Job ID = 9025660 sra ファイルのダウンロード中... Completed: 64223K bytes transferred in 3 seconds (133541K 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 --:--:-- 0:00:07 --:--:-- 0 100 12695 0 12695 0 0 1630 0 --:--:-- 0:00:07 --:--:-- 9042 100 37486 0 37486 0 0 4190 0 --:--:-- 0:00:08 --:--:-- 14614 100 43809 0 43809 0 0 4807 0 --:--:-- 0:00:09 --:--:-- 16035 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 2733404 spots for /home/okishinya/chipatlas/results/ce10/SRX2144186/SRR4188790.sra Written 2733404 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: 00:00:01 Multiseed full-index search: 00:00:36 2733404 reads; of these: 2733404 (100.00%) were unpaired; of these: 635440 (23.25%) aligned 0 times 1753602 (64.15%) aligned exactly 1 time 344362 (12.60%) aligned >1 times 76.75% overall alignment rate Time searching: 00:00:37 Overall time: 00:00:37 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] 66600 / 2097964 = 0.0317 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 04:49:21: # Command line: callpeak -t SRX2144186.bam -f BAM -g ce -n SRX2144186.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2144186.05 # format = BAM # ChIP-seq file = ['SRX2144186.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 04:49:21: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:49:21: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:49:21: # Command line: callpeak -t SRX2144186.bam -f BAM -g ce -n SRX2144186.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2144186.20 # format = BAM # ChIP-seq file = ['SRX2144186.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 04:49:21: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:49:21: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:49:21: # Command line: callpeak -t SRX2144186.bam -f BAM -g ce -n SRX2144186.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2144186.10 # format = BAM # ChIP-seq file = ['SRX2144186.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 04:49:21: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:49:21: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:49:27: 1000000 INFO @ Sat, 03 Jun 2017 04:49:27: 1000000 INFO @ Sat, 03 Jun 2017 04:49:27: 1000000 INFO @ Sat, 03 Jun 2017 04:49:33: 2000000 INFO @ Sat, 03 Jun 2017 04:49:33: 2000000 INFO @ Sat, 03 Jun 2017 04:49:33: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:49:33: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:49:33: #1 total tags in treatment: 2031364 INFO @ Sat, 03 Jun 2017 04:49:33: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:49:33: #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 04:49:33: 2000000 INFO @ Sat, 03 Jun 2017 04:49:33: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:49:33: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:49:33: #1 total tags in treatment: 2031364 INFO @ Sat, 03 Jun 2017 04:49:33: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:49:33: #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 04:49:33: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:49:33: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:49:33: #1 total tags in treatment: 2031364 INFO @ Sat, 03 Jun 2017 04:49:33: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:49:33: #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 04:49:33: #1 tags after filtering in treatment: 2031114 INFO @ Sat, 03 Jun 2017 04:49:33: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:49:33: #1 finished! INFO @ Sat, 03 Jun 2017 04:49:33: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:49:34: #1 tags after filtering in treatment: 2031114 INFO @ Sat, 03 Jun 2017 04:49:34: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:49:34: #1 finished! INFO @ Sat, 03 Jun 2017 04:49:34: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:49:34: #1 tags after filtering in treatment: 2031114 INFO @ Sat, 03 Jun 2017 04:49:34: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:49:34: #1 finished! INFO @ Sat, 03 Jun 2017 04:49:34: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:49:34: #2 number of paired peaks: 356 WARNING @ Sat, 03 Jun 2017 04:49:34: Fewer paired peaks (356) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 356 pairs to build model! INFO @ Sat, 03 Jun 2017 04:49:34: start model_add_line... INFO @ Sat, 03 Jun 2017 04:49:34: #2 number of paired peaks: 356 WARNING @ Sat, 03 Jun 2017 04:49:34: Fewer paired peaks (356) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 356 pairs to build model! INFO @ Sat, 03 Jun 2017 04:49:34: start model_add_line... INFO @ Sat, 03 Jun 2017 04:49:34: #2 number of paired peaks: 356 WARNING @ Sat, 03 Jun 2017 04:49:34: Fewer paired peaks (356) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 356 pairs to build model! INFO @ Sat, 03 Jun 2017 04:49:34: start model_add_line... INFO @ Sat, 03 Jun 2017 04:49:35: start X-correlation... INFO @ Sat, 03 Jun 2017 04:49:35: end of X-cor INFO @ Sat, 03 Jun 2017 04:49:35: #2 finished! INFO @ Sat, 03 Jun 2017 04:49:35: #2 predicted fragment length is 50 bps INFO @ Sat, 03 Jun 2017 04:49:35: #2 alternative fragment length(s) may be 50,458,482 bps INFO @ Sat, 03 Jun 2017 04:49:35: #2.2 Generate R script for model : SRX2144186.20_model.r WARNING @ Sat, 03 Jun 2017 04:49:35: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 04:49:35: #2 You may need to consider one of the other alternative d(s): 50,458,482 WARNING @ Sat, 03 Jun 2017 04:49:35: #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 04:49:35: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:49:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:49:35: start X-correlation... INFO @ Sat, 03 Jun 2017 04:49:35: end of X-cor INFO @ Sat, 03 Jun 2017 04:49:35: #2 finished! INFO @ Sat, 03 Jun 2017 04:49:35: #2 predicted fragment length is 50 bps INFO @ Sat, 03 Jun 2017 04:49:35: #2 alternative fragment length(s) may be 50,458,482 bps INFO @ Sat, 03 Jun 2017 04:49:35: #2.2 Generate R script for model : SRX2144186.05_model.r WARNING @ Sat, 03 Jun 2017 04:49:35: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 04:49:35: #2 You may need to consider one of the other alternative d(s): 50,458,482 WARNING @ Sat, 03 Jun 2017 04:49:35: #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 04:49:35: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:49:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:49:35: start X-correlation... INFO @ Sat, 03 Jun 2017 04:49:35: end of X-cor INFO @ Sat, 03 Jun 2017 04:49:35: #2 finished! INFO @ Sat, 03 Jun 2017 04:49:35: #2 predicted fragment length is 50 bps INFO @ Sat, 03 Jun 2017 04:49:35: #2 alternative fragment length(s) may be 50,458,482 bps INFO @ Sat, 03 Jun 2017 04:49:35: #2.2 Generate R script for model : SRX2144186.10_model.r WARNING @ Sat, 03 Jun 2017 04:49:35: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 04:49:35: #2 You may need to consider one of the other alternative d(s): 50,458,482 WARNING @ Sat, 03 Jun 2017 04:49:35: #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 04:49:35: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:49:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:49:47: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:49:47: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:49:48: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:49:56: #4 Write output xls file... SRX2144186.20_peaks.xls INFO @ Sat, 03 Jun 2017 04:49:56: #4 Write peak in narrowPeak format file... SRX2144186.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:49:56: #4 Write summits bed file... SRX2144186.20_summits.bed INFO @ Sat, 03 Jun 2017 04:49:56: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (62 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:49:56: #4 Write output xls file... SRX2144186.05_peaks.xls INFO @ Sat, 03 Jun 2017 04:49:56: #4 Write peak in narrowPeak format file... SRX2144186.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:49:56: #4 Write summits bed file... SRX2144186.05_summits.bed INFO @ Sat, 03 Jun 2017 04:49:56: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (282 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:49:57: #4 Write output xls file... SRX2144186.10_peaks.xls INFO @ Sat, 03 Jun 2017 04:49:57: #4 Write peak in narrowPeak format file... SRX2144186.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:49:57: #4 Write summits bed file... SRX2144186.10_summits.bed INFO @ Sat, 03 Jun 2017 04:49:57: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (169 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。