Job ID = 9028907 sra ファイルのダウンロード中... Completed: 203713K bytes transferred in 4 seconds (361840K 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 11247 0 11247 0 0 1533 0 --:--:-- 0:00:07 --:--:-- 14345 100 44726 0 44726 0 0 5369 0 --:--:-- 0:00:08 --:--:-- 25141 100 61150 0 61150 0 0 7197 0 --:--:-- 0:00:08 --:--:-- 31423 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 8813316 spots for /home/okishinya/chipatlas/results/ce10/SRX982103/SRR1956590.sra Written 8813316 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: 00:01:45 8813316 reads; of these: 8813316 (100.00%) were unpaired; of these: 3813114 (43.27%) aligned 0 times 4173189 (47.35%) aligned exactly 1 time 827013 (9.38%) aligned >1 times 56.73% overall alignment rate Time searching: 00:01:45 Overall time: 00:01:45 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] 236509 / 5000202 = 0.0473 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 12:22:33: # Command line: callpeak -t SRX982103.bam -f BAM -g ce -n SRX982103.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX982103.05 # format = BAM # ChIP-seq file = ['SRX982103.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 12:22:33: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:22:33: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:22:33: # Command line: callpeak -t SRX982103.bam -f BAM -g ce -n SRX982103.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX982103.10 # format = BAM # ChIP-seq file = ['SRX982103.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 12:22:33: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:22:33: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:22:33: # Command line: callpeak -t SRX982103.bam -f BAM -g ce -n SRX982103.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX982103.20 # format = BAM # ChIP-seq file = ['SRX982103.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 12:22:33: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:22:33: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:22:40: 1000000 INFO @ Sat, 03 Jun 2017 12:22:40: 1000000 INFO @ Sat, 03 Jun 2017 12:22:40: 1000000 INFO @ Sat, 03 Jun 2017 12:22:46: 2000000 INFO @ Sat, 03 Jun 2017 12:22:46: 2000000 INFO @ Sat, 03 Jun 2017 12:22:47: 2000000 INFO @ Sat, 03 Jun 2017 12:22:53: 3000000 INFO @ Sat, 03 Jun 2017 12:22:53: 3000000 INFO @ Sat, 03 Jun 2017 12:22:54: 3000000 INFO @ Sat, 03 Jun 2017 12:23:00: 4000000 INFO @ Sat, 03 Jun 2017 12:23:00: 4000000 INFO @ Sat, 03 Jun 2017 12:23:01: 4000000 INFO @ Sat, 03 Jun 2017 12:23:05: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 12:23:05: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 12:23:05: #1 total tags in treatment: 4763693 INFO @ Sat, 03 Jun 2017 12:23:05: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:23:05: #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 12:23:05: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 12:23:05: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 12:23:05: #1 total tags in treatment: 4763693 INFO @ Sat, 03 Jun 2017 12:23:05: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:23:05: #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 12:23:05: #1 tags after filtering in treatment: 4763249 INFO @ Sat, 03 Jun 2017 12:23:05: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:23:05: #1 finished! INFO @ Sat, 03 Jun 2017 12:23:05: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:23:06: #1 tags after filtering in treatment: 4763249 INFO @ Sat, 03 Jun 2017 12:23:06: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:23:06: #1 finished! INFO @ Sat, 03 Jun 2017 12:23:06: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:23:06: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 12:23:06: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 12:23:06: #1 total tags in treatment: 4763693 INFO @ Sat, 03 Jun 2017 12:23:06: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:23:06: #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 12:23:06: #2 number of paired peaks: 362 WARNING @ Sat, 03 Jun 2017 12:23:06: Fewer paired peaks (362) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 362 pairs to build model! INFO @ Sat, 03 Jun 2017 12:23:06: start model_add_line... INFO @ Sat, 03 Jun 2017 12:23:07: #1 tags after filtering in treatment: 4763249 INFO @ Sat, 03 Jun 2017 12:23:07: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:23:07: #1 finished! INFO @ Sat, 03 Jun 2017 12:23:07: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:23:07: #2 number of paired peaks: 362 WARNING @ Sat, 03 Jun 2017 12:23:07: Fewer paired peaks (362) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 362 pairs to build model! INFO @ Sat, 03 Jun 2017 12:23:07: start model_add_line... INFO @ Sat, 03 Jun 2017 12:23:07: #2 number of paired peaks: 362 WARNING @ Sat, 03 Jun 2017 12:23:07: Fewer paired peaks (362) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 362 pairs to build model! INFO @ Sat, 03 Jun 2017 12:23:07: start model_add_line... INFO @ Sat, 03 Jun 2017 12:23:09: start X-correlation... INFO @ Sat, 03 Jun 2017 12:23:09: end of X-cor INFO @ Sat, 03 Jun 2017 12:23:09: #2 finished! INFO @ Sat, 03 Jun 2017 12:23:09: #2 predicted fragment length is 51 bps INFO @ Sat, 03 Jun 2017 12:23:09: #2 alternative fragment length(s) may be 51,571 bps INFO @ Sat, 03 Jun 2017 12:23:09: #2.2 Generate R script for model : SRX982103.05_model.r WARNING @ Sat, 03 Jun 2017 12:23:09: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 12:23:09: #2 You may need to consider one of the other alternative d(s): 51,571 WARNING @ Sat, 03 Jun 2017 12:23:09: #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 12:23:09: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:23:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:23:10: start X-correlation... INFO @ Sat, 03 Jun 2017 12:23:10: end of X-cor INFO @ Sat, 03 Jun 2017 12:23:10: #2 finished! INFO @ Sat, 03 Jun 2017 12:23:10: #2 predicted fragment length is 51 bps INFO @ Sat, 03 Jun 2017 12:23:10: #2 alternative fragment length(s) may be 51,571 bps INFO @ Sat, 03 Jun 2017 12:23:10: #2.2 Generate R script for model : SRX982103.10_model.r WARNING @ Sat, 03 Jun 2017 12:23:10: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 12:23:10: #2 You may need to consider one of the other alternative d(s): 51,571 WARNING @ Sat, 03 Jun 2017 12:23:10: #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 12:23:10: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:23:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:23:10: start X-correlation... INFO @ Sat, 03 Jun 2017 12:23:10: end of X-cor INFO @ Sat, 03 Jun 2017 12:23:10: #2 finished! INFO @ Sat, 03 Jun 2017 12:23:10: #2 predicted fragment length is 51 bps INFO @ Sat, 03 Jun 2017 12:23:10: #2 alternative fragment length(s) may be 51,571 bps INFO @ Sat, 03 Jun 2017 12:23:10: #2.2 Generate R script for model : SRX982103.20_model.r WARNING @ Sat, 03 Jun 2017 12:23:10: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 12:23:10: #2 You may need to consider one of the other alternative d(s): 51,571 WARNING @ Sat, 03 Jun 2017 12:23:10: #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 12:23:10: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:23:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:23:38: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:23:38: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:23:39: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:23:58: #4 Write output xls file... SRX982103.10_peaks.xls INFO @ Sat, 03 Jun 2017 12:23:58: #4 Write peak in narrowPeak format file... SRX982103.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:23:58: #4 Write summits bed file... SRX982103.10_summits.bed INFO @ Sat, 03 Jun 2017 12:23:58: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (273 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 12:23:59: #4 Write output xls file... SRX982103.20_peaks.xls INFO @ Sat, 03 Jun 2017 12:23:59: #4 Write peak in narrowPeak format file... SRX982103.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:23:59: #4 Write summits bed file... SRX982103.20_summits.bed INFO @ Sat, 03 Jun 2017 12:23:59: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (117 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 12:23:59: #4 Write output xls file... SRX982103.05_peaks.xls INFO @ Sat, 03 Jun 2017 12:23:59: #4 Write peak in narrowPeak format file... SRX982103.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:23:59: #4 Write summits bed file... SRX982103.05_summits.bed INFO @ Sat, 03 Jun 2017 12:23:59: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (440 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。