Job ID = 9028893 sra ファイルのダウンロード中... Completed: 419317K bytes transferred in 7 seconds (481618K 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 1948 0 --:--:-- 0:00:07 --:--:-- 15740 100 42590 0 42590 0 0 5002 0 --:--:-- 0:00:08 --:--:-- 20564 100 56044 0 56044 0 0 6335 0 --:--:-- 0:00:08 --:--:-- 23322 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 12516168 spots for /home/okishinya/chipatlas/results/ce10/SRX982096/SRR1956583.sra Written 12516168 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: 00:03:46 12516168 reads; of these: 12516168 (100.00%) were unpaired; of these: 236830 (1.89%) aligned 0 times 10351818 (82.71%) aligned exactly 1 time 1927520 (15.40%) aligned >1 times 98.11% overall alignment rate Time searching: 00:03:46 Overall time: 00:03:46 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_sort_core] merging from 8 files... [bam_rmdupse_core] 887751 / 12279338 = 0.0723 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 12:21:35: # Command line: callpeak -t SRX982096.bam -f BAM -g ce -n SRX982096.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX982096.20 # format = BAM # ChIP-seq file = ['SRX982096.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 12:21:35: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:21:35: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:21:35: # Command line: callpeak -t SRX982096.bam -f BAM -g ce -n SRX982096.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX982096.10 # format = BAM # ChIP-seq file = ['SRX982096.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 12:21:35: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:21:35: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:21:35: # Command line: callpeak -t SRX982096.bam -f BAM -g ce -n SRX982096.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX982096.05 # format = BAM # ChIP-seq file = ['SRX982096.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 12:21:35: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:21:35: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:21:42: 1000000 INFO @ Sat, 03 Jun 2017 12:21:42: 1000000 INFO @ Sat, 03 Jun 2017 12:21:42: 1000000 INFO @ Sat, 03 Jun 2017 12:21:49: 2000000 INFO @ Sat, 03 Jun 2017 12:21:49: 2000000 INFO @ Sat, 03 Jun 2017 12:21:49: 2000000 INFO @ Sat, 03 Jun 2017 12:21:57: 3000000 INFO @ Sat, 03 Jun 2017 12:21:57: 3000000 INFO @ Sat, 03 Jun 2017 12:21:57: 3000000 INFO @ Sat, 03 Jun 2017 12:22:04: 4000000 INFO @ Sat, 03 Jun 2017 12:22:04: 4000000 INFO @ Sat, 03 Jun 2017 12:22:04: 4000000 INFO @ Sat, 03 Jun 2017 12:22:11: 5000000 INFO @ Sat, 03 Jun 2017 12:22:11: 5000000 INFO @ Sat, 03 Jun 2017 12:22:11: 5000000 INFO @ Sat, 03 Jun 2017 12:22:18: 6000000 INFO @ Sat, 03 Jun 2017 12:22:18: 6000000 INFO @ Sat, 03 Jun 2017 12:22:19: 6000000 INFO @ Sat, 03 Jun 2017 12:22:26: 7000000 INFO @ Sat, 03 Jun 2017 12:22:26: 7000000 INFO @ Sat, 03 Jun 2017 12:22:26: 7000000 INFO @ Sat, 03 Jun 2017 12:22:33: 8000000 INFO @ Sat, 03 Jun 2017 12:22:33: 8000000 INFO @ Sat, 03 Jun 2017 12:22:33: 8000000 INFO @ Sat, 03 Jun 2017 12:22:40: 9000000 INFO @ Sat, 03 Jun 2017 12:22:40: 9000000 INFO @ Sat, 03 Jun 2017 12:22:40: 9000000 INFO @ Sat, 03 Jun 2017 12:22:47: 10000000 INFO @ Sat, 03 Jun 2017 12:22:47: 10000000 INFO @ Sat, 03 Jun 2017 12:22:47: 10000000 INFO @ Sat, 03 Jun 2017 12:22:54: 11000000 INFO @ Sat, 03 Jun 2017 12:22:54: 11000000 INFO @ Sat, 03 Jun 2017 12:22:54: 11000000 INFO @ Sat, 03 Jun 2017 12:22:57: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 12:22:57: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 12:22:57: #1 total tags in treatment: 11391587 INFO @ Sat, 03 Jun 2017 12:22:57: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:22:57: #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 12:22:57: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 12:22:57: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 12:22:57: #1 total tags in treatment: 11391587 INFO @ Sat, 03 Jun 2017 12:22:57: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:22:57: #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 12:22:57: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 12:22:57: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 12:22:57: #1 total tags in treatment: 11391587 INFO @ Sat, 03 Jun 2017 12:22:57: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:22:57: #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 12:22:59: #1 tags after filtering in treatment: 11390407 INFO @ Sat, 03 Jun 2017 12:22:59: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:22:59: #1 finished! INFO @ Sat, 03 Jun 2017 12:22:59: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:23:00: #1 tags after filtering in treatment: 11390407 INFO @ Sat, 03 Jun 2017 12:23:00: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:23:00: #1 finished! INFO @ Sat, 03 Jun 2017 12:23:00: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:23:00: #1 tags after filtering in treatment: 11390407 INFO @ Sat, 03 Jun 2017 12:23:00: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:23:00: #1 finished! INFO @ Sat, 03 Jun 2017 12:23:00: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:23:01: #2 number of paired peaks: 267 WARNING @ Sat, 03 Jun 2017 12:23:01: Fewer paired peaks (267) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 267 pairs to build model! INFO @ Sat, 03 Jun 2017 12:23:01: start model_add_line... INFO @ Sat, 03 Jun 2017 12:23:02: #2 number of paired peaks: 267 WARNING @ Sat, 03 Jun 2017 12:23:02: Fewer paired peaks (267) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 267 pairs to build model! INFO @ Sat, 03 Jun 2017 12:23:02: start model_add_line... INFO @ Sat, 03 Jun 2017 12:23:02: #2 number of paired peaks: 267 WARNING @ Sat, 03 Jun 2017 12:23:02: Fewer paired peaks (267) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 267 pairs to build model! INFO @ Sat, 03 Jun 2017 12:23:02: start model_add_line... INFO @ Sat, 03 Jun 2017 12:23:06: start X-correlation... INFO @ Sat, 03 Jun 2017 12:23:06: end of X-cor INFO @ Sat, 03 Jun 2017 12:23:06: #2 finished! INFO @ Sat, 03 Jun 2017 12:23:06: #2 predicted fragment length is 49 bps INFO @ Sat, 03 Jun 2017 12:23:06: #2 alternative fragment length(s) may be 2,49 bps INFO @ Sat, 03 Jun 2017 12:23:06: #2.2 Generate R script for model : SRX982096.10_model.r WARNING @ Sat, 03 Jun 2017 12:23:06: #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 12:23:06: #2 You may need to consider one of the other alternative d(s): 2,49 WARNING @ Sat, 03 Jun 2017 12:23:06: #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 12:23:06: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:23:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:23:06: start X-correlation... INFO @ Sat, 03 Jun 2017 12:23:06: end of X-cor INFO @ Sat, 03 Jun 2017 12:23:06: #2 finished! INFO @ Sat, 03 Jun 2017 12:23:06: #2 predicted fragment length is 49 bps INFO @ Sat, 03 Jun 2017 12:23:06: #2 alternative fragment length(s) may be 2,49 bps INFO @ Sat, 03 Jun 2017 12:23:06: #2.2 Generate R script for model : SRX982096.20_model.r WARNING @ Sat, 03 Jun 2017 12:23:06: #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 12:23:06: #2 You may need to consider one of the other alternative d(s): 2,49 WARNING @ Sat, 03 Jun 2017 12:23:06: #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 12:23:06: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:23:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:23:07: start X-correlation... INFO @ Sat, 03 Jun 2017 12:23:07: end of X-cor INFO @ Sat, 03 Jun 2017 12:23:07: #2 finished! INFO @ Sat, 03 Jun 2017 12:23:07: #2 predicted fragment length is 49 bps INFO @ Sat, 03 Jun 2017 12:23:07: #2 alternative fragment length(s) may be 2,49 bps INFO @ Sat, 03 Jun 2017 12:23:07: #2.2 Generate R script for model : SRX982096.05_model.r WARNING @ Sat, 03 Jun 2017 12:23:07: #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 12:23:07: #2 You may need to consider one of the other alternative d(s): 2,49 WARNING @ Sat, 03 Jun 2017 12:23:07: #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 12:23:07: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:23:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:24:03: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:24:06: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:24:08: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:24:45: #4 Write output xls file... SRX982096.10_peaks.xls INFO @ Sat, 03 Jun 2017 12:24:45: #4 Write peak in narrowPeak format file... SRX982096.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:24:45: #4 Write summits bed file... SRX982096.10_summits.bed INFO @ Sat, 03 Jun 2017 12:24:45: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (360 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 12:24:47: #4 Write output xls file... SRX982096.05_peaks.xls INFO @ Sat, 03 Jun 2017 12:24:47: #4 Write peak in narrowPeak format file... SRX982096.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:24:47: #4 Write summits bed file... SRX982096.05_summits.bed INFO @ Sat, 03 Jun 2017 12:24:47: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (566 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 12:24:49: #4 Write output xls file... SRX982096.20_peaks.xls INFO @ Sat, 03 Jun 2017 12:24:49: #4 Write peak in narrowPeak format file... SRX982096.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:24:49: #4 Write summits bed file... SRX982096.20_summits.bed INFO @ Sat, 03 Jun 2017 12:24:49: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (138 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。