Job ID = 9157399 sra ファイルのダウンロード中... Completed: 638731K bytes transferred in 9 seconds (535049K 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 23185843 spots for /home/okishinya/chipatlas/results/ce10/SRX1936243/SRR3879850.sra Written 23185843 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: 00:05:20 23185843 reads; of these: 23185843 (100.00%) were unpaired; of these: 4434758 (19.13%) aligned 0 times 15573024 (67.17%) aligned exactly 1 time 3178061 (13.71%) aligned >1 times 80.87% overall alignment rate Time searching: 00:05:20 Overall time: 00:05:20 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] 2693774 / 18751085 = 0.1437 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 11:52:44: # Command line: callpeak -t SRX1936243.bam -f BAM -g ce -n SRX1936243.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1936243.10 # format = BAM # ChIP-seq file = ['SRX1936243.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 11:52:44: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:52:44: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:52:44: # Command line: callpeak -t SRX1936243.bam -f BAM -g ce -n SRX1936243.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1936243.05 # format = BAM # ChIP-seq file = ['SRX1936243.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 11:52:44: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:52:44: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:52:44: # Command line: callpeak -t SRX1936243.bam -f BAM -g ce -n SRX1936243.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1936243.20 # format = BAM # ChIP-seq file = ['SRX1936243.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 11:52:44: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:52:44: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:52:53: 1000000 INFO @ Tue, 27 Jun 2017 11:52:53: 1000000 INFO @ Tue, 27 Jun 2017 11:52:53: 1000000 INFO @ Tue, 27 Jun 2017 11:53:01: 2000000 INFO @ Tue, 27 Jun 2017 11:53:01: 2000000 INFO @ Tue, 27 Jun 2017 11:53:01: 2000000 INFO @ Tue, 27 Jun 2017 11:53:10: 3000000 INFO @ Tue, 27 Jun 2017 11:53:10: 3000000 INFO @ Tue, 27 Jun 2017 11:53:10: 3000000 INFO @ Tue, 27 Jun 2017 11:53:19: 4000000 INFO @ Tue, 27 Jun 2017 11:53:19: 4000000 INFO @ Tue, 27 Jun 2017 11:53:19: 4000000 INFO @ Tue, 27 Jun 2017 11:53:28: 5000000 INFO @ Tue, 27 Jun 2017 11:53:28: 5000000 INFO @ Tue, 27 Jun 2017 11:53:28: 5000000 INFO @ Tue, 27 Jun 2017 11:53:37: 6000000 INFO @ Tue, 27 Jun 2017 11:53:37: 6000000 INFO @ Tue, 27 Jun 2017 11:53:37: 6000000 INFO @ Tue, 27 Jun 2017 11:53:45: 7000000 INFO @ Tue, 27 Jun 2017 11:53:45: 7000000 INFO @ Tue, 27 Jun 2017 11:53:45: 7000000 INFO @ Tue, 27 Jun 2017 11:53:54: 8000000 INFO @ Tue, 27 Jun 2017 11:53:54: 8000000 INFO @ Tue, 27 Jun 2017 11:53:54: 8000000 INFO @ Tue, 27 Jun 2017 11:54:02: 9000000 INFO @ Tue, 27 Jun 2017 11:54:02: 9000000 INFO @ Tue, 27 Jun 2017 11:54:02: 9000000 INFO @ Tue, 27 Jun 2017 11:54:11: 10000000 INFO @ Tue, 27 Jun 2017 11:54:11: 10000000 INFO @ Tue, 27 Jun 2017 11:54:11: 10000000 INFO @ Tue, 27 Jun 2017 11:54:20: 11000000 INFO @ Tue, 27 Jun 2017 11:54:20: 11000000 INFO @ Tue, 27 Jun 2017 11:54:20: 11000000 INFO @ Tue, 27 Jun 2017 11:54:28: 12000000 INFO @ Tue, 27 Jun 2017 11:54:28: 12000000 INFO @ Tue, 27 Jun 2017 11:54:28: 12000000 INFO @ Tue, 27 Jun 2017 11:54:37: 13000000 INFO @ Tue, 27 Jun 2017 11:54:37: 13000000 INFO @ Tue, 27 Jun 2017 11:54:37: 13000000 INFO @ Tue, 27 Jun 2017 11:54:45: 14000000 INFO @ Tue, 27 Jun 2017 11:54:45: 14000000 INFO @ Tue, 27 Jun 2017 11:54:45: 14000000 INFO @ Tue, 27 Jun 2017 11:54:53: 15000000 INFO @ Tue, 27 Jun 2017 11:54:53: 15000000 INFO @ Tue, 27 Jun 2017 11:54:53: 15000000 INFO @ Tue, 27 Jun 2017 11:55:00: 16000000 INFO @ Tue, 27 Jun 2017 11:55:00: 16000000 INFO @ Tue, 27 Jun 2017 11:55:00: 16000000 INFO @ Tue, 27 Jun 2017 11:55:01: #1 tag size is determined as 52 bps INFO @ Tue, 27 Jun 2017 11:55:01: #1 tag size = 52 INFO @ Tue, 27 Jun 2017 11:55:01: #1 total tags in treatment: 16057311 INFO @ Tue, 27 Jun 2017 11:55:01: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:55:01: #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 11:55:01: #1 tag size is determined as 52 bps INFO @ Tue, 27 Jun 2017 11:55:01: #1 tag size = 52 INFO @ Tue, 27 Jun 2017 11:55:01: #1 total tags in treatment: 16057311 INFO @ Tue, 27 Jun 2017 11:55:01: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:55:01: #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 11:55:01: #1 tag size is determined as 52 bps INFO @ Tue, 27 Jun 2017 11:55:01: #1 tag size = 52 INFO @ Tue, 27 Jun 2017 11:55:01: #1 total tags in treatment: 16057311 INFO @ Tue, 27 Jun 2017 11:55:01: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:55:01: #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 11:55:01: #1 tags after filtering in treatment: 16057311 INFO @ Tue, 27 Jun 2017 11:55:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:55:01: #1 finished! INFO @ Tue, 27 Jun 2017 11:55:01: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:55:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:55:01: #1 tags after filtering in treatment: 16057311 INFO @ Tue, 27 Jun 2017 11:55:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:55:01: #1 finished! INFO @ Tue, 27 Jun 2017 11:55:01: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:55:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:55:01: #1 tags after filtering in treatment: 16057311 INFO @ Tue, 27 Jun 2017 11:55:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:55:01: #1 finished! INFO @ Tue, 27 Jun 2017 11:55:01: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:55:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:55:02: #2 number of paired peaks: 273 WARNING @ Tue, 27 Jun 2017 11:55:02: Fewer paired peaks (273) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 273 pairs to build model! INFO @ Tue, 27 Jun 2017 11:55:02: start model_add_line... INFO @ Tue, 27 Jun 2017 11:55:02: #2 number of paired peaks: 273 WARNING @ Tue, 27 Jun 2017 11:55:02: Fewer paired peaks (273) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 273 pairs to build model! INFO @ Tue, 27 Jun 2017 11:55:02: start model_add_line... INFO @ Tue, 27 Jun 2017 11:55:02: #2 number of paired peaks: 273 WARNING @ Tue, 27 Jun 2017 11:55:02: Fewer paired peaks (273) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 273 pairs to build model! INFO @ Tue, 27 Jun 2017 11:55:02: start model_add_line... INFO @ Tue, 27 Jun 2017 11:55:02: start X-correlation... INFO @ Tue, 27 Jun 2017 11:55:02: end of X-cor INFO @ Tue, 27 Jun 2017 11:55:02: #2 finished! INFO @ Tue, 27 Jun 2017 11:55:02: #2 predicted fragment length is 1 bps INFO @ Tue, 27 Jun 2017 11:55:02: #2 alternative fragment length(s) may be 1,11,50,482,582 bps INFO @ Tue, 27 Jun 2017 11:55:02: #2.2 Generate R script for model : SRX1936243.10_model.r INFO @ Tue, 27 Jun 2017 11:55:02: start X-correlation... WARNING @ Tue, 27 Jun 2017 11:55:02: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:55:02: #2 You may need to consider one of the other alternative d(s): 1,11,50,482,582 WARNING @ Tue, 27 Jun 2017 11:55:02: #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 11:55:02: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:55:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:55:02: end of X-cor INFO @ Tue, 27 Jun 2017 11:55:02: #2 finished! INFO @ Tue, 27 Jun 2017 11:55:02: #2 predicted fragment length is 1 bps INFO @ Tue, 27 Jun 2017 11:55:02: #2 alternative fragment length(s) may be 1,11,50,482,582 bps INFO @ Tue, 27 Jun 2017 11:55:02: #2.2 Generate R script for model : SRX1936243.05_model.r INFO @ Tue, 27 Jun 2017 11:55:02: start X-correlation... WARNING @ Tue, 27 Jun 2017 11:55:02: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:55:02: #2 You may need to consider one of the other alternative d(s): 1,11,50,482,582 INFO @ Tue, 27 Jun 2017 11:55:02: end of X-cor WARNING @ Tue, 27 Jun 2017 11:55:02: #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 11:55:02: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:55:02: #2 finished! INFO @ Tue, 27 Jun 2017 11:55:02: #2 predicted fragment length is 1 bps INFO @ Tue, 27 Jun 2017 11:55:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:55:02: #2 alternative fragment length(s) may be 1,11,50,482,582 bps INFO @ Tue, 27 Jun 2017 11:55:02: #2.2 Generate R script for model : SRX1936243.20_model.r WARNING @ Tue, 27 Jun 2017 11:55:02: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:55:02: #2 You may need to consider one of the other alternative d(s): 1,11,50,482,582 WARNING @ Tue, 27 Jun 2017 11:55:02: #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 11:55:02: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:55:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:55:30: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:55:31: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:55:32: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:55:44: #4 Write output xls file... SRX1936243.20_peaks.xls INFO @ Tue, 27 Jun 2017 11:55:44: #4 Write peak in narrowPeak format file... SRX1936243.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:55:44: #4 Write summits bed file... SRX1936243.20_summits.bed INFO @ Tue, 27 Jun 2017 11:55:44: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:55:46: #4 Write output xls file... SRX1936243.05_peaks.xls INFO @ Tue, 27 Jun 2017 11:55:46: #4 Write peak in narrowPeak format file... SRX1936243.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:55:46: #4 Write summits bed file... SRX1936243.05_summits.bed INFO @ Tue, 27 Jun 2017 11:55:46: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:55:47: #4 Write output xls file... SRX1936243.10_peaks.xls INFO @ Tue, 27 Jun 2017 11:55:47: #4 Write peak in narrowPeak format file... SRX1936243.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:55:47: #4 Write summits bed file... SRX1936243.10_summits.bed INFO @ Tue, 27 Jun 2017 11:55:47: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。