.2 Generate R script for model : SRX977451.20_model.r WARNING @ Sun, 04 Jun 2017 05:10:45: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Jun 2017 05:10:45: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Sun, 04 Jun 2017 05:10:45: #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 05:10:45: #3 Call peaks... INFO @ Sun, 04 Jun 2017 05:10:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 05:10:47: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 05:10:48: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 05:10:48: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 05:10:49: #4 Write output xls file... SRX977451.10_peaks.xls INFO @ Sun, 04 Jun 2017 05:10:49: #4 Write output xls file... SRX977451.20_peaks.xls INFO @ Sun, 04 Jun 2017 05:10:49: #4 Write output xls file... SRX977451.05_peaks.xls INFO @ Sun, 04 Jun 2017 05:10:50: #4 Write peak in narrowPeak format file... SRX977451.20_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 05:10:50: #4 Write peak in narrowPeak format file... SRX977451.10_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 05:10:50: #4 Write summits bed file... SRX977451.20_summits.bed INFO @ Sun, 04 Jun 2017 05:10:50: Done! INFO @ Sun, 04 Jun 2017 05:10:50: #4 Write summits bed file... SRX977451.10_summits.bed INFO @ Sun, 04 Jun 2017 05:10:50: Done! INFO @ Sun, 04 Jun 2017 05:10:50: #4 Write peak in narrowPeak format file... SRX977451.05_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 05:10:50: #4 Write summits bed file... SRX977451.05_summits.bed INFO @ Sun, 04 Jun 2017 05:10:50: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (128 records, 4 fields): 3 millis pass1 - making usageList (16 chroms): 1 millis CompletedMACS2peakCalling pass2 - checking and writing primary data (267 records, 4 fields): 3 millis CompletedMACS2peakCalling pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (621 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。