Job ID = 9029586 sra ファイルのダウンロード中... Completed: 940188K bytes transferred in 12 seconds (634504K 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 7663 0 7663 0 0 1066 0 --:--:-- 0:00:07 --:--:-- 10149 100 30246 0 30246 0 0 3773 0 --:--:-- 0:00:08 --:--:-- 19070 100 71069 0 71069 0 0 8150 0 --:--:-- 0:00:08 --:--:-- 31048 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 16543983 spots for /home/okishinya/chipatlas/results/dm3/SRX1850482/SRR3675039.sra Written 16543983 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: 00:11:55 16543983 reads; of these: 16543983 (100.00%) were unpaired; of these: 674983 (4.08%) aligned 0 times 13330139 (80.57%) aligned exactly 1 time 2538861 (15.35%) aligned >1 times 95.92% overall alignment rate Time searching: 00:11:55 Overall time: 00:11:55 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_sort_core] merging from 8 files... [bam_rmdupse_core] 9326959 / 15869000 = 0.5877 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 14:31:28: # Command line: callpeak -t SRX1850482.bam -f BAM -g dm -n SRX1850482.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1850482.20 # format = BAM # ChIP-seq file = ['SRX1850482.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 14:31:28: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:31:28: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:31:28: # Command line: callpeak -t SRX1850482.bam -f BAM -g dm -n SRX1850482.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1850482.10 # format = BAM # ChIP-seq file = ['SRX1850482.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 14:31:28: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:31:28: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:31:28: # Command line: callpeak -t SRX1850482.bam -f BAM -g dm -n SRX1850482.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1850482.05 # format = BAM # ChIP-seq file = ['SRX1850482.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 14:31:28: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:31:28: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:31:38: 1000000 INFO @ Sat, 03 Jun 2017 14:31:40: 1000000 INFO @ Sat, 03 Jun 2017 14:31:40: 1000000 INFO @ Sat, 03 Jun 2017 14:31:47: 2000000 INFO @ Sat, 03 Jun 2017 14:31:52: 2000000 INFO @ Sat, 03 Jun 2017 14:31:52: 2000000 INFO @ Sat, 03 Jun 2017 14:31:56: 3000000 INFO @ Sat, 03 Jun 2017 14:32:03: 3000000 INFO @ Sat, 03 Jun 2017 14:32:03: 3000000 INFO @ Sat, 03 Jun 2017 14:32:06: 4000000 INFO @ Sat, 03 Jun 2017 14:32:17: 4000000 INFO @ Sat, 03 Jun 2017 14:32:17: 4000000 INFO @ Sat, 03 Jun 2017 14:32:20: 5000000 INFO @ Sat, 03 Jun 2017 14:32:31: 5000000 INFO @ Sat, 03 Jun 2017 14:32:31: 5000000 INFO @ Sat, 03 Jun 2017 14:32:34: 6000000 INFO @ Sat, 03 Jun 2017 14:32:41: #1 tag size is determined as 101 bps INFO @ Sat, 03 Jun 2017 14:32:41: #1 tag size = 101 INFO @ Sat, 03 Jun 2017 14:32:41: #1 total tags in treatment: 6542041 INFO @ Sat, 03 Jun 2017 14:32:41: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:32:41: #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 14:32:42: #1 tags after filtering in treatment: 6528647 INFO @ Sat, 03 Jun 2017 14:32:42: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:32:42: #1 finished! INFO @ Sat, 03 Jun 2017 14:32:42: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:32:44: #2 number of paired peaks: 230 WARNING @ Sat, 03 Jun 2017 14:32:44: Fewer paired peaks (230) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 230 pairs to build model! INFO @ Sat, 03 Jun 2017 14:32:44: start model_add_line... INFO @ Sat, 03 Jun 2017 14:32:44: 6000000 INFO @ Sat, 03 Jun 2017 14:32:44: 6000000 INFO @ Sat, 03 Jun 2017 14:32:45: start X-correlation... INFO @ Sat, 03 Jun 2017 14:32:45: end of X-cor INFO @ Sat, 03 Jun 2017 14:32:45: #2 finished! INFO @ Sat, 03 Jun 2017 14:32:45: #2 predicted fragment length is 95 bps INFO @ Sat, 03 Jun 2017 14:32:45: #2 alternative fragment length(s) may be 95 bps INFO @ Sat, 03 Jun 2017 14:32:45: #2.2 Generate R script for model : SRX1850482.10_model.r WARNING @ Sat, 03 Jun 2017 14:32:45: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 14:32:45: #2 You may need to consider one of the other alternative d(s): 95 WARNING @ Sat, 03 Jun 2017 14:32:45: #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 14:32:45: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:32:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:32:50: #1 tag size is determined as 101 bps INFO @ Sat, 03 Jun 2017 14:32:50: #1 tag size = 101 INFO @ Sat, 03 Jun 2017 14:32:50: #1 total tags in treatment: 6542041 INFO @ Sat, 03 Jun 2017 14:32:50: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:32:50: #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 14:32:50: #1 tag size is determined as 101 bps INFO @ Sat, 03 Jun 2017 14:32:50: #1 tag size = 101 INFO @ Sat, 03 Jun 2017 14:32:50: #1 total tags in treatment: 6542041 INFO @ Sat, 03 Jun 2017 14:32:50: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:32:50: #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 14:32:51: #1 tags after filtering in treatment: 6528647 INFO @ Sat, 03 Jun 2017 14:32:51: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:32:51: #1 finished! INFO @ Sat, 03 Jun 2017 14:32:51: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:32:51: #1 tags after filtering in treatment: 6528647 INFO @ Sat, 03 Jun 2017 14:32:51: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:32:51: #1 finished! INFO @ Sat, 03 Jun 2017 14:32:51: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:32:52: #2 number of paired peaks: 230 WARNING @ Sat, 03 Jun 2017 14:32:52: Fewer paired peaks (230) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 230 pairs to build model! INFO @ Sat, 03 Jun 2017 14:32:52: start model_add_line... INFO @ Sat, 03 Jun 2017 14:32:52: #2 number of paired peaks: 230 WARNING @ Sat, 03 Jun 2017 14:32:52: Fewer paired peaks (230) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 230 pairs to build model! INFO @ Sat, 03 Jun 2017 14:32:52: start model_add_line... INFO @ Sat, 03 Jun 2017 14:32:53: start X-correlation... INFO @ Sat, 03 Jun 2017 14:32:53: end of X-cor INFO @ Sat, 03 Jun 2017 14:32:53: #2 finished! INFO @ Sat, 03 Jun 2017 14:32:53: #2 predicted fragment length is 95 bps INFO @ Sat, 03 Jun 2017 14:32:53: #2 alternative fragment length(s) may be 95 bps INFO @ Sat, 03 Jun 2017 14:32:53: #2.2 Generate R script for model : SRX1850482.20_model.r WARNING @ Sat, 03 Jun 2017 14:32:53: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 14:32:53: #2 You may need to consider one of the other alternative d(s): 95 WARNING @ Sat, 03 Jun 2017 14:32:53: #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 14:32:53: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:32:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:32:54: start X-correlation... INFO @ Sat, 03 Jun 2017 14:32:54: end of X-cor INFO @ Sat, 03 Jun 2017 14:32:54: #2 finished! INFO @ Sat, 03 Jun 2017 14:32:54: #2 predicted fragment length is 95 bps INFO @ Sat, 03 Jun 2017 14:32:54: #2 alternative fragment length(s) may be 95 bps INFO @ Sat, 03 Jun 2017 14:32:54: #2.2 Generate R script for model : SRX1850482.05_model.r WARNING @ Sat, 03 Jun 2017 14:32:54: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 14:32:54: #2 You may need to consider one of the other alternative d(s): 95 WARNING @ Sat, 03 Jun 2017 14:32:54: #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 14:32:54: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:32:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:33:22: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:33:28: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:33:31: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:33:50: #4 Write output xls file... SRX1850482.10_peaks.xls INFO @ Sat, 03 Jun 2017 14:33:50: #4 Write peak in narrowPeak format file... SRX1850482.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:33:50: #4 Write summits bed file... SRX1850482.10_summits.bed INFO @ Sat, 03 Jun 2017 14:33:50: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (754 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 14:33:56: #4 Write output xls file... SRX1850482.05_peaks.xls INFO @ Sat, 03 Jun 2017 14:33:56: #4 Write peak in narrowPeak format file... SRX1850482.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:33:56: #4 Write summits bed file... SRX1850482.05_summits.bed INFO @ Sat, 03 Jun 2017 14:33:56: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1361 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 14:33:58: #4 Write output xls file... SRX1850482.20_peaks.xls INFO @ Sat, 03 Jun 2017 14:33:58: #4 Write peak in narrowPeak format file... SRX1850482.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:33:58: #4 Write summits bed file... SRX1850482.20_summits.bed INFO @ Sat, 03 Jun 2017 14:33:58: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (388 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。