Job ID = 3001502 sra ファイルのダウンロード中... Completed: 24090K bytes transferred in 3 seconds (49473K 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 --:--:-- --:--:-- --:--:-- 0 100 4000 0 4000 0 0 6439 0 --:--:-- --:--:-- --:--:-- 9569 100 14953 0 14953 0 0 8254 0 --:--:-- 0:00:01 --:--:-- 9299 100 14953 0 14953 0 0 5315 0 --:--:-- 0:00:02 --:--:-- 5729 100 14953 0 14953 0 0 3919 0 --:--:-- 0:00:03 --:--:-- 4140 100 14953 0 14953 0 0 3104 0 --:--:-- 0:00:04 --:--:-- 3241 100 14953 0 14953 0 0 2569 0 --:--:-- 0:00:05 --:--:-- 2107 100 14953 0 14953 0 0 2192 0 --:--:-- 0:00:06 --:--:-- 0 100 16407 0 16407 0 0 2147 0 --:--:-- 0:00:07 --:--:-- 301 100 34675 0 34675 0 0 4429 0 --:--:-- 0:00:07 --:--:-- 4914 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 1576729 spots for /home/okishinya/chipatlas/results/ce10/SRX005636/SRR017605.sra Written 1576729 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: 00:00:11 1576729 reads; of these: 1576729 (100.00%) were unpaired; of these: 918695 (58.27%) aligned 0 times 491531 (31.17%) aligned exactly 1 time 166503 (10.56%) aligned >1 times 41.73% overall alignment rate Time searching: 00:00:11 Overall time: 00:00:12 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 74480 / 658034 = 0.1132 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 @ Mon, 07 Sep 2015 18:45:11: # Command line: callpeak -t SRX005636.bam -f BAM -g ce -n SRX005636.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX005636.20 # format = BAM # ChIP-seq file = ['SRX005636.bam'] # control file = None # effective genome size = 9.00e+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 @ Mon, 07 Sep 2015 18:45:11: # Command line: callpeak -t SRX005636.bam -f BAM -g ce -n SRX005636.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX005636.05 # format = BAM # ChIP-seq file = ['SRX005636.bam'] # control file = None # effective genome size = 9.00e+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 @ Mon, 07 Sep 2015 18:45:11: # Command line: callpeak -t SRX005636.bam -f BAM -g ce -n SRX005636.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX005636.10 # format = BAM # ChIP-seq file = ['SRX005636.bam'] # control file = None # effective genome size = 9.00e+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 @ Mon, 07 Sep 2015 18:45:11: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:45:11: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:45:11: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:45:11: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:45:11: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:45:11: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:45:14: #1 tag size is determined as 27 bps INFO @ Mon, 07 Sep 2015 18:45:14: #1 tag size = 27 INFO @ Mon, 07 Sep 2015 18:45:14: #1 total tags in treatment: 583554 INFO @ Mon, 07 Sep 2015 18:45:14: #1 user defined the maximum tags... INFO @ Mon, 07 Sep 2015 18:45:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 07 Sep 2015 18:45:14: #1 tag size is determined as 27 bps INFO @ Mon, 07 Sep 2015 18:45:14: #1 tag size = 27 INFO @ Mon, 07 Sep 2015 18:45:14: #1 total tags in treatment: 583554 INFO @ Mon, 07 Sep 2015 18:45:14: #1 user defined the maximum tags... INFO @ Mon, 07 Sep 2015 18:45:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 07 Sep 2015 18:45:14: #1 tags after filtering in treatment: 583552 INFO @ Mon, 07 Sep 2015 18:45:14: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 Sep 2015 18:45:14: #1 finished! INFO @ Mon, 07 Sep 2015 18:45:14: #2 Build Peak Model... INFO @ Mon, 07 Sep 2015 18:45:15: #1 tags after filtering in treatment: 583552 INFO @ Mon, 07 Sep 2015 18:45:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 Sep 2015 18:45:15: #1 finished! INFO @ Mon, 07 Sep 2015 18:45:15: #2 Build Peak Model... INFO @ Mon, 07 Sep 2015 18:45:15: #1 tag size is determined as 27 bps INFO @ Mon, 07 Sep 2015 18:45:15: #1 tag size = 27 INFO @ Mon, 07 Sep 2015 18:45:15: #1 total tags in treatment: 583554 INFO @ Mon, 07 Sep 2015 18:45:15: #1 user defined the maximum tags... INFO @ Mon, 07 Sep 2015 18:45:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 07 Sep 2015 18:45:15: #2 number of paired peaks: 339 WARNING @ Mon, 07 Sep 2015 18:45:15: Fewer paired peaks (339) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 339 pairs to build model! INFO @ Mon, 07 Sep 2015 18:45:15: start model_add_line... INFO @ Mon, 07 Sep 2015 18:45:15: #2 number of paired peaks: 339 WARNING @ Mon, 07 Sep 2015 18:45:15: Fewer paired peaks (339) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 339 pairs to build model! INFO @ Mon, 07 Sep 2015 18:45:15: start model_add_line... INFO @ Mon, 07 Sep 2015 18:45:15: #1 tags after filtering in treatment: 583552 INFO @ Mon, 07 Sep 2015 18:45:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 Sep 2015 18:45:15: #1 finished! INFO @ Mon, 07 Sep 2015 18:45:15: #2 Build Peak Model... INFO @ Mon, 07 Sep 2015 18:45:15: #2 number of paired peaks: 339 WARNING @ Mon, 07 Sep 2015 18:45:15: Fewer paired peaks (339) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 339 pairs to build model! INFO @ Mon, 07 Sep 2015 18:45:15: start model_add_line... INFO @ Mon, 07 Sep 2015 18:45:15: start X-correlation... INFO @ Mon, 07 Sep 2015 18:45:15: start X-correlation... INFO @ Mon, 07 Sep 2015 18:45:15: end of X-cor INFO @ Mon, 07 Sep 2015 18:45:15: end of X-cor INFO @ Mon, 07 Sep 2015 18:45:15: #2 finished! INFO @ Mon, 07 Sep 2015 18:45:15: #2 finished! INFO @ Mon, 07 Sep 2015 18:45:15: #2 predicted fragment length is 32 bps INFO @ Mon, 07 Sep 2015 18:45:15: #2 predicted fragment length is 32 bps INFO @ Mon, 07 Sep 2015 18:45:15: #2 alternative fragment length(s) may be 32,158,210,504,543 bps INFO @ Mon, 07 Sep 2015 18:45:15: #2 alternative fragment length(s) may be 32,158,210,504,543 bps INFO @ Mon, 07 Sep 2015 18:45:15: #2.2 Generate R script for model : SRX005636.10_model.r INFO @ Mon, 07 Sep 2015 18:45:15: #2.2 Generate R script for model : SRX005636.20_model.r WARNING @ Mon, 07 Sep 2015 18:45:15: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 07 Sep 2015 18:45:15: #2 You may need to consider one of the other alternative d(s): 32,158,210,504,543 WARNING @ Mon, 07 Sep 2015 18:45:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 07 Sep 2015 18:45:15: #3 Call peaks... WARNING @ Mon, 07 Sep 2015 18:45:15: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 07 Sep 2015 18:45:15: #2 You may need to consider one of the other alternative d(s): 32,158,210,504,543 WARNING @ Mon, 07 Sep 2015 18:45:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 07 Sep 2015 18:45:15: #3 Call peaks... INFO @ Mon, 07 Sep 2015 18:45:15: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 Sep 2015 18:45:15: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 Sep 2015 18:45:15: start X-correlation... INFO @ Mon, 07 Sep 2015 18:45:15: end of X-cor INFO @ Mon, 07 Sep 2015 18:45:15: #2 finished! INFO @ Mon, 07 Sep 2015 18:45:15: #2 predicted fragment length is 32 bps INFO @ Mon, 07 Sep 2015 18:45:15: #2 alternative fragment length(s) may be 32,158,210,504,543 bps INFO @ Mon, 07 Sep 2015 18:45:15: #2.2 Generate R script for model : SRX005636.05_model.r WARNING @ Mon, 07 Sep 2015 18:45:15: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 07 Sep 2015 18:45:15: #2 You may need to consider one of the other alternative d(s): 32,158,210,504,543 WARNING @ Mon, 07 Sep 2015 18:45:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 07 Sep 2015 18:45:15: #3 Call peaks... INFO @ Mon, 07 Sep 2015 18:45:15: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 Sep 2015 18:45:19: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:45:19: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:45:19: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:45:21: #4 Write output xls file... SRX005636.20_peaks.xls INFO @ Mon, 07 Sep 2015 18:45:21: #4 Write peak in narrowPeak format file... SRX005636.20_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:45:21: #4 Write summits bed file... SRX005636.20_summits.bed INFO @ Mon, 07 Sep 2015 18:45:21: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (11 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 07 Sep 2015 18:45:21: #4 Write output xls file... SRX005636.10_peaks.xls INFO @ Mon, 07 Sep 2015 18:45:21: #4 Write peak in narrowPeak format file... SRX005636.10_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:45:21: #4 Write summits bed file... SRX005636.10_summits.bed INFO @ Mon, 07 Sep 2015 18:45:21: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (61 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Mon, 07 Sep 2015 18:45:22: #4 Write output xls file... SRX005636.05_peaks.xls INFO @ Mon, 07 Sep 2015 18:45:22: #4 Write peak in narrowPeak format file... SRX005636.05_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:45:22: #4 Write summits bed file... SRX005636.05_summits.bed INFO @ Mon, 07 Sep 2015 18:45:22: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (139 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。