Job ID = 9157186 sra ファイルのダウンロード中... Completed: 247215K bytes transferred in 5 seconds (399084K 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 10896785 spots for /home/okishinya/chipatlas/results/ce10/SRX2228903/SRR4380359.sra Written 10896785 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: 00:01:58 10896785 reads; of these: 10896785 (100.00%) were unpaired; of these: 6495976 (59.61%) aligned 0 times 3120217 (28.63%) aligned exactly 1 time 1280592 (11.75%) aligned >1 times 40.39% overall alignment rate Time searching: 00:01:58 Overall time: 00:01:58 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] 1132214 / 4400809 = 0.2573 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 10:58:16: # Command line: callpeak -t SRX2228903.bam -f BAM -g ce -n SRX2228903.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2228903.20 # format = BAM # ChIP-seq file = ['SRX2228903.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 10:58:16: #1 read tag files... INFO @ Tue, 27 Jun 2017 10:58:16: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 10:58:16: # Command line: callpeak -t SRX2228903.bam -f BAM -g ce -n SRX2228903.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2228903.05 # format = BAM # ChIP-seq file = ['SRX2228903.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 10:58:16: #1 read tag files... INFO @ Tue, 27 Jun 2017 10:58:16: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 10:58:16: # Command line: callpeak -t SRX2228903.bam -f BAM -g ce -n SRX2228903.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2228903.10 # format = BAM # ChIP-seq file = ['SRX2228903.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 10:58:16: #1 read tag files... INFO @ Tue, 27 Jun 2017 10:58:16: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 10:58:23: 1000000 INFO @ Tue, 27 Jun 2017 10:58:23: 1000000 INFO @ Tue, 27 Jun 2017 10:58:23: 1000000 INFO @ Tue, 27 Jun 2017 10:58:30: 2000000 INFO @ Tue, 27 Jun 2017 10:58:30: 2000000 INFO @ Tue, 27 Jun 2017 10:58:30: 2000000 INFO @ Tue, 27 Jun 2017 10:58:37: 3000000 INFO @ Tue, 27 Jun 2017 10:58:37: 3000000 INFO @ Tue, 27 Jun 2017 10:58:37: 3000000 INFO @ Tue, 27 Jun 2017 10:58:38: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 10:58:38: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 10:58:38: #1 total tags in treatment: 3268595 INFO @ Tue, 27 Jun 2017 10:58:38: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 10:58:38: #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 10:58:38: #1 tags after filtering in treatment: 3268595 INFO @ Tue, 27 Jun 2017 10:58:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 10:58:38: #1 finished! INFO @ Tue, 27 Jun 2017 10:58:38: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 10:58:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 10:58:39: #2 number of paired peaks: 737 WARNING @ Tue, 27 Jun 2017 10:58:39: Fewer paired peaks (737) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 737 pairs to build model! INFO @ Tue, 27 Jun 2017 10:58:39: start model_add_line... INFO @ Tue, 27 Jun 2017 10:58:39: start X-correlation... INFO @ Tue, 27 Jun 2017 10:58:39: end of X-cor INFO @ Tue, 27 Jun 2017 10:58:39: #2 finished! INFO @ Tue, 27 Jun 2017 10:58:39: #2 predicted fragment length is 49 bps INFO @ Tue, 27 Jun 2017 10:58:39: #2 alternative fragment length(s) may be 4,49 bps INFO @ Tue, 27 Jun 2017 10:58:39: #2.2 Generate R script for model : SRX2228903.20_model.r WARNING @ Tue, 27 Jun 2017 10:58:39: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 10:58:39: #2 You may need to consider one of the other alternative d(s): 4,49 WARNING @ Tue, 27 Jun 2017 10:58:39: #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 10:58:39: #3 Call peaks... INFO @ Tue, 27 Jun 2017 10:58:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 10:58:39: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 10:58:39: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 10:58:39: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 10:58:39: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 10:58:39: #1 total tags in treatment: 3268595 INFO @ Tue, 27 Jun 2017 10:58:39: #1 total tags in treatment: 3268595 INFO @ Tue, 27 Jun 2017 10:58:39: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 10:58:39: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 10:58:39: #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 10:58:39: #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 10:58:39: #1 tags after filtering in treatment: 3268595 INFO @ Tue, 27 Jun 2017 10:58:39: #1 tags after filtering in treatment: 3268595 INFO @ Tue, 27 Jun 2017 10:58:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 10:58:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 10:58:39: #1 finished! INFO @ Tue, 27 Jun 2017 10:58:39: #1 finished! INFO @ Tue, 27 Jun 2017 10:58:39: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 10:58:39: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 10:58:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 10:58:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 10:58:39: #2 number of paired peaks: 737 WARNING @ Tue, 27 Jun 2017 10:58:39: Fewer paired peaks (737) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 737 pairs to build model! INFO @ Tue, 27 Jun 2017 10:58:39: start model_add_line... INFO @ Tue, 27 Jun 2017 10:58:39: #2 number of paired peaks: 737 WARNING @ Tue, 27 Jun 2017 10:58:39: Fewer paired peaks (737) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 737 pairs to build model! INFO @ Tue, 27 Jun 2017 10:58:39: start model_add_line... INFO @ Tue, 27 Jun 2017 10:58:39: start X-correlation... INFO @ Tue, 27 Jun 2017 10:58:39: end of X-cor INFO @ Tue, 27 Jun 2017 10:58:39: #2 finished! INFO @ Tue, 27 Jun 2017 10:58:39: #2 predicted fragment length is 49 bps INFO @ Tue, 27 Jun 2017 10:58:39: #2 alternative fragment length(s) may be 4,49 bps INFO @ Tue, 27 Jun 2017 10:58:39: #2.2 Generate R script for model : SRX2228903.05_model.r WARNING @ Tue, 27 Jun 2017 10:58:39: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 10:58:39: #2 You may need to consider one of the other alternative d(s): 4,49 WARNING @ Tue, 27 Jun 2017 10:58:39: #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 10:58:39: #3 Call peaks... INFO @ Tue, 27 Jun 2017 10:58:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 10:58:39: start X-correlation... INFO @ Tue, 27 Jun 2017 10:58:39: end of X-cor INFO @ Tue, 27 Jun 2017 10:58:39: #2 finished! INFO @ Tue, 27 Jun 2017 10:58:39: #2 predicted fragment length is 49 bps INFO @ Tue, 27 Jun 2017 10:58:39: #2 alternative fragment length(s) may be 4,49 bps INFO @ Tue, 27 Jun 2017 10:58:39: #2.2 Generate R script for model : SRX2228903.10_model.r WARNING @ Tue, 27 Jun 2017 10:58:39: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 10:58:39: #2 You may need to consider one of the other alternative d(s): 4,49 WARNING @ Tue, 27 Jun 2017 10:58:39: #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 10:58:39: #3 Call peaks... INFO @ Tue, 27 Jun 2017 10:58:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 10:58:47: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 10:58:47: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 10:58:47: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 10:58:51: #4 Write output xls file... SRX2228903.20_peaks.xls INFO @ Tue, 27 Jun 2017 10:58:51: #4 Write peak in narrowPeak format file... SRX2228903.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 10:58:51: #4 Write summits bed file... SRX2228903.20_summits.bed INFO @ Tue, 27 Jun 2017 10:58:51: Done! INFO @ Tue, 27 Jun 2017 10:58:51: #4 Write output xls file... SRX2228903.05_peaks.xls INFO @ Tue, 27 Jun 2017 10:58:51: #4 Write peak in narrowPeak format file... SRX2228903.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 10:58:51: #4 Write summits bed file... SRX2228903.05_summits.bed pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (281 records, 4 fields): 2 millis INFO @ Tue, 27 Jun 2017 10:58:51: Done! CompletedMACS2peakCalling pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (685 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 10:58:52: #4 Write output xls file... SRX2228903.10_peaks.xls INFO @ Tue, 27 Jun 2017 10:58:52: #4 Write peak in narrowPeak format file... SRX2228903.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 10:58:52: #4 Write summits bed file... SRX2228903.10_summits.bed INFO @ Tue, 27 Jun 2017 10:58:52: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (512 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。