Job ID = 9157349 sra ファイルのダウンロード中... Completed: 381891K bytes transferred in 7 seconds (399127K 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 16560194 spots for /home/okishinya/chipatlas/results/ce10/SRX059251/SRR190691.sra Written 16560194 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: 00:00:01 Multiseed full-index search: 00:03:17 16560194 reads; of these: 16560194 (100.00%) were unpaired; of these: 532563 (3.22%) aligned 0 times 13113630 (79.19%) aligned exactly 1 time 2914001 (17.60%) aligned >1 times 96.78% overall alignment rate Time searching: 00:03:18 Overall time: 00:03:18 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] 1975911 / 16027631 = 0.1233 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 11:33:13: # Command line: callpeak -t SRX059251.bam -f BAM -g ce -n SRX059251.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX059251.10 # format = BAM # ChIP-seq file = ['SRX059251.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 11:33:13: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:33:13: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:33:13: # Command line: callpeak -t SRX059251.bam -f BAM -g ce -n SRX059251.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX059251.05 # format = BAM # ChIP-seq file = ['SRX059251.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 11:33:13: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:33:13: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:33:13: # Command line: callpeak -t SRX059251.bam -f BAM -g ce -n SRX059251.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX059251.20 # format = BAM # ChIP-seq file = ['SRX059251.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 11:33:13: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:33:13: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:33:19: 1000000 INFO @ Tue, 27 Jun 2017 11:33:20: 1000000 INFO @ Tue, 27 Jun 2017 11:33:20: 1000000 INFO @ Tue, 27 Jun 2017 11:33:25: 2000000 INFO @ Tue, 27 Jun 2017 11:33:27: 2000000 INFO @ Tue, 27 Jun 2017 11:33:27: 2000000 INFO @ Tue, 27 Jun 2017 11:33:32: 3000000 INFO @ Tue, 27 Jun 2017 11:33:34: 3000000 INFO @ Tue, 27 Jun 2017 11:33:34: 3000000 INFO @ Tue, 27 Jun 2017 11:33:38: 4000000 INFO @ Tue, 27 Jun 2017 11:33:41: 4000000 INFO @ Tue, 27 Jun 2017 11:33:41: 4000000 INFO @ Tue, 27 Jun 2017 11:33:45: 5000000 INFO @ Tue, 27 Jun 2017 11:33:48: 5000000 INFO @ Tue, 27 Jun 2017 11:33:48: 5000000 INFO @ Tue, 27 Jun 2017 11:33:51: 6000000 INFO @ Tue, 27 Jun 2017 11:33:54: 6000000 INFO @ Tue, 27 Jun 2017 11:33:54: 6000000 INFO @ Tue, 27 Jun 2017 11:33:58: 7000000 INFO @ Tue, 27 Jun 2017 11:34:01: 7000000 INFO @ Tue, 27 Jun 2017 11:34:01: 7000000 INFO @ Tue, 27 Jun 2017 11:34:04: 8000000 INFO @ Tue, 27 Jun 2017 11:34:08: 8000000 INFO @ Tue, 27 Jun 2017 11:34:08: 8000000 INFO @ Tue, 27 Jun 2017 11:34:10: 9000000 INFO @ Tue, 27 Jun 2017 11:34:16: 9000000 INFO @ Tue, 27 Jun 2017 11:34:16: 9000000 INFO @ Tue, 27 Jun 2017 11:34:17: 10000000 INFO @ Tue, 27 Jun 2017 11:34:22: 10000000 INFO @ Tue, 27 Jun 2017 11:34:22: 10000000 INFO @ Tue, 27 Jun 2017 11:34:23: 11000000 INFO @ Tue, 27 Jun 2017 11:34:29: 11000000 INFO @ Tue, 27 Jun 2017 11:34:29: 11000000 INFO @ Tue, 27 Jun 2017 11:34:30: 12000000 INFO @ Tue, 27 Jun 2017 11:34:36: 13000000 INFO @ Tue, 27 Jun 2017 11:34:36: 12000000 INFO @ Tue, 27 Jun 2017 11:34:36: 12000000 INFO @ Tue, 27 Jun 2017 11:34:42: 14000000 INFO @ Tue, 27 Jun 2017 11:34:43: #1 tag size is determined as 36 bps INFO @ Tue, 27 Jun 2017 11:34:43: #1 tag size = 36 INFO @ Tue, 27 Jun 2017 11:34:43: #1 total tags in treatment: 14051720 INFO @ Tue, 27 Jun 2017 11:34:43: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:34:43: #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 11:34:43: 13000000 INFO @ Tue, 27 Jun 2017 11:34:43: 13000000 INFO @ Tue, 27 Jun 2017 11:34:43: #1 tags after filtering in treatment: 14051720 INFO @ Tue, 27 Jun 2017 11:34:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:34:43: #1 finished! INFO @ Tue, 27 Jun 2017 11:34:43: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:34:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:34:44: #2 number of paired peaks: 266 WARNING @ Tue, 27 Jun 2017 11:34:44: Fewer paired peaks (266) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 266 pairs to build model! INFO @ Tue, 27 Jun 2017 11:34:44: start model_add_line... INFO @ Tue, 27 Jun 2017 11:34:44: start X-correlation... INFO @ Tue, 27 Jun 2017 11:34:44: end of X-cor INFO @ Tue, 27 Jun 2017 11:34:44: #2 finished! INFO @ Tue, 27 Jun 2017 11:34:44: #2 predicted fragment length is 1 bps INFO @ Tue, 27 Jun 2017 11:34:44: #2 alternative fragment length(s) may be 1,32,565,597 bps INFO @ Tue, 27 Jun 2017 11:34:44: #2.2 Generate R script for model : SRX059251.10_model.r WARNING @ Tue, 27 Jun 2017 11:34:44: #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 11:34:44: #2 You may need to consider one of the other alternative d(s): 1,32,565,597 WARNING @ Tue, 27 Jun 2017 11:34:44: #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 11:34:44: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:34:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:34:49: 14000000 INFO @ Tue, 27 Jun 2017 11:34:49: 14000000 INFO @ Tue, 27 Jun 2017 11:34:50: #1 tag size is determined as 36 bps INFO @ Tue, 27 Jun 2017 11:34:50: #1 tag size = 36 INFO @ Tue, 27 Jun 2017 11:34:50: #1 total tags in treatment: 14051720 INFO @ Tue, 27 Jun 2017 11:34:50: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:34:50: #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 11:34:50: #1 tag size is determined as 36 bps INFO @ Tue, 27 Jun 2017 11:34:50: #1 tag size = 36 INFO @ Tue, 27 Jun 2017 11:34:50: #1 total tags in treatment: 14051720 INFO @ Tue, 27 Jun 2017 11:34:50: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:34:50: #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 11:34:50: #1 tags after filtering in treatment: 14051720 INFO @ Tue, 27 Jun 2017 11:34:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:34:50: #1 finished! INFO @ Tue, 27 Jun 2017 11:34:50: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:34:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:34:50: #1 tags after filtering in treatment: 14051720 INFO @ Tue, 27 Jun 2017 11:34:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:34:50: #1 finished! INFO @ Tue, 27 Jun 2017 11:34:50: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:34:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:34:51: #2 number of paired peaks: 266 WARNING @ Tue, 27 Jun 2017 11:34:51: Fewer paired peaks (266) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 266 pairs to build model! INFO @ Tue, 27 Jun 2017 11:34:51: start model_add_line... INFO @ Tue, 27 Jun 2017 11:34:51: #2 number of paired peaks: 266 WARNING @ Tue, 27 Jun 2017 11:34:51: Fewer paired peaks (266) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 266 pairs to build model! INFO @ Tue, 27 Jun 2017 11:34:51: start model_add_line... INFO @ Tue, 27 Jun 2017 11:34:51: start X-correlation... INFO @ Tue, 27 Jun 2017 11:34:51: end of X-cor INFO @ Tue, 27 Jun 2017 11:34:51: #2 finished! INFO @ Tue, 27 Jun 2017 11:34:51: #2 predicted fragment length is 1 bps INFO @ Tue, 27 Jun 2017 11:34:51: #2 alternative fragment length(s) may be 1,32,565,597 bps INFO @ Tue, 27 Jun 2017 11:34:51: #2.2 Generate R script for model : SRX059251.20_model.r WARNING @ Tue, 27 Jun 2017 11:34:51: #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 11:34:51: #2 You may need to consider one of the other alternative d(s): 1,32,565,597 WARNING @ Tue, 27 Jun 2017 11:34:51: #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 11:34:51: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:34:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:34:51: start X-correlation... INFO @ Tue, 27 Jun 2017 11:34:51: end of X-cor INFO @ Tue, 27 Jun 2017 11:34:51: #2 finished! INFO @ Tue, 27 Jun 2017 11:34:51: #2 predicted fragment length is 1 bps INFO @ Tue, 27 Jun 2017 11:34:51: #2 alternative fragment length(s) may be 1,32,565,597 bps INFO @ Tue, 27 Jun 2017 11:34:51: #2.2 Generate R script for model : SRX059251.05_model.r WARNING @ Tue, 27 Jun 2017 11:34:51: #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 11:34:51: #2 You may need to consider one of the other alternative d(s): 1,32,565,597 WARNING @ Tue, 27 Jun 2017 11:34:51: #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 11:34:51: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:34:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:35:12: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:35:16: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:35:18: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:35:27: #4 Write output xls file... SRX059251.10_peaks.xls INFO @ Tue, 27 Jun 2017 11:35:27: #4 Write peak in narrowPeak format file... SRX059251.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:35:27: #4 Write summits bed file... SRX059251.10_summits.bed INFO @ Tue, 27 Jun 2017 11:35:27: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:35:30: #4 Write output xls file... SRX059251.05_peaks.xls INFO @ Tue, 27 Jun 2017 11:35:30: #4 Write peak in narrowPeak format file... SRX059251.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:35:30: #4 Write summits bed file... SRX059251.05_summits.bed INFO @ Tue, 27 Jun 2017 11:35:30: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:35:32: #4 Write output xls file... SRX059251.20_peaks.xls INFO @ Tue, 27 Jun 2017 11:35:32: #4 Write peak in narrowPeak format file... SRX059251.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:35:32: #4 Write summits bed file... SRX059251.20_summits.bed INFO @ Tue, 27 Jun 2017 11:35:32: 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。