Job ID = 6983656 sra ファイルのダウンロード中... Completed: 288357K bytes transferred in 7 seconds (312412K 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 35003 0 35003 0 0 45355 0 --:--:-- --:--:-- --:--:-- 58927 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 11549071 spots for /home/okishinya/chipatlas/results/dm3/SRX017463/SRR037520.sra Written 11549071 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: 00:01:57 11549071 reads; of these: 11549071 (100.00%) were unpaired; of these: 7213586 (62.46%) aligned 0 times 3126844 (27.07%) aligned exactly 1 time 1208641 (10.47%) aligned >1 times 37.54% overall alignment rate Time searching: 00:01:57 Overall time: 00:01:57 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] 986838 / 4335485 = 0.2276 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, 05 Jun 2016 15:34:00: # Command line: callpeak -t SRX017463.bam -f BAM -g dm -n SRX017463.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX017463.20 # format = BAM # ChIP-seq file = ['SRX017463.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 @ Sun, 05 Jun 2016 15:34:00: # Command line: callpeak -t SRX017463.bam -f BAM -g dm -n SRX017463.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX017463.10 # format = BAM # ChIP-seq file = ['SRX017463.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 @ Sun, 05 Jun 2016 15:34:00: #1 read tag files... INFO @ Sun, 05 Jun 2016 15:34:00: #1 read tag files... INFO @ Sun, 05 Jun 2016 15:34:00: # Command line: callpeak -t SRX017463.bam -f BAM -g dm -n SRX017463.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX017463.05 # format = BAM # ChIP-seq file = ['SRX017463.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 @ Sun, 05 Jun 2016 15:34:00: #1 read treatment tags... INFO @ Sun, 05 Jun 2016 15:34:00: #1 read treatment tags... INFO @ Sun, 05 Jun 2016 15:34:00: #1 read tag files... INFO @ Sun, 05 Jun 2016 15:34:00: #1 read treatment tags... INFO @ Sun, 05 Jun 2016 15:34:05: 1000000 INFO @ Sun, 05 Jun 2016 15:34:05: 1000000 INFO @ Sun, 05 Jun 2016 15:34:05: 1000000 INFO @ Sun, 05 Jun 2016 15:34:10: 2000000 INFO @ Sun, 05 Jun 2016 15:34:10: 2000000 INFO @ Sun, 05 Jun 2016 15:34:10: 2000000 INFO @ Sun, 05 Jun 2016 15:34:15: 3000000 INFO @ Sun, 05 Jun 2016 15:34:15: 3000000 INFO @ Sun, 05 Jun 2016 15:34:15: 3000000 INFO @ Sun, 05 Jun 2016 15:34:17: #1 tag size is determined as 36 bps INFO @ Sun, 05 Jun 2016 15:34:17: #1 tag size = 36 INFO @ Sun, 05 Jun 2016 15:34:17: #1 total tags in treatment: 3348647 INFO @ Sun, 05 Jun 2016 15:34:17: #1 user defined the maximum tags... INFO @ Sun, 05 Jun 2016 15:34:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 05 Jun 2016 15:34:17: #1 tag size is determined as 36 bps INFO @ Sun, 05 Jun 2016 15:34:17: #1 tag size = 36 INFO @ Sun, 05 Jun 2016 15:34:17: #1 total tags in treatment: 3348647 INFO @ Sun, 05 Jun 2016 15:34:17: #1 user defined the maximum tags... INFO @ Sun, 05 Jun 2016 15:34:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 05 Jun 2016 15:34:17: #1 tag size is determined as 36 bps INFO @ Sun, 05 Jun 2016 15:34:17: #1 tag size = 36 INFO @ Sun, 05 Jun 2016 15:34:17: #1 total tags in treatment: 3348647 INFO @ Sun, 05 Jun 2016 15:34:17: #1 user defined the maximum tags... INFO @ Sun, 05 Jun 2016 15:34:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 05 Jun 2016 15:34:17: #1 tags after filtering in treatment: 3348517 INFO @ Sun, 05 Jun 2016 15:34:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 05 Jun 2016 15:34:17: #1 finished! INFO @ Sun, 05 Jun 2016 15:34:17: #2 Build Peak Model... INFO @ Sun, 05 Jun 2016 15:34:17: #1 tags after filtering in treatment: 3348517 INFO @ Sun, 05 Jun 2016 15:34:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 05 Jun 2016 15:34:17: #1 finished! INFO @ Sun, 05 Jun 2016 15:34:17: #2 Build Peak Model... INFO @ Sun, 05 Jun 2016 15:34:17: #1 tags after filtering in treatment: 3348517 INFO @ Sun, 05 Jun 2016 15:34:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 05 Jun 2016 15:34:17: #1 finished! INFO @ Sun, 05 Jun 2016 15:34:17: #2 Build Peak Model... INFO @ Sun, 05 Jun 2016 15:34:18: #2 number of paired peaks: 1305 INFO @ Sun, 05 Jun 2016 15:34:18: start model_add_line... INFO @ Sun, 05 Jun 2016 15:34:18: #2 number of paired peaks: 1305 INFO @ Sun, 05 Jun 2016 15:34:18: start model_add_line... INFO @ Sun, 05 Jun 2016 15:34:18: #2 number of paired peaks: 1305 INFO @ Sun, 05 Jun 2016 15:34:18: start model_add_line... INFO @ Sun, 05 Jun 2016 15:34:21: start X-correlation... INFO @ Sun, 05 Jun 2016 15:34:21: start X-correlation... INFO @ Sun, 05 Jun 2016 15:34:21: end of X-cor INFO @ Sun, 05 Jun 2016 15:34:21: #2 finished! INFO @ Sun, 05 Jun 2016 15:34:21: #2 predicted fragment length is 66 bps INFO @ Sun, 05 Jun 2016 15:34:21: #2 alternative fragment length(s) may be 66 bps INFO @ Sun, 05 Jun 2016 15:34:21: #2.2 Generate R script for model : SRX017463.20_model.r INFO @ Sun, 05 Jun 2016 15:34:21: end of X-cor INFO @ Sun, 05 Jun 2016 15:34:21: #2 finished! INFO @ Sun, 05 Jun 2016 15:34:21: #2 predicted fragment length is 66 bps INFO @ Sun, 05 Jun 2016 15:34:21: #2 alternative fragment length(s) may be 66 bps INFO @ Sun, 05 Jun 2016 15:34:21: #2.2 Generate R script for model : SRX017463.10_model.r WARNING @ Sun, 05 Jun 2016 15:34:21: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 05 Jun 2016 15:34:21: #2 You may need to consider one of the other alternative d(s): 66 WARNING @ Sun, 05 Jun 2016 15:34:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 05 Jun 2016 15:34:21: #3 Call peaks... WARNING @ Sun, 05 Jun 2016 15:34:21: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 05 Jun 2016 15:34:21: #2 You may need to consider one of the other alternative d(s): 66 WARNING @ Sun, 05 Jun 2016 15:34:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 05 Jun 2016 15:34:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 05 Jun 2016 15:34:21: #3 Call peaks... INFO @ Sun, 05 Jun 2016 15:34:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 05 Jun 2016 15:34:21: start X-correlation... INFO @ Sun, 05 Jun 2016 15:34:21: end of X-cor INFO @ Sun, 05 Jun 2016 15:34:21: #2 finished! INFO @ Sun, 05 Jun 2016 15:34:21: #2 predicted fragment length is 66 bps INFO @ Sun, 05 Jun 2016 15:34:21: #2 alternative fragment length(s) may be 66 bps INFO @ Sun, 05 Jun 2016 15:34:21: #2.2 Generate R script for model : SRX017463.05_model.r WARNING @ Sun, 05 Jun 2016 15:34:21: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 05 Jun 2016 15:34:21: #2 You may need to consider one of the other alternative d(s): 66 WARNING @ Sun, 05 Jun 2016 15:34:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 05 Jun 2016 15:34:21: #3 Call peaks... INFO @ Sun, 05 Jun 2016 15:34:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 05 Jun 2016 15:34:40: #3 Call peaks for each chromosome... INFO @ Sun, 05 Jun 2016 15:34:41: #3 Call peaks for each chromosome... INFO @ Sun, 05 Jun 2016 15:34:41: #3 Call peaks for each chromosome... INFO @ Sun, 05 Jun 2016 15:34:54: #4 Write output xls file... SRX017463.10_peaks.xls INFO @ Sun, 05 Jun 2016 15:34:54: #4 Write peak in narrowPeak format file... SRX017463.10_peaks.narrowPeak INFO @ Sun, 05 Jun 2016 15:34:54: #4 Write summits bed file... SRX017463.10_summits.bed INFO @ Sun, 05 Jun 2016 15:34:54: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1574 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 05 Jun 2016 15:34:56: #4 Write output xls file... SRX017463.20_peaks.xls INFO @ Sun, 05 Jun 2016 15:34:56: #4 Write peak in narrowPeak format file... SRX017463.20_peaks.narrowPeak INFO @ Sun, 05 Jun 2016 15:34:56: #4 Write summits bed file... SRX017463.20_summits.bed INFO @ Sun, 05 Jun 2016 15:34:56: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (485 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 05 Jun 2016 15:34:58: #4 Write output xls file... SRX017463.05_peaks.xls INFO @ Sun, 05 Jun 2016 15:34:58: #4 Write peak in narrowPeak format file... SRX017463.05_peaks.narrowPeak INFO @ Sun, 05 Jun 2016 15:34:58: #4 Write summits bed file... SRX017463.05_summits.bed INFO @ Sun, 05 Jun 2016 15:34:58: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3905 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。