Job ID = 9035829 sra ファイルのダウンロード中... Completed: 1097273K bytes transferred in 13 seconds (687444K 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 0 0 0 0 0 0 0 0 --:--:-- 0:00:11 --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:12 --:--:-- 0 100 7663 0 7663 0 0 593 0 --:--:-- 0:00:12 --:--:-- 1690 100 30317 0 30317 0 0 2178 0 --:--:-- 0:00:13 --:--:-- 6698 100 53413 0 53413 0 0 3622 0 --:--:-- 0:00:14 --:--:-- 12264 100 58342 0 58342 0 0 3956 0 --:--:-- 0:00:14 --:--:-- 17394 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 27547055 spots for /home/okishinya/chipatlas/results/sacCer3/SRX079681/SRR292352.sra Written 27547055 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: 00:09:29 27547055 reads; of these: 27547055 (100.00%) were unpaired; of these: 27535174 (99.96%) aligned 0 times 9564 (0.03%) aligned exactly 1 time 2317 (0.01%) aligned >1 times 0.04% overall alignment rate Time searching: 00:09:29 Overall time: 00:09:29 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] 1218 / 11881 = 0.1025 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 01:54:46: # Command line: callpeak -t SRX079681.bam -f BAM -g 12100000 -n SRX079681.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX079681.05 # format = BAM # ChIP-seq file = ['SRX079681.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 01:54:46: #1 read tag files... INFO @ Sun, 04 Jun 2017 01:54:46: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 01:54:46: # Command line: callpeak -t SRX079681.bam -f BAM -g 12100000 -n SRX079681.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX079681.20 # format = BAM # ChIP-seq file = ['SRX079681.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 01:54:46: #1 read tag files... INFO @ Sun, 04 Jun 2017 01:54:46: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 01:54:46: # Command line: callpeak -t SRX079681.bam -f BAM -g 12100000 -n SRX079681.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX079681.10 # format = BAM # ChIP-seq file = ['SRX079681.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 01:54:46: #1 read tag files... INFO @ Sun, 04 Jun 2017 01:54:46: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 04 Jun 2017 01:54:47: #1 tag size is determined as 72 bps INFO @ Sun, 04 Jun 2017 01:54:47: #1 tag size = 72 INFO @ Sun, 04 Jun 2017 01:54:47: #1 total tags in treatment: 10663 INFO @ Sun, 04 Jun 2017 01:54:47: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 01:54:47: #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 01:54:47: #1 tag size is determined as 72 bps INFO @ Sun, 04 Jun 2017 01:54:47: #1 tag size = 72 INFO @ Sun, 04 Jun 2017 01:54:47: #1 total tags in treatment: 10663 INFO @ Sun, 04 Jun 2017 01:54:47: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 01:54:47: #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 01:54:47: #1 tag size is determined as 72 bps INFO @ Sun, 04 Jun 2017 01:54:47: #1 tag size = 72 INFO @ Sun, 04 Jun 2017 01:54:47: #1 total tags in treatment: 10663 INFO @ Sun, 04 Jun 2017 01:54:47: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 01:54:47: #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 01:54:47: #1 tags after filtering in treatment: 10480 INFO @ Sun, 04 Jun 2017 01:54:47: #1 Redundant rate of treatment: 0.02 INFO @ Sun, 04 Jun 2017 01:54:47: #1 finished! INFO @ Sun, 04 Jun 2017 01:54:47: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 01:54:47: #1 tags after filtering in treatment: 10480 INFO @ Sun, 04 Jun 2017 01:54:47: #1 Redundant rate of treatment: 0.02 INFO @ Sun, 04 Jun 2017 01:54:47: #1 finished! INFO @ Sun, 04 Jun 2017 01:54:47: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 01:54:47: #1 tags after filtering in treatment: 10480 INFO @ Sun, 04 Jun 2017 01:54:47: #1 Redundant rate of treatment: 0.02 INFO @ Sun, 04 Jun 2017 01:54:47: #1 finished! INFO @ Sun, 04 Jun 2017 01:54:47: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 01:54:47: #2 number of paired peaks: 122 WARNING @ Sun, 04 Jun 2017 01:54:47: Fewer paired peaks (122) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 122 pairs to build model! INFO @ Sun, 04 Jun 2017 01:54:47: start model_add_line... INFO @ Sun, 04 Jun 2017 01:54:47: #2 number of paired peaks: 122 WARNING @ Sun, 04 Jun 2017 01:54:47: Fewer paired peaks (122) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 122 pairs to build model! INFO @ Sun, 04 Jun 2017 01:54:47: start model_add_line... INFO @ Sun, 04 Jun 2017 01:54:47: #2 number of paired peaks: 122 WARNING @ Sun, 04 Jun 2017 01:54:47: Fewer paired peaks (122) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 122 pairs to build model! INFO @ Sun, 04 Jun 2017 01:54:47: start model_add_line... INFO @ Sun, 04 Jun 2017 01:54:47: start X-correlation... INFO @ Sun, 04 Jun 2017 01:54:47: start X-correlation... INFO @ Sun, 04 Jun 2017 01:54:47: start X-correlation... BigWig に変換しました。 INFO @ Sun, 04 Jun 2017 01:54:47: end of X-cor INFO @ Sun, 04 Jun 2017 01:54:47: end of X-cor INFO @ Sun, 04 Jun 2017 01:54:47: #2 finished! INFO @ Sun, 04 Jun 2017 01:54:47: #2 finished! INFO @ Sun, 04 Jun 2017 01:54:47: #2 predicted fragment length is 87 bps INFO @ Sun, 04 Jun 2017 01:54:47: #2 predicted fragment length is 87 bps INFO @ Sun, 04 Jun 2017 01:54:47: #2 alternative fragment length(s) may be 2,87,130,161,225,284,343,374,404,445,524,551,586 bps INFO @ Sun, 04 Jun 2017 01:54:47: #2 alternative fragment length(s) may be 2,87,130,161,225,284,343,374,404,445,524,551,586 bps INFO @ Sun, 04 Jun 2017 01:54:47: #2.2 Generate R script for model : SRX079681.10_model.r INFO @ Sun, 04 Jun 2017 01:54:47: #2.2 Generate R script for model : SRX079681.20_model.r INFO @ Sun, 04 Jun 2017 01:54:47: end of X-cor INFO @ Sun, 04 Jun 2017 01:54:47: #2 finished! INFO @ Sun, 04 Jun 2017 01:54:47: #2 predicted fragment length is 87 bps INFO @ Sun, 04 Jun 2017 01:54:47: #2 alternative fragment length(s) may be 2,87,130,161,225,284,343,374,404,445,524,551,586 bps INFO @ Sun, 04 Jun 2017 01:54:47: #2.2 Generate R script for model : SRX079681.05_model.r WARNING @ Sun, 04 Jun 2017 01:54:47: #2 Since the d (87) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Jun 2017 01:54:47: #2 You may need to consider one of the other alternative d(s): 2,87,130,161,225,284,343,374,404,445,524,551,586 WARNING @ Sun, 04 Jun 2017 01:54:47: #2 Since the d (87) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Jun 2017 01:54:47: #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 01:54:47: #3 Call peaks... WARNING @ Sun, 04 Jun 2017 01:54:47: #2 You may need to consider one of the other alternative d(s): 2,87,130,161,225,284,343,374,404,445,524,551,586 WARNING @ Sun, 04 Jun 2017 01:54:47: #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 01:54:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 01:54:47: #3 Call peaks... INFO @ Sun, 04 Jun 2017 01:54:47: #3 Pre-compute pvalue-qvalue table... WARNING @ Sun, 04 Jun 2017 01:54:47: #2 Since the d (87) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Jun 2017 01:54:47: #2 You may need to consider one of the other alternative d(s): 2,87,130,161,225,284,343,374,404,445,524,551,586 WARNING @ Sun, 04 Jun 2017 01:54:47: #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 01:54:47: #3 Call peaks... INFO @ Sun, 04 Jun 2017 01:54:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 01:54:47: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 01:54:47: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 01:54:47: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 01:54:47: #4 Write output xls file... SRX079681.20_peaks.xls INFO @ Sun, 04 Jun 2017 01:54:47: #4 Write output xls file... SRX079681.10_peaks.xls INFO @ Sun, 04 Jun 2017 01:54:47: #4 Write output xls file... SRX079681.05_peaks.xls INFO @ Sun, 04 Jun 2017 01:54:47: #4 Write peak in narrowPeak format file... SRX079681.10_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 01:54:47: #4 Write peak in narrowPeak format file... SRX079681.20_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 01:54:47: #4 Write peak in narrowPeak format file... SRX079681.05_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 01:54:47: #4 Write summits bed file... SRX079681.20_summits.bed INFO @ Sun, 04 Jun 2017 01:54:47: #4 Write summits bed file... SRX079681.10_summits.bed INFO @ Sun, 04 Jun 2017 01:54:47: #4 Write summits bed file... SRX079681.05_summits.bed INFO @ Sun, 04 Jun 2017 01:54:47: Done! INFO @ Sun, 04 Jun 2017 01:54:47: Done! INFO @ Sun, 04 Jun 2017 01:54:47: Done! pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (1 records, 4 fields): 2 millis pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (3 records, 4 fields): 2 millis CompletedMACS2peakCalling pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (11 records, 4 fields): 2 millis CompletedMACS2peakCalling CompletedMACS2peakCalling