Job ID = 2236684 sra ファイルのダウンロード中... Completed: 96670K bytes transferred in 4 seconds (180138K 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 --:--:-- --:--:-- --:--:-- 0 101 2547 0 2547 0 0 4854 0 --:--:-- --:--:-- --:--:-- 7625 100 34341 0 34341 0 0 48054 0 --:--:-- --:--:-- --:--:-- 65536 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 4009487 spots for /home/okishinya/chipatlas/results/ce10/SRX015093/SRR032437.sra Written 4009487 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: 00:00:33 4009487 reads; of these: 4009487 (100.00%) were unpaired; of these: 2265088 (56.49%) aligned 0 times 1529154 (38.14%) aligned exactly 1 time 215245 (5.37%) aligned >1 times 43.51% overall alignment rate Time searching: 00:00:33 Overall time: 00:00:33 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] 130763 / 1744399 = 0.0750 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 @ Thu, 30 Apr 2015 10:55:00: # Command line: callpeak -t SRX015093.bam -f BAM -g ce -n SRX015093.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX015093.05 # format = BAM # ChIP-seq file = ['SRX015093.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 @ Thu, 30 Apr 2015 10:55:00: # Command line: callpeak -t SRX015093.bam -f BAM -g ce -n SRX015093.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX015093.10 # format = BAM # ChIP-seq file = ['SRX015093.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 @ Thu, 30 Apr 2015 10:55:00: #1 read tag files... INFO @ Thu, 30 Apr 2015 10:55:00: #1 read tag files... INFO @ Thu, 30 Apr 2015 10:55:00: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 10:55:00: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 10:55:00: # Command line: callpeak -t SRX015093.bam -f BAM -g ce -n SRX015093.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX015093.20 # format = BAM # ChIP-seq file = ['SRX015093.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 @ Thu, 30 Apr 2015 10:55:00: #1 read tag files... INFO @ Thu, 30 Apr 2015 10:55:00: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 10:55:05: 1000000 INFO @ Thu, 30 Apr 2015 10:55:05: 1000000 INFO @ Thu, 30 Apr 2015 10:55:05: 1000000 INFO @ Thu, 30 Apr 2015 10:55:08: #1 tag size is determined as 34 bps INFO @ Thu, 30 Apr 2015 10:55:08: #1 tag size = 34 INFO @ Thu, 30 Apr 2015 10:55:08: #1 total tags in treatment: 1613636 INFO @ Thu, 30 Apr 2015 10:55:08: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 10:55:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 30 Apr 2015 10:55:08: #1 tag size is determined as 34 bps INFO @ Thu, 30 Apr 2015 10:55:08: #1 tag size = 34 INFO @ Thu, 30 Apr 2015 10:55:08: #1 total tags in treatment: 1613636 INFO @ Thu, 30 Apr 2015 10:55:08: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 10:55:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 30 Apr 2015 10:55:09: #1 tag size is determined as 34 bps INFO @ Thu, 30 Apr 2015 10:55:09: #1 tag size = 34 INFO @ Thu, 30 Apr 2015 10:55:09: #1 total tags in treatment: 1613636 INFO @ Thu, 30 Apr 2015 10:55:09: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 10:55:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 30 Apr 2015 10:55:09: #1 tags after filtering in treatment: 1612480 INFO @ Thu, 30 Apr 2015 10:55:09: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 10:55:09: #1 finished! INFO @ Thu, 30 Apr 2015 10:55:09: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 10:55:09: #1 tags after filtering in treatment: 1612480 INFO @ Thu, 30 Apr 2015 10:55:09: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 10:55:09: #1 finished! INFO @ Thu, 30 Apr 2015 10:55:09: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 10:55:09: #1 tags after filtering in treatment: 1612480 INFO @ Thu, 30 Apr 2015 10:55:09: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 10:55:09: #1 finished! INFO @ Thu, 30 Apr 2015 10:55:09: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 10:55:09: #2 number of paired peaks: 238 WARNING @ Thu, 30 Apr 2015 10:55:09: Fewer paired peaks (238) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 238 pairs to build model! INFO @ Thu, 30 Apr 2015 10:55:09: start model_add_line... INFO @ Thu, 30 Apr 2015 10:55:09: #2 number of paired peaks: 238 WARNING @ Thu, 30 Apr 2015 10:55:09: Fewer paired peaks (238) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 238 pairs to build model! INFO @ Thu, 30 Apr 2015 10:55:09: start model_add_line... INFO @ Thu, 30 Apr 2015 10:55:09: #2 number of paired peaks: 238 WARNING @ Thu, 30 Apr 2015 10:55:09: Fewer paired peaks (238) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 238 pairs to build model! INFO @ Thu, 30 Apr 2015 10:55:09: start model_add_line... INFO @ Thu, 30 Apr 2015 10:55:10: start X-correlation... INFO @ Thu, 30 Apr 2015 10:55:10: end of X-cor INFO @ Thu, 30 Apr 2015 10:55:10: #2 finished! INFO @ Thu, 30 Apr 2015 10:55:10: #2 predicted fragment length is 39 bps INFO @ Thu, 30 Apr 2015 10:55:10: #2 alternative fragment length(s) may be 39,89,538,574,598 bps INFO @ Thu, 30 Apr 2015 10:55:10: #2.2 Generate R script for model : SRX015093.05_model.r WARNING @ Thu, 30 Apr 2015 10:55:10: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 30 Apr 2015 10:55:10: #2 You may need to consider one of the other alternative d(s): 39,89,538,574,598 WARNING @ Thu, 30 Apr 2015 10:55:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 30 Apr 2015 10:55:10: #3 Call peaks... INFO @ Thu, 30 Apr 2015 10:55:10: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 10:55:10: start X-correlation... INFO @ Thu, 30 Apr 2015 10:55:10: end of X-cor INFO @ Thu, 30 Apr 2015 10:55:10: #2 finished! INFO @ Thu, 30 Apr 2015 10:55:10: #2 predicted fragment length is 39 bps INFO @ Thu, 30 Apr 2015 10:55:10: #2 alternative fragment length(s) may be 39,89,538,574,598 bps INFO @ Thu, 30 Apr 2015 10:55:10: #2.2 Generate R script for model : SRX015093.20_model.r INFO @ Thu, 30 Apr 2015 10:55:10: start X-correlation... INFO @ Thu, 30 Apr 2015 10:55:10: end of X-cor INFO @ Thu, 30 Apr 2015 10:55:10: #2 finished! INFO @ Thu, 30 Apr 2015 10:55:10: #2 predicted fragment length is 39 bps INFO @ Thu, 30 Apr 2015 10:55:10: #2 alternative fragment length(s) may be 39,89,538,574,598 bps INFO @ Thu, 30 Apr 2015 10:55:10: #2.2 Generate R script for model : SRX015093.10_model.r WARNING @ Thu, 30 Apr 2015 10:55:10: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 30 Apr 2015 10:55:10: #2 You may need to consider one of the other alternative d(s): 39,89,538,574,598 WARNING @ Thu, 30 Apr 2015 10:55:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 30 Apr 2015 10:55:10: #3 Call peaks... INFO @ Thu, 30 Apr 2015 10:55:10: #3 Pre-compute pvalue-qvalue table... WARNING @ Thu, 30 Apr 2015 10:55:10: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 30 Apr 2015 10:55:10: #2 You may need to consider one of the other alternative d(s): 39,89,538,574,598 WARNING @ Thu, 30 Apr 2015 10:55:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 30 Apr 2015 10:55:10: #3 Call peaks... INFO @ Thu, 30 Apr 2015 10:55:10: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 10:55:19: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 10:55:19: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 10:55:20: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 10:55:26: #4 Write output xls file... SRX015093.20_peaks.xls INFO @ Thu, 30 Apr 2015 10:55:26: #4 Write peak in narrowPeak format file... SRX015093.20_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 10:55:26: #4 Write summits bed file... SRX015093.20_summits.bed INFO @ Thu, 30 Apr 2015 10:55:26: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (3 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 10:55:26: #4 Write output xls file... SRX015093.10_peaks.xls INFO @ Thu, 30 Apr 2015 10:55:26: #4 Write peak in narrowPeak format file... SRX015093.10_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 10:55:26: #4 Write summits bed file... SRX015093.10_summits.bed INFO @ Thu, 30 Apr 2015 10:55:26: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (30 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 10:55:27: #4 Write output xls file... SRX015093.05_peaks.xls INFO @ Thu, 30 Apr 2015 10:55:27: #4 Write peak in narrowPeak format file... SRX015093.05_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 10:55:27: #4 Write summits bed file... SRX015093.05_summits.bed INFO @ Thu, 30 Apr 2015 10:55:27: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (97 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。