Job ID = 9157255 sra ファイルのダウンロード中... Completed: 377320K bytes transferred in 6 seconds (482039K bits/sec), in 1 file, 2 directories. 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 8201532 spots for /home/okishinya/chipatlas/results/ce10/SRX2350739/SRR5024048.sra Written 8201532 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: 00:02:06 8201532 reads; of these: 8201532 (100.00%) were unpaired; of these: 133471 (1.63%) aligned 0 times 7082306 (86.35%) aligned exactly 1 time 985755 (12.02%) aligned >1 times 98.37% overall alignment rate Time searching: 00:02:06 Overall time: 00:02:06 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] 726307 / 8068061 = 0.0900 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 @ Tue, 27 Jun 2017 11:16:30: # Command line: callpeak -t SRX2350739.bam -f BAM -g ce -n SRX2350739.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2350739.10 # format = BAM # ChIP-seq file = ['SRX2350739.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 # Paired-End mode is off INFO @ Tue, 27 Jun 2017 11:16:30: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:16:30: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:16:30: # Command line: callpeak -t SRX2350739.bam -f BAM -g ce -n SRX2350739.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2350739.20 # format = BAM # ChIP-seq file = ['SRX2350739.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 # Paired-End mode is off INFO @ Tue, 27 Jun 2017 11:16:30: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:16:30: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:16:30: # Command line: callpeak -t SRX2350739.bam -f BAM -g ce -n SRX2350739.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2350739.05 # format = BAM # ChIP-seq file = ['SRX2350739.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 # Paired-End mode is off INFO @ Tue, 27 Jun 2017 11:16:30: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:16:30: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:16:37: 1000000 INFO @ Tue, 27 Jun 2017 11:16:37: 1000000 INFO @ Tue, 27 Jun 2017 11:16:37: 1000000 INFO @ Tue, 27 Jun 2017 11:16:44: 2000000 INFO @ Tue, 27 Jun 2017 11:16:45: 2000000 INFO @ Tue, 27 Jun 2017 11:16:45: 2000000 INFO @ Tue, 27 Jun 2017 11:16:51: 3000000 INFO @ Tue, 27 Jun 2017 11:16:53: 3000000 INFO @ Tue, 27 Jun 2017 11:16:53: 3000000 INFO @ Tue, 27 Jun 2017 11:16:59: 4000000 INFO @ Tue, 27 Jun 2017 11:17:01: 4000000 INFO @ Tue, 27 Jun 2017 11:17:01: 4000000 INFO @ Tue, 27 Jun 2017 11:17:06: 5000000 INFO @ Tue, 27 Jun 2017 11:17:09: 5000000 INFO @ Tue, 27 Jun 2017 11:17:09: 5000000 INFO @ Tue, 27 Jun 2017 11:17:13: 6000000 INFO @ Tue, 27 Jun 2017 11:17:17: 6000000 INFO @ Tue, 27 Jun 2017 11:17:17: 6000000 INFO @ Tue, 27 Jun 2017 11:17:20: 7000000 INFO @ Tue, 27 Jun 2017 11:17:23: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:17:23: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:17:23: #1 total tags in treatment: 7341754 INFO @ Tue, 27 Jun 2017 11:17:23: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:17:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 11:17:23: #1 tags after filtering in treatment: 7341754 INFO @ Tue, 27 Jun 2017 11:17:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:17:23: #1 finished! INFO @ Tue, 27 Jun 2017 11:17:23: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:17:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:17:24: #2 number of paired peaks: 155 WARNING @ Tue, 27 Jun 2017 11:17:24: Fewer paired peaks (155) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 155 pairs to build model! INFO @ Tue, 27 Jun 2017 11:17:24: start model_add_line... INFO @ Tue, 27 Jun 2017 11:17:24: start X-correlation... INFO @ Tue, 27 Jun 2017 11:17:24: end of X-cor INFO @ Tue, 27 Jun 2017 11:17:24: #2 finished! INFO @ Tue, 27 Jun 2017 11:17:24: #2 predicted fragment length is 51 bps INFO @ Tue, 27 Jun 2017 11:17:24: #2 alternative fragment length(s) may be 4,51,179,202,400,417,486 bps INFO @ Tue, 27 Jun 2017 11:17:24: #2.2 Generate R script for model : SRX2350739.10_model.r WARNING @ Tue, 27 Jun 2017 11:17:24: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:17:24: #2 You may need to consider one of the other alternative d(s): 4,51,179,202,400,417,486 WARNING @ Tue, 27 Jun 2017 11:17:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 11:17:24: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:17:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:17:26: 7000000 INFO @ Tue, 27 Jun 2017 11:17:26: 7000000 INFO @ Tue, 27 Jun 2017 11:17:28: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:17:28: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:17:28: #1 total tags in treatment: 7341754 INFO @ Tue, 27 Jun 2017 11:17:28: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:17:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 11:17:28: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:17:28: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:17:28: #1 total tags in treatment: 7341754 INFO @ Tue, 27 Jun 2017 11:17:28: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:17:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 11:17:28: #1 tags after filtering in treatment: 7341754 INFO @ Tue, 27 Jun 2017 11:17:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:17:28: #1 finished! INFO @ Tue, 27 Jun 2017 11:17:28: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:17:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:17:28: #1 tags after filtering in treatment: 7341754 INFO @ Tue, 27 Jun 2017 11:17:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:17:28: #1 finished! INFO @ Tue, 27 Jun 2017 11:17:28: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:17:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:17:29: #2 number of paired peaks: 155 WARNING @ Tue, 27 Jun 2017 11:17:29: Fewer paired peaks (155) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 155 pairs to build model! INFO @ Tue, 27 Jun 2017 11:17:29: start model_add_line... INFO @ Tue, 27 Jun 2017 11:17:29: #2 number of paired peaks: 155 WARNING @ Tue, 27 Jun 2017 11:17:29: Fewer paired peaks (155) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 155 pairs to build model! INFO @ Tue, 27 Jun 2017 11:17:29: start model_add_line... INFO @ Tue, 27 Jun 2017 11:17:29: start X-correlation... INFO @ Tue, 27 Jun 2017 11:17:29: end of X-cor INFO @ Tue, 27 Jun 2017 11:17:29: #2 finished! INFO @ Tue, 27 Jun 2017 11:17:29: #2 predicted fragment length is 51 bps INFO @ Tue, 27 Jun 2017 11:17:29: #2 alternative fragment length(s) may be 4,51,179,202,400,417,486 bps INFO @ Tue, 27 Jun 2017 11:17:29: #2.2 Generate R script for model : SRX2350739.05_model.r WARNING @ Tue, 27 Jun 2017 11:17:29: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:17:29: #2 You may need to consider one of the other alternative d(s): 4,51,179,202,400,417,486 WARNING @ Tue, 27 Jun 2017 11:17:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 11:17:29: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:17:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:17:29: start X-correlation... INFO @ Tue, 27 Jun 2017 11:17:29: end of X-cor INFO @ Tue, 27 Jun 2017 11:17:29: #2 finished! INFO @ Tue, 27 Jun 2017 11:17:29: #2 predicted fragment length is 51 bps INFO @ Tue, 27 Jun 2017 11:17:29: #2 alternative fragment length(s) may be 4,51,179,202,400,417,486 bps INFO @ Tue, 27 Jun 2017 11:17:29: #2.2 Generate R script for model : SRX2350739.20_model.r WARNING @ Tue, 27 Jun 2017 11:17:29: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:17:29: #2 You may need to consider one of the other alternative d(s): 4,51,179,202,400,417,486 WARNING @ Tue, 27 Jun 2017 11:17:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 11:17:29: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:17:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:17:39: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:17:45: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:17:45: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:17:49: #4 Write output xls file... SRX2350739.10_peaks.xls INFO @ Tue, 27 Jun 2017 11:17:49: #4 Write peak in narrowPeak format file... SRX2350739.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:17:49: #4 Write summits bed file... SRX2350739.10_summits.bed INFO @ Tue, 27 Jun 2017 11:17:49: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (163 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:17:54: #4 Write output xls file... SRX2350739.20_peaks.xls INFO @ Tue, 27 Jun 2017 11:17:54: #4 Write peak in narrowPeak format file... SRX2350739.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:17:54: #4 Write summits bed file... SRX2350739.20_summits.bed INFO @ Tue, 27 Jun 2017 11:17:54: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (52 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:17:54: #4 Write output xls file... SRX2350739.05_peaks.xls INFO @ Tue, 27 Jun 2017 11:17:54: #4 Write peak in narrowPeak format file... SRX2350739.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:17:54: #4 Write summits bed file... SRX2350739.05_summits.bed INFO @ Tue, 27 Jun 2017 11:17:54: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (293 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。