Job ID = 9157306 sra ファイルのダウンロード中... Completed: 807416K bytes transferred in 27 seconds (238285K 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 16597750 spots for /home/okishinya/chipatlas/results/ce10/SRX2761390/SRR5476964.sra Written 16597750 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: 00:04:28 16597750 reads; of these: 16597750 (100.00%) were unpaired; of these: 721101 (4.34%) aligned 0 times 12951909 (78.03%) aligned exactly 1 time 2924740 (17.62%) aligned >1 times 95.66% overall alignment rate Time searching: 00:04:28 Overall time: 00:04:28 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_sort_core] merging from 8 files... [bam_rmdupse_core] 1350668 / 15876649 = 0.0851 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 11:31:46: # Command line: callpeak -t SRX2761390.bam -f BAM -g ce -n SRX2761390.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2761390.05 # format = BAM # ChIP-seq file = ['SRX2761390.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 11:31:46: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:31:46: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:31:46: # Command line: callpeak -t SRX2761390.bam -f BAM -g ce -n SRX2761390.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2761390.20 # format = BAM # ChIP-seq file = ['SRX2761390.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 11:31:46: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:31:46: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:31:46: # Command line: callpeak -t SRX2761390.bam -f BAM -g ce -n SRX2761390.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2761390.10 # format = BAM # ChIP-seq file = ['SRX2761390.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 11:31:46: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:31:46: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:31:53: 1000000 INFO @ Tue, 27 Jun 2017 11:31:54: 1000000 INFO @ Tue, 27 Jun 2017 11:31:54: 1000000 INFO @ Tue, 27 Jun 2017 11:31:59: 2000000 INFO @ Tue, 27 Jun 2017 11:32:02: 2000000 INFO @ Tue, 27 Jun 2017 11:32:02: 2000000 INFO @ Tue, 27 Jun 2017 11:32:06: 3000000 INFO @ Tue, 27 Jun 2017 11:32:10: 3000000 INFO @ Tue, 27 Jun 2017 11:32:11: 3000000 INFO @ Tue, 27 Jun 2017 11:32:13: 4000000 INFO @ Tue, 27 Jun 2017 11:32:18: 4000000 INFO @ Tue, 27 Jun 2017 11:32:20: 4000000 INFO @ Tue, 27 Jun 2017 11:32:20: 5000000 INFO @ Tue, 27 Jun 2017 11:32:26: 5000000 INFO @ Tue, 27 Jun 2017 11:32:27: 6000000 INFO @ Tue, 27 Jun 2017 11:32:28: 5000000 INFO @ Tue, 27 Jun 2017 11:32:33: 7000000 INFO @ Tue, 27 Jun 2017 11:32:34: 6000000 INFO @ Tue, 27 Jun 2017 11:32:37: 6000000 INFO @ Tue, 27 Jun 2017 11:32:40: 8000000 INFO @ Tue, 27 Jun 2017 11:32:42: 7000000 INFO @ Tue, 27 Jun 2017 11:32:46: 7000000 INFO @ Tue, 27 Jun 2017 11:32:47: 9000000 INFO @ Tue, 27 Jun 2017 11:32:51: 8000000 INFO @ Tue, 27 Jun 2017 11:32:54: 10000000 INFO @ Tue, 27 Jun 2017 11:32:54: 8000000 INFO @ Tue, 27 Jun 2017 11:32:59: 9000000 INFO @ Tue, 27 Jun 2017 11:33:01: 11000000 INFO @ Tue, 27 Jun 2017 11:33:03: 9000000 INFO @ Tue, 27 Jun 2017 11:33:07: 10000000 INFO @ Tue, 27 Jun 2017 11:33:08: 12000000 INFO @ Tue, 27 Jun 2017 11:33:11: 10000000 INFO @ Tue, 27 Jun 2017 11:33:14: 13000000 INFO @ Tue, 27 Jun 2017 11:33:15: 11000000 INFO @ Tue, 27 Jun 2017 11:33:20: 11000000 INFO @ Tue, 27 Jun 2017 11:33:21: 14000000 INFO @ Tue, 27 Jun 2017 11:33:24: 12000000 INFO @ Tue, 27 Jun 2017 11:33:25: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:33:25: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:33:25: #1 total tags in treatment: 14525981 INFO @ Tue, 27 Jun 2017 11:33:25: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:33:25: #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 11:33:25: #1 tags after filtering in treatment: 14525981 INFO @ Tue, 27 Jun 2017 11:33:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:33:25: #1 finished! INFO @ Tue, 27 Jun 2017 11:33:25: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:33:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:33:26: #2 number of paired peaks: 370 WARNING @ Tue, 27 Jun 2017 11:33:26: Fewer paired peaks (370) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 370 pairs to build model! INFO @ Tue, 27 Jun 2017 11:33:26: start model_add_line... INFO @ Tue, 27 Jun 2017 11:33:27: start X-correlation... INFO @ Tue, 27 Jun 2017 11:33:27: end of X-cor INFO @ Tue, 27 Jun 2017 11:33:27: #2 finished! INFO @ Tue, 27 Jun 2017 11:33:27: #2 predicted fragment length is 44 bps INFO @ Tue, 27 Jun 2017 11:33:27: #2 alternative fragment length(s) may be 2,44 bps INFO @ Tue, 27 Jun 2017 11:33:27: #2.2 Generate R script for model : SRX2761390.10_model.r WARNING @ Tue, 27 Jun 2017 11:33:27: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:33:27: #2 You may need to consider one of the other alternative d(s): 2,44 WARNING @ Tue, 27 Jun 2017 11:33:27: #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 11:33:27: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:33:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:33:28: 12000000 INFO @ Tue, 27 Jun 2017 11:33:32: 13000000 INFO @ Tue, 27 Jun 2017 11:33:37: 13000000 INFO @ Tue, 27 Jun 2017 11:33:40: 14000000 INFO @ Tue, 27 Jun 2017 11:33:44: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:33:44: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:33:44: #1 total tags in treatment: 14525981 INFO @ Tue, 27 Jun 2017 11:33:44: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:33:44: #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 11:33:45: #1 tags after filtering in treatment: 14525981 INFO @ Tue, 27 Jun 2017 11:33:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:33:45: #1 finished! INFO @ Tue, 27 Jun 2017 11:33:45: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:33:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:33:45: 14000000 INFO @ Tue, 27 Jun 2017 11:33:46: #2 number of paired peaks: 370 WARNING @ Tue, 27 Jun 2017 11:33:46: Fewer paired peaks (370) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 370 pairs to build model! INFO @ Tue, 27 Jun 2017 11:33:46: start model_add_line... INFO @ Tue, 27 Jun 2017 11:33:46: start X-correlation... INFO @ Tue, 27 Jun 2017 11:33:46: end of X-cor INFO @ Tue, 27 Jun 2017 11:33:46: #2 finished! INFO @ Tue, 27 Jun 2017 11:33:46: #2 predicted fragment length is 44 bps INFO @ Tue, 27 Jun 2017 11:33:46: #2 alternative fragment length(s) may be 2,44 bps INFO @ Tue, 27 Jun 2017 11:33:46: #2.2 Generate R script for model : SRX2761390.20_model.r WARNING @ Tue, 27 Jun 2017 11:33:46: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:33:46: #2 You may need to consider one of the other alternative d(s): 2,44 WARNING @ Tue, 27 Jun 2017 11:33:46: #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 11:33:46: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:33:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:33:49: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:33:49: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:33:49: #1 total tags in treatment: 14525981 INFO @ Tue, 27 Jun 2017 11:33:49: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:33:49: #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 11:33:50: #1 tags after filtering in treatment: 14525981 INFO @ Tue, 27 Jun 2017 11:33:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:33:50: #1 finished! INFO @ Tue, 27 Jun 2017 11:33:50: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:33:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:33:51: #2 number of paired peaks: 370 WARNING @ Tue, 27 Jun 2017 11:33:51: Fewer paired peaks (370) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 370 pairs to build model! INFO @ Tue, 27 Jun 2017 11:33:51: start model_add_line... INFO @ Tue, 27 Jun 2017 11:33:51: start X-correlation... INFO @ Tue, 27 Jun 2017 11:33:51: end of X-cor INFO @ Tue, 27 Jun 2017 11:33:51: #2 finished! INFO @ Tue, 27 Jun 2017 11:33:51: #2 predicted fragment length is 44 bps INFO @ Tue, 27 Jun 2017 11:33:51: #2 alternative fragment length(s) may be 2,44 bps INFO @ Tue, 27 Jun 2017 11:33:51: #2.2 Generate R script for model : SRX2761390.05_model.r WARNING @ Tue, 27 Jun 2017 11:33:51: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:33:51: #2 You may need to consider one of the other alternative d(s): 2,44 WARNING @ Tue, 27 Jun 2017 11:33:51: #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 11:33:51: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:33:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:33:57: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:34:11: #4 Write output xls file... SRX2761390.10_peaks.xls INFO @ Tue, 27 Jun 2017 11:34:11: #4 Write peak in narrowPeak format file... SRX2761390.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:34:11: #4 Write summits bed file... SRX2761390.10_summits.bed INFO @ Tue, 27 Jun 2017 11:34:11: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (511 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:34:14: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:34:20: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:34:28: #4 Write output xls file... SRX2761390.20_peaks.xls INFO @ Tue, 27 Jun 2017 11:34:28: #4 Write peak in narrowPeak format file... SRX2761390.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:34:28: #4 Write summits bed file... SRX2761390.20_summits.bed INFO @ Tue, 27 Jun 2017 11:34:28: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (197 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:34:35: #4 Write output xls file... SRX2761390.05_peaks.xls INFO @ Tue, 27 Jun 2017 11:34:35: #4 Write peak in narrowPeak format file... SRX2761390.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:34:35: #4 Write summits bed file... SRX2761390.05_summits.bed INFO @ Tue, 27 Jun 2017 11:34:35: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (755 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。