Job ID = 2162165 sra ファイルのダウンロード中... Completed: 136271K bytes transferred in 4 seconds (248810K 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 6919 0 6919 0 0 14057 0 --:--:-- --:--:-- --:--:-- 22986 100 35455 0 35455 0 0 51991 0 --:--:-- --:--:-- --:--:-- 72209 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 6948791 spots for /home/okishinya/chipatlas/results/dm3/SRX050601/SRR139083.sra Written 6948791 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: 00:02:09 6948791 reads; of these: 6948791 (100.00%) were unpaired; of these: 270276 (3.89%) aligned 0 times 4927986 (70.92%) aligned exactly 1 time 1750529 (25.19%) aligned >1 times 96.11% overall alignment rate Time searching: 00:02:09 Overall time: 00:02:09 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 214279 / 6678515 = 0.0321 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 @ Tue, 21 Apr 2015 13:35:33: # Command line: callpeak -t SRX050601.bam -f BAM -g dm -n SRX050601.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX050601.10 # format = BAM # ChIP-seq file = ['SRX050601.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Tue, 21 Apr 2015 13:35:33: # Command line: callpeak -t SRX050601.bam -f BAM -g dm -n SRX050601.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX050601.05 # format = BAM # ChIP-seq file = ['SRX050601.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Tue, 21 Apr 2015 13:35:33: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:35:33: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:35:33: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:35:33: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:35:33: # Command line: callpeak -t SRX050601.bam -f BAM -g dm -n SRX050601.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX050601.20 # format = BAM # ChIP-seq file = ['SRX050601.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Tue, 21 Apr 2015 13:35:33: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:35:33: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:35:38: 1000000 INFO @ Tue, 21 Apr 2015 13:35:38: 1000000 INFO @ Tue, 21 Apr 2015 13:35:38: 1000000 INFO @ Tue, 21 Apr 2015 13:35:43: 2000000 INFO @ Tue, 21 Apr 2015 13:35:43: 2000000 INFO @ Tue, 21 Apr 2015 13:35:43: 2000000 INFO @ Tue, 21 Apr 2015 13:35:48: 3000000 INFO @ Tue, 21 Apr 2015 13:35:48: 3000000 INFO @ Tue, 21 Apr 2015 13:35:48: 3000000 INFO @ Tue, 21 Apr 2015 13:35:52: 4000000 INFO @ Tue, 21 Apr 2015 13:35:53: 4000000 INFO @ Tue, 21 Apr 2015 13:35:53: 4000000 INFO @ Tue, 21 Apr 2015 13:35:57: 5000000 INFO @ Tue, 21 Apr 2015 13:35:58: 5000000 INFO @ Tue, 21 Apr 2015 13:35:58: 5000000 INFO @ Tue, 21 Apr 2015 13:36:02: 6000000 INFO @ Tue, 21 Apr 2015 13:36:03: 6000000 INFO @ Tue, 21 Apr 2015 13:36:03: 6000000 INFO @ Tue, 21 Apr 2015 13:36:04: #1 tag size is determined as 30 bps INFO @ Tue, 21 Apr 2015 13:36:04: #1 tag size = 30 INFO @ Tue, 21 Apr 2015 13:36:04: #1 total tags in treatment: 6464236 INFO @ Tue, 21 Apr 2015 13:36:04: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:36:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 21 Apr 2015 13:36:05: #1 tag size is determined as 30 bps INFO @ Tue, 21 Apr 2015 13:36:05: #1 tag size = 30 INFO @ Tue, 21 Apr 2015 13:36:05: #1 total tags in treatment: 6464236 INFO @ Tue, 21 Apr 2015 13:36:05: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:36:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 21 Apr 2015 13:36:05: #1 tags after filtering in treatment: 6464117 INFO @ Tue, 21 Apr 2015 13:36:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:36:05: #1 finished! INFO @ Tue, 21 Apr 2015 13:36:05: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:36:05: #1 tag size is determined as 30 bps INFO @ Tue, 21 Apr 2015 13:36:05: #1 tag size = 30 INFO @ Tue, 21 Apr 2015 13:36:05: #1 total tags in treatment: 6464236 INFO @ Tue, 21 Apr 2015 13:36:05: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:36:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 21 Apr 2015 13:36:06: #1 tags after filtering in treatment: 6464117 INFO @ Tue, 21 Apr 2015 13:36:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:36:06: #1 finished! INFO @ Tue, 21 Apr 2015 13:36:06: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:36:06: #2 number of paired peaks: 163 WARNING @ Tue, 21 Apr 2015 13:36:06: Fewer paired peaks (163) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 163 pairs to build model! INFO @ Tue, 21 Apr 2015 13:36:06: start model_add_line... INFO @ Tue, 21 Apr 2015 13:36:06: #1 tags after filtering in treatment: 6464117 INFO @ Tue, 21 Apr 2015 13:36:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:36:06: #1 finished! INFO @ Tue, 21 Apr 2015 13:36:06: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:36:07: start X-correlation... INFO @ Tue, 21 Apr 2015 13:36:07: end of X-cor INFO @ Tue, 21 Apr 2015 13:36:07: #2 finished! INFO @ Tue, 21 Apr 2015 13:36:07: #2 predicted fragment length is 36 bps INFO @ Tue, 21 Apr 2015 13:36:07: #2 alternative fragment length(s) may be 36 bps INFO @ Tue, 21 Apr 2015 13:36:07: #2.2 Generate R script for model : SRX050601.20_model.r WARNING @ Tue, 21 Apr 2015 13:36:07: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 13:36:07: #2 You may need to consider one of the other alternative d(s): 36 WARNING @ Tue, 21 Apr 2015 13:36:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 21 Apr 2015 13:36:07: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:36:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:36:07: #2 number of paired peaks: 163 WARNING @ Tue, 21 Apr 2015 13:36:07: Fewer paired peaks (163) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 163 pairs to build model! INFO @ Tue, 21 Apr 2015 13:36:07: start model_add_line... INFO @ Tue, 21 Apr 2015 13:36:08: #2 number of paired peaks: 163 WARNING @ Tue, 21 Apr 2015 13:36:08: Fewer paired peaks (163) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 163 pairs to build model! INFO @ Tue, 21 Apr 2015 13:36:08: start model_add_line... INFO @ Tue, 21 Apr 2015 13:36:08: start X-correlation... INFO @ Tue, 21 Apr 2015 13:36:08: end of X-cor INFO @ Tue, 21 Apr 2015 13:36:08: #2 finished! INFO @ Tue, 21 Apr 2015 13:36:08: #2 predicted fragment length is 36 bps INFO @ Tue, 21 Apr 2015 13:36:08: #2 alternative fragment length(s) may be 36 bps INFO @ Tue, 21 Apr 2015 13:36:08: #2.2 Generate R script for model : SRX050601.10_model.r WARNING @ Tue, 21 Apr 2015 13:36:08: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 13:36:08: #2 You may need to consider one of the other alternative d(s): 36 WARNING @ Tue, 21 Apr 2015 13:36:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 21 Apr 2015 13:36:08: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:36:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:36:08: start X-correlation... INFO @ Tue, 21 Apr 2015 13:36:08: end of X-cor INFO @ Tue, 21 Apr 2015 13:36:08: #2 finished! INFO @ Tue, 21 Apr 2015 13:36:08: #2 predicted fragment length is 36 bps INFO @ Tue, 21 Apr 2015 13:36:08: #2 alternative fragment length(s) may be 36 bps INFO @ Tue, 21 Apr 2015 13:36:08: #2.2 Generate R script for model : SRX050601.05_model.r WARNING @ Tue, 21 Apr 2015 13:36:08: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 13:36:08: #2 You may need to consider one of the other alternative d(s): 36 WARNING @ Tue, 21 Apr 2015 13:36:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 21 Apr 2015 13:36:08: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:36:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:36:43: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:36:44: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:36:45: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:37:11: #4 Write output xls file... SRX050601.20_peaks.xls INFO @ Tue, 21 Apr 2015 13:37:11: #4 Write peak in narrowPeak format file... SRX050601.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:37:11: #4 Write summits bed file... SRX050601.20_summits.bed INFO @ Tue, 21 Apr 2015 13:37:11: Done! pass1 - making usageList (7 chroms): 1 millis INFO @ Tue, 21 Apr 2015 13:37:11: #4 Write output xls file... SRX050601.05_peaks.xls pass2 - checking and writing primary data (551 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:37:11: #4 Write peak in narrowPeak format file... SRX050601.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:37:11: #4 Write summits bed file... SRX050601.05_summits.bed INFO @ Tue, 21 Apr 2015 13:37:11: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (1286 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:37:11: #4 Write output xls file... SRX050601.10_peaks.xls INFO @ Tue, 21 Apr 2015 13:37:11: #4 Write peak in narrowPeak format file... SRX050601.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:37:11: #4 Write summits bed file... SRX050601.10_summits.bed INFO @ Tue, 21 Apr 2015 13:37:11: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (937 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。