Job ID = 9157197 sra ファイルのダウンロード中... Completed: 205493K bytes transferred in 4 seconds (342675K 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 6722011 spots for /home/okishinya/chipatlas/results/ce10/SRX2228912/SRR4380368.sra Written 6722011 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: 00:01:46 6722011 reads; of these: 6722011 (100.00%) were unpaired; of these: 301557 (4.49%) aligned 0 times 5375836 (79.97%) aligned exactly 1 time 1044618 (15.54%) aligned >1 times 95.51% overall alignment rate Time searching: 00:01:46 Overall time: 00:01:46 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_rmdupse_core] 326584 / 6420454 = 0.0509 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 11:01:26: # Command line: callpeak -t SRX2228912.bam -f BAM -g ce -n SRX2228912.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2228912.05 # format = BAM # ChIP-seq file = ['SRX2228912.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 11:01:26: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:01:26: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:01:26: # Command line: callpeak -t SRX2228912.bam -f BAM -g ce -n SRX2228912.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2228912.20 # format = BAM # ChIP-seq file = ['SRX2228912.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 11:01:26: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:01:26: # Command line: callpeak -t SRX2228912.bam -f BAM -g ce -n SRX2228912.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2228912.10 # format = BAM # ChIP-seq file = ['SRX2228912.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 11:01:26: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:01:26: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:01:26: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:01:35: 1000000 INFO @ Tue, 27 Jun 2017 11:01:36: 1000000 INFO @ Tue, 27 Jun 2017 11:01:36: 1000000 INFO @ Tue, 27 Jun 2017 11:01:44: 2000000 INFO @ Tue, 27 Jun 2017 11:01:45: 2000000 INFO @ Tue, 27 Jun 2017 11:01:45: 2000000 INFO @ Tue, 27 Jun 2017 11:01:52: 3000000 INFO @ Tue, 27 Jun 2017 11:01:54: 3000000 INFO @ Tue, 27 Jun 2017 11:01:54: 3000000 INFO @ Tue, 27 Jun 2017 11:02:00: 4000000 INFO @ Tue, 27 Jun 2017 11:02:04: 4000000 INFO @ Tue, 27 Jun 2017 11:02:04: 4000000 INFO @ Tue, 27 Jun 2017 11:02:07: 5000000 INFO @ Tue, 27 Jun 2017 11:02:13: 5000000 INFO @ Tue, 27 Jun 2017 11:02:13: 5000000 INFO @ Tue, 27 Jun 2017 11:02:14: 6000000 INFO @ Tue, 27 Jun 2017 11:02:15: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:02:15: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:02:15: #1 total tags in treatment: 6093870 INFO @ Tue, 27 Jun 2017 11:02:15: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:02:15: #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 11:02:15: #1 tags after filtering in treatment: 6093870 INFO @ Tue, 27 Jun 2017 11:02:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:02:15: #1 finished! INFO @ Tue, 27 Jun 2017 11:02:15: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:02:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:02:16: #2 number of paired peaks: 338 WARNING @ Tue, 27 Jun 2017 11:02:16: Fewer paired peaks (338) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 338 pairs to build model! INFO @ Tue, 27 Jun 2017 11:02:16: start model_add_line... INFO @ Tue, 27 Jun 2017 11:02:16: start X-correlation... INFO @ Tue, 27 Jun 2017 11:02:16: end of X-cor INFO @ Tue, 27 Jun 2017 11:02:16: #2 finished! INFO @ Tue, 27 Jun 2017 11:02:16: #2 predicted fragment length is 51 bps INFO @ Tue, 27 Jun 2017 11:02:16: #2 alternative fragment length(s) may be 4,51,559,576,592 bps INFO @ Tue, 27 Jun 2017 11:02:16: #2.2 Generate R script for model : SRX2228912.05_model.r WARNING @ Tue, 27 Jun 2017 11:02:16: #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 11:02:16: #2 You may need to consider one of the other alternative d(s): 4,51,559,576,592 WARNING @ Tue, 27 Jun 2017 11:02:16: #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 11:02:16: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:02:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:02:21: 6000000 INFO @ Tue, 27 Jun 2017 11:02:21: 6000000 INFO @ Tue, 27 Jun 2017 11:02:22: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:02:22: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:02:22: #1 total tags in treatment: 6093870 INFO @ Tue, 27 Jun 2017 11:02:22: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:02:22: #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 11:02:22: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:02:22: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:02:22: #1 total tags in treatment: 6093870 INFO @ Tue, 27 Jun 2017 11:02:22: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:02:22: #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 11:02:22: #1 tags after filtering in treatment: 6093870 INFO @ Tue, 27 Jun 2017 11:02:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:02:22: #1 finished! INFO @ Tue, 27 Jun 2017 11:02:22: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:02:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:02:22: #1 tags after filtering in treatment: 6093870 INFO @ Tue, 27 Jun 2017 11:02:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:02:22: #1 finished! INFO @ Tue, 27 Jun 2017 11:02:22: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:02:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:02:22: #2 number of paired peaks: 338 WARNING @ Tue, 27 Jun 2017 11:02:22: Fewer paired peaks (338) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 338 pairs to build model! INFO @ Tue, 27 Jun 2017 11:02:22: start model_add_line... INFO @ Tue, 27 Jun 2017 11:02:22: #2 number of paired peaks: 338 WARNING @ Tue, 27 Jun 2017 11:02:22: Fewer paired peaks (338) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 338 pairs to build model! INFO @ Tue, 27 Jun 2017 11:02:22: start model_add_line... INFO @ Tue, 27 Jun 2017 11:02:23: start X-correlation... INFO @ Tue, 27 Jun 2017 11:02:23: start X-correlation... INFO @ Tue, 27 Jun 2017 11:02:23: end of X-cor INFO @ Tue, 27 Jun 2017 11:02:23: #2 finished! INFO @ Tue, 27 Jun 2017 11:02:23: #2 predicted fragment length is 51 bps INFO @ Tue, 27 Jun 2017 11:02:23: #2 alternative fragment length(s) may be 4,51,559,576,592 bps INFO @ Tue, 27 Jun 2017 11:02:23: #2.2 Generate R script for model : SRX2228912.10_model.r INFO @ Tue, 27 Jun 2017 11:02:23: end of X-cor INFO @ Tue, 27 Jun 2017 11:02:23: #2 finished! INFO @ Tue, 27 Jun 2017 11:02:23: #2 predicted fragment length is 51 bps INFO @ Tue, 27 Jun 2017 11:02:23: #2 alternative fragment length(s) may be 4,51,559,576,592 bps INFO @ Tue, 27 Jun 2017 11:02:23: #2.2 Generate R script for model : SRX2228912.20_model.r WARNING @ Tue, 27 Jun 2017 11:02:23: #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 11:02:23: #2 You may need to consider one of the other alternative d(s): 4,51,559,576,592 WARNING @ Tue, 27 Jun 2017 11:02:23: #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 11:02:23: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:02:23: #3 Pre-compute pvalue-qvalue table... WARNING @ Tue, 27 Jun 2017 11:02:23: #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 11:02:23: #2 You may need to consider one of the other alternative d(s): 4,51,559,576,592 WARNING @ Tue, 27 Jun 2017 11:02:23: #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 11:02:23: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:02:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:02:29: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:02:36: #4 Write output xls file... SRX2228912.05_peaks.xls INFO @ Tue, 27 Jun 2017 11:02:36: #4 Write peak in narrowPeak format file... SRX2228912.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:02:36: #4 Write summits bed file... SRX2228912.05_summits.bed INFO @ Tue, 27 Jun 2017 11:02:36: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (480 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:02:36: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:02:37: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:02:44: #4 Write output xls file... SRX2228912.20_peaks.xls INFO @ Tue, 27 Jun 2017 11:02:44: #4 Write peak in narrowPeak format file... SRX2228912.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:02:44: #4 Write summits bed file... SRX2228912.20_summits.bed INFO @ Tue, 27 Jun 2017 11:02:44: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (119 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:02:44: #4 Write output xls file... SRX2228912.10_peaks.xls INFO @ Tue, 27 Jun 2017 11:02:44: #4 Write peak in narrowPeak format file... SRX2228912.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:02:44: #4 Write summits bed file... SRX2228912.10_summits.bed INFO @ Tue, 27 Jun 2017 11:02:44: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (296 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。