Job ID = 9029554 sra ファイルのダウンロード中... Completed: 1325161K bytes transferred in 14 seconds (745976K 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 14324 0 14324 0 0 1895 0 --:--:-- 0:00:07 --:--:-- 13214 100 46317 0 46317 0 0 5496 0 --:--:-- 0:00:08 --:--:-- 23667 100 107k 0 107k 0 0 11702 0 --:--:-- 0:00:09 --:--:-- 37700 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 20514613 spots for /home/okishinya/chipatlas/results/dm3/SRX1840067/SRR3661293.sra Written 20514613 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: 00:13:06 20514613 reads; of these: 20514613 (100.00%) were unpaired; of these: 4934931 (24.06%) aligned 0 times 11978815 (58.39%) aligned exactly 1 time 3600867 (17.55%) aligned >1 times 75.94% overall alignment rate Time searching: 00:13:06 Overall time: 00:13:06 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] 11831695 / 15579682 = 0.7594 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 14:26:16: # Command line: callpeak -t SRX1840067.bam -f BAM -g dm -n SRX1840067.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1840067.10 # format = BAM # ChIP-seq file = ['SRX1840067.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 14:26:16: # Command line: callpeak -t SRX1840067.bam -f BAM -g dm -n SRX1840067.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1840067.20 # format = BAM # ChIP-seq file = ['SRX1840067.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 14:26:16: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:26:16: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:26:16: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:26:16: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:26:16: # Command line: callpeak -t SRX1840067.bam -f BAM -g dm -n SRX1840067.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1840067.05 # format = BAM # ChIP-seq file = ['SRX1840067.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 14:26:16: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:26:16: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:26:25: 1000000 INFO @ Sat, 03 Jun 2017 14:26:28: 1000000 INFO @ Sat, 03 Jun 2017 14:26:28: 1000000 INFO @ Sat, 03 Jun 2017 14:26:35: 2000000 INFO @ Sat, 03 Jun 2017 14:26:40: 2000000 INFO @ Sat, 03 Jun 2017 14:26:40: 2000000 INFO @ Sat, 03 Jun 2017 14:26:47: 3000000 INFO @ Sat, 03 Jun 2017 14:26:53: 3000000 INFO @ Sat, 03 Jun 2017 14:26:53: 3000000 INFO @ Sat, 03 Jun 2017 14:26:56: #1 tag size is determined as 101 bps INFO @ Sat, 03 Jun 2017 14:26:56: #1 tag size = 101 INFO @ Sat, 03 Jun 2017 14:26:56: #1 total tags in treatment: 3747987 INFO @ Sat, 03 Jun 2017 14:26:56: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:26:56: #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 14:26:57: #1 tags after filtering in treatment: 3743577 INFO @ Sat, 03 Jun 2017 14:26:57: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:26:57: #1 finished! INFO @ Sat, 03 Jun 2017 14:26:57: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:26:58: #2 number of paired peaks: 1272 INFO @ Sat, 03 Jun 2017 14:26:58: start model_add_line... INFO @ Sat, 03 Jun 2017 14:27:01: start X-correlation... INFO @ Sat, 03 Jun 2017 14:27:01: end of X-cor INFO @ Sat, 03 Jun 2017 14:27:01: #2 finished! INFO @ Sat, 03 Jun 2017 14:27:01: #2 predicted fragment length is 163 bps INFO @ Sat, 03 Jun 2017 14:27:01: #2 alternative fragment length(s) may be 163 bps INFO @ Sat, 03 Jun 2017 14:27:01: #2.2 Generate R script for model : SRX1840067.20_model.r WARNING @ Sat, 03 Jun 2017 14:27:01: #2 Since the d (163) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 14:27:01: #2 You may need to consider one of the other alternative d(s): 163 WARNING @ Sat, 03 Jun 2017 14:27:01: #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 14:27:01: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:27:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:27:02: #1 tag size is determined as 101 bps INFO @ Sat, 03 Jun 2017 14:27:02: #1 tag size = 101 INFO @ Sat, 03 Jun 2017 14:27:02: #1 total tags in treatment: 3747987 INFO @ Sat, 03 Jun 2017 14:27:02: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:27:02: #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 14:27:02: #1 tag size is determined as 101 bps INFO @ Sat, 03 Jun 2017 14:27:02: #1 tag size = 101 INFO @ Sat, 03 Jun 2017 14:27:02: #1 total tags in treatment: 3747987 INFO @ Sat, 03 Jun 2017 14:27:02: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:27:02: #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 14:27:03: #1 tags after filtering in treatment: 3743577 INFO @ Sat, 03 Jun 2017 14:27:03: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:27:03: #1 finished! INFO @ Sat, 03 Jun 2017 14:27:03: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:27:03: #1 tags after filtering in treatment: 3743577 INFO @ Sat, 03 Jun 2017 14:27:03: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:27:03: #1 finished! INFO @ Sat, 03 Jun 2017 14:27:03: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:27:04: #2 number of paired peaks: 1272 INFO @ Sat, 03 Jun 2017 14:27:04: start model_add_line... INFO @ Sat, 03 Jun 2017 14:27:04: #2 number of paired peaks: 1272 INFO @ Sat, 03 Jun 2017 14:27:04: start model_add_line... INFO @ Sat, 03 Jun 2017 14:27:07: start X-correlation... INFO @ Sat, 03 Jun 2017 14:27:07: start X-correlation... INFO @ Sat, 03 Jun 2017 14:27:07: end of X-cor INFO @ Sat, 03 Jun 2017 14:27:07: end of X-cor INFO @ Sat, 03 Jun 2017 14:27:07: #2 finished! INFO @ Sat, 03 Jun 2017 14:27:07: #2 finished! INFO @ Sat, 03 Jun 2017 14:27:07: #2 predicted fragment length is 163 bps INFO @ Sat, 03 Jun 2017 14:27:07: #2 predicted fragment length is 163 bps INFO @ Sat, 03 Jun 2017 14:27:07: #2 alternative fragment length(s) may be 163 bps INFO @ Sat, 03 Jun 2017 14:27:07: #2 alternative fragment length(s) may be 163 bps INFO @ Sat, 03 Jun 2017 14:27:07: #2.2 Generate R script for model : SRX1840067.10_model.r INFO @ Sat, 03 Jun 2017 14:27:07: #2.2 Generate R script for model : SRX1840067.05_model.r WARNING @ Sat, 03 Jun 2017 14:27:07: #2 Since the d (163) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 14:27:07: #2 You may need to consider one of the other alternative d(s): 163 WARNING @ Sat, 03 Jun 2017 14:27:07: #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 14:27:07: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:27:07: #3 Pre-compute pvalue-qvalue table... WARNING @ Sat, 03 Jun 2017 14:27:07: #2 Since the d (163) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 14:27:07: #2 You may need to consider one of the other alternative d(s): 163 WARNING @ Sat, 03 Jun 2017 14:27:07: #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 14:27:07: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:27:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:27:25: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:27:30: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:27:30: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:27:44: #4 Write output xls file... SRX1840067.20_peaks.xls INFO @ Sat, 03 Jun 2017 14:27:44: #4 Write peak in narrowPeak format file... SRX1840067.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:27:44: #4 Write summits bed file... SRX1840067.20_summits.bed INFO @ Sat, 03 Jun 2017 14:27:44: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (792 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 14:27:48: #4 Write output xls file... SRX1840067.05_peaks.xls INFO @ Sat, 03 Jun 2017 14:27:48: #4 Write peak in narrowPeak format file... SRX1840067.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:27:48: #4 Write summits bed file... SRX1840067.05_summits.bed INFO @ Sat, 03 Jun 2017 14:27:48: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3134 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 14:27:48: #4 Write output xls file... SRX1840067.10_peaks.xls INFO @ Sat, 03 Jun 2017 14:27:48: #4 Write peak in narrowPeak format file... SRX1840067.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:27:48: #4 Write summits bed file... SRX1840067.10_summits.bed INFO @ Sat, 03 Jun 2017 14:27:48: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1646 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。