Job ID = 9037683 sra ファイルのダウンロード中... Completed: 191512K bytes transferred in 4 seconds (324036K 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 --:--:-- 0:00:06 --:--:-- 0 100 21558 0 21558 0 0 2797 0 --:--:-- 0:00:07 --:--:-- 16431 100 46496 0 46496 0 0 5554 0 --:--:-- 0:00:08 --:--:-- 23542 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 9673296 spots for /home/okishinya/chipatlas/results/sacCer3/SRX977474/SRR1951320.sra Written 9673296 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: 00:01:16 9673296 reads; of these: 9673296 (100.00%) were unpaired; of these: 1184751 (12.25%) aligned 0 times 7416203 (76.67%) aligned exactly 1 time 1072342 (11.09%) aligned >1 times 87.75% overall alignment rate Time searching: 00:01:16 Overall time: 00:01:16 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] 8249970 / 8488545 = 0.9719 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 05:11:38: # Command line: callpeak -t SRX977474.bam -f BAM -g 12100000 -n SRX977474.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX977474.10 # format = BAM # ChIP-seq file = ['SRX977474.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 05:11:38: #1 read tag files... INFO @ Sun, 04 Jun 2017 05:11:38: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 05:11:38: # Command line: callpeak -t SRX977474.bam -f BAM -g 12100000 -n SRX977474.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX977474.05 # format = BAM # ChIP-seq file = ['SRX977474.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 05:11:38: #1 read tag files... INFO @ Sun, 04 Jun 2017 05:11:38: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 05:11:38: # Command line: callpeak -t SRX977474.bam -f BAM -g 12100000 -n SRX977474.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX977474.20 # format = BAM # ChIP-seq file = ['SRX977474.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 05:11:38: #1 read tag files... INFO @ Sun, 04 Jun 2017 05:11:38: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 05:11:40: #1 tag size is determined as 40 bps INFO @ Sun, 04 Jun 2017 05:11:40: #1 tag size is determined as 40 bps INFO @ Sun, 04 Jun 2017 05:11:40: #1 tag size = 40 INFO @ Sun, 04 Jun 2017 05:11:40: #1 tag size = 40 INFO @ Sun, 04 Jun 2017 05:11:40: #1 total tags in treatment: 238575 INFO @ Sun, 04 Jun 2017 05:11:40: #1 total tags in treatment: 238575 INFO @ Sun, 04 Jun 2017 05:11:40: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 05:11:40: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 05:11:40: #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 05:11:40: #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 05:11:40: #1 tag size is determined as 40 bps INFO @ Sun, 04 Jun 2017 05:11:40: #1 tag size = 40 INFO @ Sun, 04 Jun 2017 05:11:40: #1 total tags in treatment: 238575 INFO @ Sun, 04 Jun 2017 05:11:40: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 05:11:40: #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 05:11:40: #1 tags after filtering in treatment: 238183 INFO @ Sun, 04 Jun 2017 05:11:40: #1 tags after filtering in treatment: 238183 INFO @ Sun, 04 Jun 2017 05:11:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 05:11:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 05:11:40: #1 finished! INFO @ Sun, 04 Jun 2017 05:11:40: #1 finished! INFO @ Sun, 04 Jun 2017 05:11:40: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 05:11:40: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 05:11:40: #1 tags after filtering in treatment: 238183 INFO @ Sun, 04 Jun 2017 05:11:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 05:11:40: #1 finished! INFO @ Sun, 04 Jun 2017 05:11:40: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 05:11:40: #2 number of paired peaks: 577 WARNING @ Sun, 04 Jun 2017 05:11:40: Fewer paired peaks (577) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 577 pairs to build model! INFO @ Sun, 04 Jun 2017 05:11:40: start model_add_line... INFO @ Sun, 04 Jun 2017 05:11:40: #2 number of paired peaks: 577 WARNING @ Sun, 04 Jun 2017 05:11:40: Fewer paired peaks (577) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 577 pairs to build model! INFO @ Sun, 04 Jun 2017 05:11:40: start model_add_line... INFO @ Sun, 04 Jun 2017 05:11:40: #2 number of paired peaks: 577 WARNING @ Sun, 04 Jun 2017 05:11:40: Fewer paired peaks (577) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 577 pairs to build model! INFO @ Sun, 04 Jun 2017 05:11:40: start model_add_line... INFO @ Sun, 04 Jun 2017 05:11:41: start X-correlation... INFO @ Sun, 04 Jun 2017 05:11:41: start X-correlation... INFO @ Sun, 04 Jun 2017 05:11:41: end of X-cor INFO @ Sun, 04 Jun 2017 05:11:41: #2 finished! INFO @ Sun, 04 Jun 2017 05:11:41: #2 predicted fragment length is 58 bps INFO @ Sun, 04 Jun 2017 05:11:41: #2 alternative fragment length(s) may be 58,418,464,486,518,548,570 bps INFO @ Sun, 04 Jun 2017 05:11:41: #2.2 Generate R script for model : SRX977474.05_model.r INFO @ Sun, 04 Jun 2017 05:11:41: end of X-cor INFO @ Sun, 04 Jun 2017 05:11:41: #2 finished! INFO @ Sun, 04 Jun 2017 05:11:41: #2 predicted fragment length is 58 bps INFO @ Sun, 04 Jun 2017 05:11:41: #2 alternative fragment length(s) may be 58,418,464,486,518,548,570 bps INFO @ Sun, 04 Jun 2017 05:11:41: #2.2 Generate R script for model : SRX977474.10_model.r WARNING @ Sun, 04 Jun 2017 05:11:41: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Jun 2017 05:11:41: #2 You may need to consider one of the other alternative d(s): 58,418,464,486,518,548,570 WARNING @ Sun, 04 Jun 2017 05:11:41: #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 05:11:41: #3 Call peaks... INFO @ Sun, 04 Jun 2017 05:11:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 05:11:41: start X-correlation... WARNING @ Sun, 04 Jun 2017 05:11:41: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Jun 2017 05:11:41: #2 You may need to consider one of the other alternative d(s): 58,418,464,486,518,548,570 WARNING @ Sun, 04 Jun 2017 05:11:41: #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 05:11:41: #3 Call peaks... INFO @ Sun, 04 Jun 2017 05:11:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 05:11:41: end of X-cor INFO @ Sun, 04 Jun 2017 05:11:41: #2 finished! INFO @ Sun, 04 Jun 2017 05:11:41: #2 predicted fragment length is 58 bps INFO @ Sun, 04 Jun 2017 05:11:41: #2 alternative fragment length(s) may be 58,418,464,486,518,548,570 bps INFO @ Sun, 04 Jun 2017 05:11:41: #2.2 Generate R script for model : SRX977474.20_model.r WARNING @ Sun, 04 Jun 2017 05:11:41: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Jun 2017 05:11:41: #2 You may need to consider one of the other alternative d(s): 58,418,464,486,518,548,570 WARNING @ Sun, 04 Jun 2017 05:11:41: #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 05:11:41: #3 Call peaks... INFO @ Sun, 04 Jun 2017 05:11:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 05:11:43: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 05:11:43: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 05:11:43: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 04 Jun 2017 05:11:44: #4 Write output xls file... SRX977474.10_peaks.xls INFO @ Sun, 04 Jun 2017 05:11:44: #4 Write peak in narrowPeak format file... SRX977474.10_peaks.narrowPeak BigWig に変換しました。 INFO @ Sun, 04 Jun 2017 05:11:44: #4 Write summits bed file... SRX977474.10_summits.bed INFO @ Sun, 04 Jun 2017 05:11:44: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (168 records, 4 fields): 3 millis INFO @ Sun, 04 Jun 2017 05:11:44: #4 Write output xls file... SRX977474.05_peaks.xls CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 05:11:44: #4 Write peak in narrowPeak format file... SRX977474.05_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 05:11:44: #4 Write summits bed file... SRX977474.05_summits.bed INFO @ Sun, 04 Jun 2017 05:11:44: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (366 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 05:11:44: #4 Write output xls file... SRX977474.20_peaks.xls INFO @ Sun, 04 Jun 2017 05:11:44: #4 Write peak in narrowPeak format file... SRX977474.20_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 05:11:44: #4 Write summits bed file... SRX977474.20_summits.bed INFO @ Sun, 04 Jun 2017 05:11:44: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (30 records, 4 fields): 2 millis CompletedMACS2peakCalling