Job ID = 9025499 sra ファイルのダウンロード中... Completed: 18098K bytes transferred in 3 seconds (47461K 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 9111 0 9111 0 0 1283 0 --:--:-- 0:00:07 --:--:-- 12941 100 33902 0 33902 0 0 4189 0 --:--:-- 0:00:08 --:--:-- 19942 100 42731 0 42731 0 0 5173 0 --:--:-- 0:00:08 --:--:-- 22887 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 766043 spots for /home/okishinya/chipatlas/results/ce10/SRX1388748/SRR2832464.sra Written 766043 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: 00:00:15 766043 reads; of these: 766043 (100.00%) were unpaired; of these: 95413 (12.46%) aligned 0 times 531307 (69.36%) aligned exactly 1 time 139323 (18.19%) aligned >1 times 87.54% overall alignment rate Time searching: 00:00:15 Overall time: 00:00:15 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] 18716 / 670630 = 0.0279 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 04:08:00: # Command line: callpeak -t SRX1388748.bam -f BAM -g ce -n SRX1388748.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1388748.10 # format = BAM # ChIP-seq file = ['SRX1388748.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 04:08:00: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:08:00: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:08:00: # Command line: callpeak -t SRX1388748.bam -f BAM -g ce -n SRX1388748.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1388748.05 # format = BAM # ChIP-seq file = ['SRX1388748.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 04:08:00: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:08:00: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:08:00: # Command line: callpeak -t SRX1388748.bam -f BAM -g ce -n SRX1388748.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1388748.20 # format = BAM # ChIP-seq file = ['SRX1388748.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 04:08:00: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:08:00: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:08:03: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:08:03: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:08:03: #1 total tags in treatment: 651914 INFO @ Sat, 03 Jun 2017 04:08:03: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:08:03: #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 04:08:03: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:08:03: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:08:03: #1 total tags in treatment: 651914 INFO @ Sat, 03 Jun 2017 04:08:03: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:08:03: #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 04:08:03: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:08:03: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:08:03: #1 total tags in treatment: 651914 INFO @ Sat, 03 Jun 2017 04:08:03: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:08:03: #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 04:08:03: #1 tags after filtering in treatment: 651852 INFO @ Sat, 03 Jun 2017 04:08:03: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:08:03: #1 finished! INFO @ Sat, 03 Jun 2017 04:08:03: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:08:03: #1 tags after filtering in treatment: 651852 INFO @ Sat, 03 Jun 2017 04:08:03: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:08:03: #1 finished! INFO @ Sat, 03 Jun 2017 04:08:03: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:08:03: #1 tags after filtering in treatment: 651852 INFO @ Sat, 03 Jun 2017 04:08:03: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:08:03: #1 finished! INFO @ Sat, 03 Jun 2017 04:08:03: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:08:03: #2 number of paired peaks: 323 WARNING @ Sat, 03 Jun 2017 04:08:03: Fewer paired peaks (323) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 323 pairs to build model! INFO @ Sat, 03 Jun 2017 04:08:03: start model_add_line... INFO @ Sat, 03 Jun 2017 04:08:03: #2 number of paired peaks: 323 WARNING @ Sat, 03 Jun 2017 04:08:03: Fewer paired peaks (323) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 323 pairs to build model! INFO @ Sat, 03 Jun 2017 04:08:03: start model_add_line... INFO @ Sat, 03 Jun 2017 04:08:04: #2 number of paired peaks: 323 WARNING @ Sat, 03 Jun 2017 04:08:04: Fewer paired peaks (323) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 323 pairs to build model! INFO @ Sat, 03 Jun 2017 04:08:04: start model_add_line... INFO @ Sat, 03 Jun 2017 04:08:04: start X-correlation... INFO @ Sat, 03 Jun 2017 04:08:04: end of X-cor INFO @ Sat, 03 Jun 2017 04:08:04: #2 finished! INFO @ Sat, 03 Jun 2017 04:08:04: #2 predicted fragment length is 49 bps INFO @ Sat, 03 Jun 2017 04:08:04: #2 alternative fragment length(s) may be 49,151,214,368,424,462,508,554,580 bps INFO @ Sat, 03 Jun 2017 04:08:04: #2.2 Generate R script for model : SRX1388748.10_model.r WARNING @ Sat, 03 Jun 2017 04:08:04: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 04:08:04: #2 You may need to consider one of the other alternative d(s): 49,151,214,368,424,462,508,554,580 WARNING @ Sat, 03 Jun 2017 04:08:04: #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 04:08:04: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:08:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:08:04: start X-correlation... INFO @ Sat, 03 Jun 2017 04:08:04: end of X-cor INFO @ Sat, 03 Jun 2017 04:08:04: #2 finished! INFO @ Sat, 03 Jun 2017 04:08:04: #2 predicted fragment length is 49 bps INFO @ Sat, 03 Jun 2017 04:08:04: #2 alternative fragment length(s) may be 49,151,214,368,424,462,508,554,580 bps INFO @ Sat, 03 Jun 2017 04:08:04: #2.2 Generate R script for model : SRX1388748.05_model.r WARNING @ Sat, 03 Jun 2017 04:08:04: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 04:08:04: #2 You may need to consider one of the other alternative d(s): 49,151,214,368,424,462,508,554,580 WARNING @ Sat, 03 Jun 2017 04:08:04: #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 04:08:04: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:08:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:08:04: start X-correlation... INFO @ Sat, 03 Jun 2017 04:08:04: end of X-cor INFO @ Sat, 03 Jun 2017 04:08:04: #2 finished! INFO @ Sat, 03 Jun 2017 04:08:04: #2 predicted fragment length is 49 bps INFO @ Sat, 03 Jun 2017 04:08:04: #2 alternative fragment length(s) may be 49,151,214,368,424,462,508,554,580 bps INFO @ Sat, 03 Jun 2017 04:08:04: #2.2 Generate R script for model : SRX1388748.20_model.r WARNING @ Sat, 03 Jun 2017 04:08:04: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 04:08:04: #2 You may need to consider one of the other alternative d(s): 49,151,214,368,424,462,508,554,580 WARNING @ Sat, 03 Jun 2017 04:08:04: #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 04:08:04: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:08:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:08:08: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:08:08: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:08:08: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:08:11: #4 Write output xls file... SRX1388748.05_peaks.xls INFO @ Sat, 03 Jun 2017 04:08:11: #4 Write peak in narrowPeak format file... SRX1388748.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:08:11: #4 Write summits bed file... SRX1388748.05_summits.bed INFO @ Sat, 03 Jun 2017 04:08:11: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (131 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:08:11: #4 Write output xls file... SRX1388748.10_peaks.xls INFO @ Sat, 03 Jun 2017 04:08:11: #4 Write peak in narrowPeak format file... SRX1388748.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:08:11: #4 Write summits bed file... SRX1388748.10_summits.bed INFO @ Sat, 03 Jun 2017 04:08:11: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (73 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:08:11: #4 Write output xls file... SRX1388748.20_peaks.xls INFO @ Sat, 03 Jun 2017 04:08:11: #4 Write peak in narrowPeak format file... SRX1388748.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:08:11: #4 Write summits bed file... SRX1388748.20_summits.bed INFO @ Sat, 03 Jun 2017 04:08:11: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (29 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。