Job ID = 9157233 sra ファイルのダウンロード中... Completed: 662604K bytes transferred in 8 seconds (669546K 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 14583103 spots for /home/okishinya/chipatlas/results/ce10/SRX2350732/SRR5024041.sra Written 14583103 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: 00:04:24 14583103 reads; of these: 14583103 (100.00%) were unpaired; of these: 236228 (1.62%) aligned 0 times 11446904 (78.49%) aligned exactly 1 time 2899971 (19.89%) aligned >1 times 98.38% overall alignment rate Time searching: 00:04:24 Overall time: 00:04:24 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] 1835154 / 14346875 = 0.1279 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 11:15:18: # Command line: callpeak -t SRX2350732.bam -f BAM -g ce -n SRX2350732.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2350732.10 # format = BAM # ChIP-seq file = ['SRX2350732.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 11:15:18: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:15:18: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:15:18: # Command line: callpeak -t SRX2350732.bam -f BAM -g ce -n SRX2350732.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2350732.20 # format = BAM # ChIP-seq file = ['SRX2350732.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 11:15:18: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:15:18: # Command line: callpeak -t SRX2350732.bam -f BAM -g ce -n SRX2350732.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2350732.05 # format = BAM # ChIP-seq file = ['SRX2350732.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 11:15:18: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:15:18: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:15:18: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:15:25: 1000000 INFO @ Tue, 27 Jun 2017 11:15:26: 1000000 INFO @ Tue, 27 Jun 2017 11:15:26: 1000000 INFO @ Tue, 27 Jun 2017 11:15:32: 2000000 INFO @ Tue, 27 Jun 2017 11:15:34: 2000000 INFO @ Tue, 27 Jun 2017 11:15:34: 2000000 INFO @ Tue, 27 Jun 2017 11:15:39: 3000000 INFO @ Tue, 27 Jun 2017 11:15:42: 3000000 INFO @ Tue, 27 Jun 2017 11:15:42: 3000000 INFO @ Tue, 27 Jun 2017 11:15:46: 4000000 INFO @ Tue, 27 Jun 2017 11:15:51: 4000000 INFO @ Tue, 27 Jun 2017 11:15:51: 4000000 INFO @ Tue, 27 Jun 2017 11:15:53: 5000000 INFO @ Tue, 27 Jun 2017 11:15:59: 5000000 INFO @ Tue, 27 Jun 2017 11:15:59: 5000000 INFO @ Tue, 27 Jun 2017 11:16:00: 6000000 INFO @ Tue, 27 Jun 2017 11:16:07: 6000000 INFO @ Tue, 27 Jun 2017 11:16:07: 6000000 INFO @ Tue, 27 Jun 2017 11:16:08: 7000000 INFO @ Tue, 27 Jun 2017 11:16:15: 7000000 INFO @ Tue, 27 Jun 2017 11:16:15: 7000000 INFO @ Tue, 27 Jun 2017 11:16:15: 8000000 INFO @ Tue, 27 Jun 2017 11:16:22: 9000000 INFO @ Tue, 27 Jun 2017 11:16:23: 8000000 INFO @ Tue, 27 Jun 2017 11:16:23: 8000000 INFO @ Tue, 27 Jun 2017 11:16:29: 10000000 INFO @ Tue, 27 Jun 2017 11:16:31: 9000000 INFO @ Tue, 27 Jun 2017 11:16:31: 9000000 INFO @ Tue, 27 Jun 2017 11:16:36: 11000000 INFO @ Tue, 27 Jun 2017 11:16:39: 10000000 INFO @ Tue, 27 Jun 2017 11:16:39: 10000000 INFO @ Tue, 27 Jun 2017 11:16:43: 12000000 INFO @ Tue, 27 Jun 2017 11:16:47: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:16:47: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:16:47: #1 total tags in treatment: 12511721 INFO @ Tue, 27 Jun 2017 11:16:47: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:16:47: #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 11:16:47: #1 tags after filtering in treatment: 12511721 INFO @ Tue, 27 Jun 2017 11:16:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:16:47: #1 finished! INFO @ Tue, 27 Jun 2017 11:16:47: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:16:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:16:48: 11000000 INFO @ Tue, 27 Jun 2017 11:16:48: 11000000 INFO @ Tue, 27 Jun 2017 11:16:48: #2 number of paired peaks: 339 WARNING @ Tue, 27 Jun 2017 11:16:48: Fewer paired peaks (339) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 339 pairs to build model! INFO @ Tue, 27 Jun 2017 11:16:48: start model_add_line... INFO @ Tue, 27 Jun 2017 11:16:48: start X-correlation... INFO @ Tue, 27 Jun 2017 11:16:48: end of X-cor INFO @ Tue, 27 Jun 2017 11:16:48: #2 finished! INFO @ Tue, 27 Jun 2017 11:16:48: #2 predicted fragment length is 49 bps INFO @ Tue, 27 Jun 2017 11:16:48: #2 alternative fragment length(s) may be 2,49,579 bps INFO @ Tue, 27 Jun 2017 11:16:48: #2.2 Generate R script for model : SRX2350732.20_model.r WARNING @ Tue, 27 Jun 2017 11:16:48: #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 11:16:48: #2 You may need to consider one of the other alternative d(s): 2,49,579 WARNING @ Tue, 27 Jun 2017 11:16:48: #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 11:16:48: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:16:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:16:56: 12000000 INFO @ Tue, 27 Jun 2017 11:16:57: 12000000 INFO @ Tue, 27 Jun 2017 11:17:00: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:17:00: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:17:00: #1 total tags in treatment: 12511721 INFO @ Tue, 27 Jun 2017 11:17:00: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:17:00: #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 11:17:01: #1 tags after filtering in treatment: 12511721 INFO @ Tue, 27 Jun 2017 11:17:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:17:01: #1 finished! INFO @ Tue, 27 Jun 2017 11:17:01: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:17:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:17:01: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:17:01: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:17:01: #1 total tags in treatment: 12511721 INFO @ Tue, 27 Jun 2017 11:17:01: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:17:01: #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 11:17:01: #1 tags after filtering in treatment: 12511721 INFO @ Tue, 27 Jun 2017 11:17:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:17:01: #1 finished! INFO @ Tue, 27 Jun 2017 11:17:01: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:17:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:17:01: #2 number of paired peaks: 339 WARNING @ Tue, 27 Jun 2017 11:17:01: Fewer paired peaks (339) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 339 pairs to build model! INFO @ Tue, 27 Jun 2017 11:17:01: start model_add_line... INFO @ Tue, 27 Jun 2017 11:17:02: start X-correlation... INFO @ Tue, 27 Jun 2017 11:17:02: end of X-cor INFO @ Tue, 27 Jun 2017 11:17:02: #2 finished! INFO @ Tue, 27 Jun 2017 11:17:02: #2 predicted fragment length is 49 bps INFO @ Tue, 27 Jun 2017 11:17:02: #2 alternative fragment length(s) may be 2,49,579 bps INFO @ Tue, 27 Jun 2017 11:17:02: #2.2 Generate R script for model : SRX2350732.05_model.r WARNING @ Tue, 27 Jun 2017 11:17:02: #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 11:17:02: #2 You may need to consider one of the other alternative d(s): 2,49,579 WARNING @ Tue, 27 Jun 2017 11:17:02: #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 11:17:02: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:17:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:17:02: #2 number of paired peaks: 339 WARNING @ Tue, 27 Jun 2017 11:17:02: Fewer paired peaks (339) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 339 pairs to build model! INFO @ Tue, 27 Jun 2017 11:17:02: start model_add_line... INFO @ Tue, 27 Jun 2017 11:17:02: start X-correlation... INFO @ Tue, 27 Jun 2017 11:17:02: end of X-cor INFO @ Tue, 27 Jun 2017 11:17:02: #2 finished! INFO @ Tue, 27 Jun 2017 11:17:02: #2 predicted fragment length is 49 bps INFO @ Tue, 27 Jun 2017 11:17:02: #2 alternative fragment length(s) may be 2,49,579 bps INFO @ Tue, 27 Jun 2017 11:17:02: #2.2 Generate R script for model : SRX2350732.10_model.r WARNING @ Tue, 27 Jun 2017 11:17:02: #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 11:17:02: #2 You may need to consider one of the other alternative d(s): 2,49,579 WARNING @ Tue, 27 Jun 2017 11:17:02: #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 11:17:02: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:17:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:17:16: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:17:26: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:17:29: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:17:29: #4 Write output xls file... SRX2350732.20_peaks.xls INFO @ Tue, 27 Jun 2017 11:17:29: #4 Write peak in narrowPeak format file... SRX2350732.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:17:29: #4 Write summits bed file... SRX2350732.20_summits.bed INFO @ Tue, 27 Jun 2017 11:17:29: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (196 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:17:40: #4 Write output xls file... SRX2350732.10_peaks.xls INFO @ Tue, 27 Jun 2017 11:17:40: #4 Write peak in narrowPeak format file... SRX2350732.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:17:40: #4 Write summits bed file... SRX2350732.10_summits.bed INFO @ Tue, 27 Jun 2017 11:17:40: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (449 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:17:43: #4 Write output xls file... SRX2350732.05_peaks.xls INFO @ Tue, 27 Jun 2017 11:17:43: #4 Write peak in narrowPeak format file... SRX2350732.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:17:43: #4 Write summits bed file... SRX2350732.05_summits.bed INFO @ Tue, 27 Jun 2017 11:17:43: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (759 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。