Job ID = 9025665 sra ファイルのダウンロード中... Completed: 161820K bytes transferred in 5 seconds (251366K 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 0 0 0 0 0 0 0 0 --:--:-- 0:00:06 --:--:-- 0 100 14324 0 14324 0 0 1887 0 --:--:-- 0:00:07 --:--:-- 10705 100 44795 0 44795 0 0 5218 0 --:--:-- 0:00:08 --:--:-- 19192 100 46666 0 46666 0 0 5333 0 --:--:-- 0:00:08 --:--:-- 18666 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 6821424 spots for /home/okishinya/chipatlas/results/ce10/SRX2144191/SRR4188795.sra Written 6821424 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: 00:01:41 6821424 reads; of these: 6821424 (100.00%) were unpaired; of these: 1078291 (15.81%) aligned 0 times 4455965 (65.32%) aligned exactly 1 time 1287168 (18.87%) aligned >1 times 84.19% overall alignment rate Time searching: 00:01:41 Overall time: 00:01:41 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 411013 / 5743133 = 0.0716 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 04:52:48: # Command line: callpeak -t SRX2144191.bam -f BAM -g ce -n SRX2144191.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2144191.20 # format = BAM # ChIP-seq file = ['SRX2144191.bam'] # control file = None # effective genome size = 9.00e+07 # 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 04:52:48: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:52:48: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:52:48: # Command line: callpeak -t SRX2144191.bam -f BAM -g ce -n SRX2144191.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2144191.05 # format = BAM # ChIP-seq file = ['SRX2144191.bam'] # control file = None # effective genome size = 9.00e+07 # 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 04:52:48: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:52:48: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:52:48: # Command line: callpeak -t SRX2144191.bam -f BAM -g ce -n SRX2144191.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2144191.10 # format = BAM # ChIP-seq file = ['SRX2144191.bam'] # control file = None # effective genome size = 9.00e+07 # 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 04:52:48: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:52:48: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:52:55: 1000000 INFO @ Sat, 03 Jun 2017 04:52:55: 1000000 INFO @ Sat, 03 Jun 2017 04:52:55: 1000000 INFO @ Sat, 03 Jun 2017 04:53:02: 2000000 INFO @ Sat, 03 Jun 2017 04:53:02: 2000000 INFO @ Sat, 03 Jun 2017 04:53:02: 2000000 INFO @ Sat, 03 Jun 2017 04:53:09: 3000000 INFO @ Sat, 03 Jun 2017 04:53:09: 3000000 INFO @ Sat, 03 Jun 2017 04:53:09: 3000000 INFO @ Sat, 03 Jun 2017 04:53:15: 4000000 INFO @ Sat, 03 Jun 2017 04:53:15: 4000000 INFO @ Sat, 03 Jun 2017 04:53:15: 4000000 INFO @ Sat, 03 Jun 2017 04:53:22: 5000000 INFO @ Sat, 03 Jun 2017 04:53:22: 5000000 INFO @ Sat, 03 Jun 2017 04:53:22: 5000000 INFO @ Sat, 03 Jun 2017 04:53:24: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:53:24: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:53:24: #1 total tags in treatment: 5332120 INFO @ Sat, 03 Jun 2017 04:53:24: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:53:24: #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 04:53:24: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:53:24: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:53:24: #1 total tags in treatment: 5332120 INFO @ Sat, 03 Jun 2017 04:53:24: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:53:24: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:53:24: #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 04:53:24: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:53:24: #1 total tags in treatment: 5332120 INFO @ Sat, 03 Jun 2017 04:53:24: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:53:24: #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 04:53:25: #1 tags after filtering in treatment: 5330610 INFO @ Sat, 03 Jun 2017 04:53:25: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:53:25: #1 finished! INFO @ Sat, 03 Jun 2017 04:53:25: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:53:25: #1 tags after filtering in treatment: 5330610 INFO @ Sat, 03 Jun 2017 04:53:25: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:53:25: #1 finished! INFO @ Sat, 03 Jun 2017 04:53:25: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:53:25: #1 tags after filtering in treatment: 5330610 INFO @ Sat, 03 Jun 2017 04:53:25: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:53:25: #1 finished! INFO @ Sat, 03 Jun 2017 04:53:25: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:53:26: #2 number of paired peaks: 497 WARNING @ Sat, 03 Jun 2017 04:53:26: Fewer paired peaks (497) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 497 pairs to build model! INFO @ Sat, 03 Jun 2017 04:53:26: start model_add_line... INFO @ Sat, 03 Jun 2017 04:53:26: #2 number of paired peaks: 497 WARNING @ Sat, 03 Jun 2017 04:53:26: Fewer paired peaks (497) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 497 pairs to build model! INFO @ Sat, 03 Jun 2017 04:53:26: start model_add_line... INFO @ Sat, 03 Jun 2017 04:53:26: #2 number of paired peaks: 497 WARNING @ Sat, 03 Jun 2017 04:53:26: Fewer paired peaks (497) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 497 pairs to build model! INFO @ Sat, 03 Jun 2017 04:53:26: start model_add_line... INFO @ Sat, 03 Jun 2017 04:53:31: start X-correlation... INFO @ Sat, 03 Jun 2017 04:53:31: end of X-cor INFO @ Sat, 03 Jun 2017 04:53:31: #2 finished! INFO @ Sat, 03 Jun 2017 04:53:31: #2 predicted fragment length is 47 bps INFO @ Sat, 03 Jun 2017 04:53:31: #2 alternative fragment length(s) may be 4,47,539 bps INFO @ Sat, 03 Jun 2017 04:53:31: #2.2 Generate R script for model : SRX2144191.20_model.r WARNING @ Sat, 03 Jun 2017 04:53:31: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 04:53:31: #2 You may need to consider one of the other alternative d(s): 4,47,539 WARNING @ Sat, 03 Jun 2017 04:53:31: #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 04:53:31: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:53:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:53:31: start X-correlation... INFO @ Sat, 03 Jun 2017 04:53:31: end of X-cor INFO @ Sat, 03 Jun 2017 04:53:31: #2 finished! INFO @ Sat, 03 Jun 2017 04:53:31: #2 predicted fragment length is 47 bps INFO @ Sat, 03 Jun 2017 04:53:31: #2 alternative fragment length(s) may be 4,47,539 bps INFO @ Sat, 03 Jun 2017 04:53:31: #2.2 Generate R script for model : SRX2144191.10_model.r INFO @ Sat, 03 Jun 2017 04:53:31: start X-correlation... INFO @ Sat, 03 Jun 2017 04:53:31: end of X-cor INFO @ Sat, 03 Jun 2017 04:53:31: #2 finished! INFO @ Sat, 03 Jun 2017 04:53:31: #2 predicted fragment length is 47 bps INFO @ Sat, 03 Jun 2017 04:53:31: #2 alternative fragment length(s) may be 4,47,539 bps INFO @ Sat, 03 Jun 2017 04:53:31: #2.2 Generate R script for model : SRX2144191.05_model.r WARNING @ Sat, 03 Jun 2017 04:53:31: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 04:53:31: #2 You may need to consider one of the other alternative d(s): 4,47,539 WARNING @ Sat, 03 Jun 2017 04:53:31: #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 04:53:31: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:53:31: #3 Pre-compute pvalue-qvalue table... WARNING @ Sat, 03 Jun 2017 04:53:31: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 04:53:31: #2 You may need to consider one of the other alternative d(s): 4,47,539 WARNING @ Sat, 03 Jun 2017 04:53:31: #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 04:53:31: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:53:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:54:02: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:54:03: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:54:04: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:54:23: #4 Write output xls file... SRX2144191.05_peaks.xls INFO @ Sat, 03 Jun 2017 04:54:23: #4 Write peak in narrowPeak format file... SRX2144191.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:54:23: #4 Write summits bed file... SRX2144191.05_summits.bed INFO @ Sat, 03 Jun 2017 04:54:23: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (598 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:54:24: #4 Write output xls file... SRX2144191.20_peaks.xls INFO @ Sat, 03 Jun 2017 04:54:24: #4 Write peak in narrowPeak format file... SRX2144191.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:54:24: #4 Write summits bed file... SRX2144191.20_summits.bed INFO @ Sat, 03 Jun 2017 04:54:24: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (162 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:54:25: #4 Write output xls file... SRX2144191.10_peaks.xls INFO @ Sat, 03 Jun 2017 04:54:25: #4 Write peak in narrowPeak format file... SRX2144191.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:54:25: #4 Write summits bed file... SRX2144191.10_summits.bed INFO @ Sat, 03 Jun 2017 04:54:25: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (378 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。