Job ID = 9029358 sra ファイルのダウンロード中... Completed: 97607K bytes transferred in 4 seconds (186297K 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 --:--:-- 0 100 12695 0 12695 0 0 1732 0 --:--:-- 0:00:07 --:--:-- 13476 100 43278 0 43278 0 0 5198 0 --:--:-- 0:00:08 --:--:-- 22319 100 55806 0 55806 0 0 6572 0 --:--:-- 0:00:08 --:--:-- 26523 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 1722828 spots for /home/okishinya/chipatlas/results/dm3/SRX1600271/SRR3187700.sra Written 1722828 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: 00:00:34 1722828 reads; of these: 1722828 (100.00%) were unpaired; of these: 610079 (35.41%) aligned 0 times 981036 (56.94%) aligned exactly 1 time 131713 (7.65%) aligned >1 times 64.59% overall alignment rate Time searching: 00:00:34 Overall time: 00:00:34 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] 882698 / 1112749 = 0.7933 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 @ Sat, 03 Jun 2017 13:17:38: # Command line: callpeak -t SRX1600271.bam -f BAM -g dm -n SRX1600271.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1600271.10 # format = BAM # ChIP-seq file = ['SRX1600271.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 @ Sat, 03 Jun 2017 13:17:38: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:17:38: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:17:38: # Command line: callpeak -t SRX1600271.bam -f BAM -g dm -n SRX1600271.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1600271.05 # format = BAM # ChIP-seq file = ['SRX1600271.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 @ Sat, 03 Jun 2017 13:17:38: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:17:38: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:17:38: # Command line: callpeak -t SRX1600271.bam -f BAM -g dm -n SRX1600271.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1600271.20 # format = BAM # ChIP-seq file = ['SRX1600271.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 @ Sat, 03 Jun 2017 13:17:38: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:17:38: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:17:39: #1 tag size is determined as 76 bps INFO @ Sat, 03 Jun 2017 13:17:39: #1 tag size = 76 INFO @ Sat, 03 Jun 2017 13:17:39: #1 total tags in treatment: 230051 INFO @ Sat, 03 Jun 2017 13:17:39: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:17:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 13:17:40: #1 tags after filtering in treatment: 229969 INFO @ Sat, 03 Jun 2017 13:17:40: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:17:40: #1 finished! INFO @ Sat, 03 Jun 2017 13:17:40: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:17:40: #1 tag size is determined as 76 bps INFO @ Sat, 03 Jun 2017 13:17:40: #1 tag size = 76 INFO @ Sat, 03 Jun 2017 13:17:40: #1 total tags in treatment: 230051 INFO @ Sat, 03 Jun 2017 13:17:40: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:17:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 13:17:40: #1 tag size is determined as 76 bps INFO @ Sat, 03 Jun 2017 13:17:40: #1 tag size = 76 INFO @ Sat, 03 Jun 2017 13:17:40: #1 total tags in treatment: 230051 INFO @ Sat, 03 Jun 2017 13:17:40: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:17:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 13:17:40: #1 tags after filtering in treatment: 229969 INFO @ Sat, 03 Jun 2017 13:17:40: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:17:40: #1 finished! INFO @ Sat, 03 Jun 2017 13:17:40: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:17:40: #1 tags after filtering in treatment: 229969 INFO @ Sat, 03 Jun 2017 13:17:40: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:17:40: #1 finished! INFO @ Sat, 03 Jun 2017 13:17:40: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:17:40: #2 number of paired peaks: 5777 INFO @ Sat, 03 Jun 2017 13:17:40: start model_add_line... INFO @ Sat, 03 Jun 2017 13:17:40: #2 number of paired peaks: 5777 INFO @ Sat, 03 Jun 2017 13:17:40: start model_add_line... INFO @ Sat, 03 Jun 2017 13:17:40: #2 number of paired peaks: 5777 INFO @ Sat, 03 Jun 2017 13:17:40: start model_add_line... INFO @ Sat, 03 Jun 2017 13:17:41: start X-correlation... INFO @ Sat, 03 Jun 2017 13:17:41: end of X-cor INFO @ Sat, 03 Jun 2017 13:17:41: #2 finished! INFO @ Sat, 03 Jun 2017 13:17:41: #2 predicted fragment length is 136 bps INFO @ Sat, 03 Jun 2017 13:17:41: #2 alternative fragment length(s) may be 136,215 bps INFO @ Sat, 03 Jun 2017 13:17:41: #2.2 Generate R script for model : SRX1600271.20_model.r WARNING @ Sat, 03 Jun 2017 13:17:41: #2 Since the d (136) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:17:41: #2 You may need to consider one of the other alternative d(s): 136,215 WARNING @ Sat, 03 Jun 2017 13:17:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 13:17:41: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:17:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:17:41: start X-correlation... INFO @ Sat, 03 Jun 2017 13:17:41: end of X-cor INFO @ Sat, 03 Jun 2017 13:17:41: #2 finished! INFO @ Sat, 03 Jun 2017 13:17:41: #2 predicted fragment length is 136 bps INFO @ Sat, 03 Jun 2017 13:17:41: #2 alternative fragment length(s) may be 136,215 bps INFO @ Sat, 03 Jun 2017 13:17:41: #2.2 Generate R script for model : SRX1600271.05_model.r WARNING @ Sat, 03 Jun 2017 13:17:41: #2 Since the d (136) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:17:41: #2 You may need to consider one of the other alternative d(s): 136,215 WARNING @ Sat, 03 Jun 2017 13:17:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 13:17:41: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:17:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:17:41: start X-correlation... INFO @ Sat, 03 Jun 2017 13:17:41: end of X-cor INFO @ Sat, 03 Jun 2017 13:17:41: #2 finished! INFO @ Sat, 03 Jun 2017 13:17:41: #2 predicted fragment length is 136 bps INFO @ Sat, 03 Jun 2017 13:17:41: #2 alternative fragment length(s) may be 136,215 bps INFO @ Sat, 03 Jun 2017 13:17:41: #2.2 Generate R script for model : SRX1600271.10_model.r WARNING @ Sat, 03 Jun 2017 13:17:41: #2 Since the d (136) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:17:41: #2 You may need to consider one of the other alternative d(s): 136,215 WARNING @ Sat, 03 Jun 2017 13:17:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 13:17:41: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:17:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:17:43: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:17:43: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:17:43: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:17:44: #4 Write output xls file... SRX1600271.20_peaks.xls INFO @ Sat, 03 Jun 2017 13:17:44: #4 Write peak in narrowPeak format file... SRX1600271.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:17:44: #4 Write summits bed file... SRX1600271.20_summits.bed INFO @ Sat, 03 Jun 2017 13:17:44: Done! pass1 - making usageList (5 chroms): 0 millis pass2 - checking and writing primary data (123 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Jun 2017 13:17:44: #4 Write output xls file... SRX1600271.10_peaks.xls INFO @ Sat, 03 Jun 2017 13:17:44: #4 Write peak in narrowPeak format file... SRX1600271.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:17:44: #4 Write summits bed file... SRX1600271.10_summits.bed INFO @ Sat, 03 Jun 2017 13:17:44: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (218 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:17:44: #4 Write output xls file... SRX1600271.05_peaks.xls INFO @ Sat, 03 Jun 2017 13:17:44: #4 Write peak in narrowPeak format file... SRX1600271.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:17:44: #4 Write summits bed file... SRX1600271.05_summits.bed INFO @ Sat, 03 Jun 2017 13:17:44: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (661 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。