Job ID = 9028839 sra ファイルのダウンロード中... Completed: 201131K bytes transferred in 5 seconds (315237K 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 7663 0 7663 0 0 1089 0 --:--:-- 0:00:07 --:--:-- 12419 100 36038 0 36038 0 0 4486 0 --:--:-- 0:00:08 --:--:-- 22342 100 52344 0 52344 0 0 6383 0 --:--:-- 0:00:08 --:--:-- 29390 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 5885804 spots for /home/okishinya/chipatlas/results/ce10/SRX982071/SRR1956549.sra Written 5885804 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: 00:01:35 5885804 reads; of these: 5885804 (100.00%) were unpaired; of these: 213507 (3.63%) aligned 0 times 4672343 (79.38%) aligned exactly 1 time 999954 (16.99%) aligned >1 times 96.37% overall alignment rate Time searching: 00:01:35 Overall time: 00:01:35 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] 1590998 / 5672297 = 0.2805 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 12:00:49: # Command line: callpeak -t SRX982071.bam -f BAM -g ce -n SRX982071.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX982071.05 # format = BAM # ChIP-seq file = ['SRX982071.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 12:00:49: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:00:49: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:00:49: # Command line: callpeak -t SRX982071.bam -f BAM -g ce -n SRX982071.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX982071.20 # format = BAM # ChIP-seq file = ['SRX982071.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 12:00:49: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:00:49: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:00:49: # Command line: callpeak -t SRX982071.bam -f BAM -g ce -n SRX982071.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX982071.10 # format = BAM # ChIP-seq file = ['SRX982071.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 12:00:49: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:00:49: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:00:55: 1000000 INFO @ Sat, 03 Jun 2017 12:00:56: 1000000 INFO @ Sat, 03 Jun 2017 12:00:56: 1000000 INFO @ Sat, 03 Jun 2017 12:01:01: 2000000 INFO @ Sat, 03 Jun 2017 12:01:03: 2000000 INFO @ Sat, 03 Jun 2017 12:01:03: 2000000 INFO @ Sat, 03 Jun 2017 12:01:06: 3000000 INFO @ Sat, 03 Jun 2017 12:01:10: 3000000 INFO @ Sat, 03 Jun 2017 12:01:10: 3000000 INFO @ Sat, 03 Jun 2017 12:01:12: 4000000 INFO @ Sat, 03 Jun 2017 12:01:13: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 12:01:13: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 12:01:13: #1 total tags in treatment: 4081299 INFO @ Sat, 03 Jun 2017 12:01:13: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:01:13: #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 12:01:13: #1 tags after filtering in treatment: 4080799 INFO @ Sat, 03 Jun 2017 12:01:13: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:01:13: #1 finished! INFO @ Sat, 03 Jun 2017 12:01:13: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:01:14: #2 number of paired peaks: 463 WARNING @ Sat, 03 Jun 2017 12:01:14: Fewer paired peaks (463) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 463 pairs to build model! INFO @ Sat, 03 Jun 2017 12:01:14: start model_add_line... INFO @ Sat, 03 Jun 2017 12:01:17: 4000000 INFO @ Sat, 03 Jun 2017 12:01:17: 4000000 INFO @ Sat, 03 Jun 2017 12:01:17: start X-correlation... INFO @ Sat, 03 Jun 2017 12:01:17: end of X-cor INFO @ Sat, 03 Jun 2017 12:01:17: #2 finished! INFO @ Sat, 03 Jun 2017 12:01:17: #2 predicted fragment length is 50 bps INFO @ Sat, 03 Jun 2017 12:01:17: #2 alternative fragment length(s) may be 50,487 bps INFO @ Sat, 03 Jun 2017 12:01:17: #2.2 Generate R script for model : SRX982071.05_model.r WARNING @ Sat, 03 Jun 2017 12:01:18: #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 12:01:18: #2 You may need to consider one of the other alternative d(s): 50,487 WARNING @ Sat, 03 Jun 2017 12:01:18: #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 12:01:18: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:01:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:01:18: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 12:01:18: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 12:01:18: #1 total tags in treatment: 4081299 INFO @ Sat, 03 Jun 2017 12:01:18: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:01:18: #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 12:01:18: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 12:01:18: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 12:01:18: #1 total tags in treatment: 4081299 INFO @ Sat, 03 Jun 2017 12:01:18: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:01:18: #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 12:01:19: #1 tags after filtering in treatment: 4080799 INFO @ Sat, 03 Jun 2017 12:01:19: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:01:19: #1 finished! INFO @ Sat, 03 Jun 2017 12:01:19: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:01:19: #1 tags after filtering in treatment: 4080799 INFO @ Sat, 03 Jun 2017 12:01:19: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:01:19: #1 finished! INFO @ Sat, 03 Jun 2017 12:01:19: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:01:20: #2 number of paired peaks: 463 WARNING @ Sat, 03 Jun 2017 12:01:20: Fewer paired peaks (463) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 463 pairs to build model! INFO @ Sat, 03 Jun 2017 12:01:20: start model_add_line... INFO @ Sat, 03 Jun 2017 12:01:20: #2 number of paired peaks: 463 WARNING @ Sat, 03 Jun 2017 12:01:20: Fewer paired peaks (463) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 463 pairs to build model! INFO @ Sat, 03 Jun 2017 12:01:20: start model_add_line... INFO @ Sat, 03 Jun 2017 12:01:23: start X-correlation... INFO @ Sat, 03 Jun 2017 12:01:23: start X-correlation... INFO @ Sat, 03 Jun 2017 12:01:23: end of X-cor INFO @ Sat, 03 Jun 2017 12:01:23: #2 finished! INFO @ Sat, 03 Jun 2017 12:01:23: #2 predicted fragment length is 50 bps INFO @ Sat, 03 Jun 2017 12:01:23: #2 alternative fragment length(s) may be 50,487 bps INFO @ Sat, 03 Jun 2017 12:01:23: #2.2 Generate R script for model : SRX982071.20_model.r INFO @ Sat, 03 Jun 2017 12:01:23: end of X-cor INFO @ Sat, 03 Jun 2017 12:01:23: #2 finished! INFO @ Sat, 03 Jun 2017 12:01:23: #2 predicted fragment length is 50 bps INFO @ Sat, 03 Jun 2017 12:01:23: #2 alternative fragment length(s) may be 50,487 bps INFO @ Sat, 03 Jun 2017 12:01:23: #2.2 Generate R script for model : SRX982071.10_model.r WARNING @ Sat, 03 Jun 2017 12:01:23: #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 12:01:23: #2 You may need to consider one of the other alternative d(s): 50,487 WARNING @ Sat, 03 Jun 2017 12:01:23: #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 12:01:23: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:01:23: #3 Pre-compute pvalue-qvalue table... WARNING @ Sat, 03 Jun 2017 12:01:23: #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 12:01:23: #2 You may need to consider one of the other alternative d(s): 50,487 WARNING @ Sat, 03 Jun 2017 12:01:23: #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 12:01:23: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:01:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:01:42: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:01:48: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:01:48: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:02:00: #4 Write output xls file... SRX982071.05_peaks.xls INFO @ Sat, 03 Jun 2017 12:02:00: #4 Write peak in narrowPeak format file... SRX982071.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:02:00: #4 Write summits bed file... SRX982071.05_summits.bed INFO @ Sat, 03 Jun 2017 12:02:00: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (543 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 12:02:06: #4 Write output xls file... SRX982071.20_peaks.xls INFO @ Sat, 03 Jun 2017 12:02:06: #4 Write peak in narrowPeak format file... SRX982071.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:02:06: #4 Write summits bed file... SRX982071.20_summits.bed INFO @ Sat, 03 Jun 2017 12:02:06: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (138 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 12:02:06: #4 Write output xls file... SRX982071.10_peaks.xls INFO @ Sat, 03 Jun 2017 12:02:06: #4 Write peak in narrowPeak format file... SRX982071.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:02:06: #4 Write summits bed file... SRX982071.10_summits.bed INFO @ Sat, 03 Jun 2017 12:02:06: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (324 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。