Job ID = 9157346 sra ファイルのダウンロード中... Completed: 381313K bytes transferred in 7 seconds (391757K 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 16535439 spots for /home/okishinya/chipatlas/results/ce10/SRX059227/SRR190667.sra Written 16535439 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:31 16535439 reads; of these: 16535439 (100.00%) were unpaired; of these: 461486 (2.79%) aligned 0 times 13204060 (79.85%) aligned exactly 1 time 2869893 (17.36%) aligned >1 times 97.21% overall alignment rate Time searching: 00:04:32 Overall time: 00:04:32 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] 1508149 / 16073953 = 0.0938 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 11:34:21: # Command line: callpeak -t SRX059227.bam -f BAM -g ce -n SRX059227.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX059227.20 # format = BAM # ChIP-seq file = ['SRX059227.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 11:34:21: # Command line: callpeak -t SRX059227.bam -f BAM -g ce -n SRX059227.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX059227.05 # format = BAM # ChIP-seq file = ['SRX059227.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 11:34:21: # Command line: callpeak -t SRX059227.bam -f BAM -g ce -n SRX059227.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX059227.10 # format = BAM # ChIP-seq file = ['SRX059227.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 11:34:21: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:34:21: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:34:21: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:34:21: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:34:21: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:34:21: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:34:27: 1000000 INFO @ Tue, 27 Jun 2017 11:34:27: 1000000 INFO @ Tue, 27 Jun 2017 11:34:27: 1000000 INFO @ Tue, 27 Jun 2017 11:34:33: 2000000 INFO @ Tue, 27 Jun 2017 11:34:33: 2000000 INFO @ Tue, 27 Jun 2017 11:34:33: 2000000 INFO @ Tue, 27 Jun 2017 11:34:39: 3000000 INFO @ Tue, 27 Jun 2017 11:34:39: 3000000 INFO @ Tue, 27 Jun 2017 11:34:40: 3000000 INFO @ Tue, 27 Jun 2017 11:34:45: 4000000 INFO @ Tue, 27 Jun 2017 11:34:45: 4000000 INFO @ Tue, 27 Jun 2017 11:34:46: 4000000 INFO @ Tue, 27 Jun 2017 11:34:50: 5000000 INFO @ Tue, 27 Jun 2017 11:34:51: 5000000 INFO @ Tue, 27 Jun 2017 11:34:53: 5000000 INFO @ Tue, 27 Jun 2017 11:34:56: 6000000 INFO @ Tue, 27 Jun 2017 11:34:57: 6000000 INFO @ Tue, 27 Jun 2017 11:35:00: 6000000 INFO @ Tue, 27 Jun 2017 11:35:02: 7000000 INFO @ Tue, 27 Jun 2017 11:35:04: 7000000 INFO @ Tue, 27 Jun 2017 11:35:06: 7000000 INFO @ Tue, 27 Jun 2017 11:35:08: 8000000 INFO @ Tue, 27 Jun 2017 11:35:10: 8000000 INFO @ Tue, 27 Jun 2017 11:35:13: 8000000 INFO @ Tue, 27 Jun 2017 11:35:14: 9000000 INFO @ Tue, 27 Jun 2017 11:35:16: 9000000 INFO @ Tue, 27 Jun 2017 11:35:20: 9000000 INFO @ Tue, 27 Jun 2017 11:35:20: 10000000 INFO @ Tue, 27 Jun 2017 11:35:23: 10000000 INFO @ Tue, 27 Jun 2017 11:35:26: 11000000 INFO @ Tue, 27 Jun 2017 11:35:27: 10000000 INFO @ Tue, 27 Jun 2017 11:35:29: 11000000 INFO @ Tue, 27 Jun 2017 11:35:32: 12000000 INFO @ Tue, 27 Jun 2017 11:35:33: 11000000 INFO @ Tue, 27 Jun 2017 11:35:35: 12000000 INFO @ Tue, 27 Jun 2017 11:35:38: 13000000 INFO @ Tue, 27 Jun 2017 11:35:40: 12000000 INFO @ Tue, 27 Jun 2017 11:35:42: 13000000 INFO @ Tue, 27 Jun 2017 11:35:44: 14000000 INFO @ Tue, 27 Jun 2017 11:35:47: 13000000 INFO @ Tue, 27 Jun 2017 11:35:47: #1 tag size is determined as 36 bps INFO @ Tue, 27 Jun 2017 11:35:47: #1 tag size = 36 INFO @ Tue, 27 Jun 2017 11:35:47: #1 total tags in treatment: 14565804 INFO @ Tue, 27 Jun 2017 11:35:47: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:35:47: #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 11:35:48: #1 tags after filtering in treatment: 14565804 INFO @ Tue, 27 Jun 2017 11:35:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:35:48: #1 finished! INFO @ Tue, 27 Jun 2017 11:35:48: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:35:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:35:48: 14000000 INFO @ Tue, 27 Jun 2017 11:35:49: #2 number of paired peaks: 268 WARNING @ Tue, 27 Jun 2017 11:35:49: Fewer paired peaks (268) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 268 pairs to build model! INFO @ Tue, 27 Jun 2017 11:35:49: start model_add_line... INFO @ Tue, 27 Jun 2017 11:35:49: start X-correlation... INFO @ Tue, 27 Jun 2017 11:35:49: end of X-cor INFO @ Tue, 27 Jun 2017 11:35:49: #2 finished! INFO @ Tue, 27 Jun 2017 11:35:49: #2 predicted fragment length is 1 bps INFO @ Tue, 27 Jun 2017 11:35:49: #2 alternative fragment length(s) may be 1,35,554,557,560 bps INFO @ Tue, 27 Jun 2017 11:35:49: #2.2 Generate R script for model : SRX059227.20_model.r WARNING @ Tue, 27 Jun 2017 11:35:49: #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 11:35:49: #2 You may need to consider one of the other alternative d(s): 1,35,554,557,560 WARNING @ Tue, 27 Jun 2017 11:35:49: #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 11:35:49: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:35:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:35:51: #1 tag size is determined as 36 bps INFO @ Tue, 27 Jun 2017 11:35:51: #1 tag size = 36 INFO @ Tue, 27 Jun 2017 11:35:51: #1 total tags in treatment: 14565804 INFO @ Tue, 27 Jun 2017 11:35:51: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:35:51: #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 11:35:52: #1 tags after filtering in treatment: 14565804 INFO @ Tue, 27 Jun 2017 11:35:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:35:52: #1 finished! INFO @ Tue, 27 Jun 2017 11:35:52: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:35:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:35:53: #2 number of paired peaks: 268 WARNING @ Tue, 27 Jun 2017 11:35:53: Fewer paired peaks (268) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 268 pairs to build model! INFO @ Tue, 27 Jun 2017 11:35:53: start model_add_line... INFO @ Tue, 27 Jun 2017 11:35:53: start X-correlation... INFO @ Tue, 27 Jun 2017 11:35:53: end of X-cor INFO @ Tue, 27 Jun 2017 11:35:53: #2 finished! INFO @ Tue, 27 Jun 2017 11:35:53: #2 predicted fragment length is 1 bps INFO @ Tue, 27 Jun 2017 11:35:53: #2 alternative fragment length(s) may be 1,35,554,557,560 bps INFO @ Tue, 27 Jun 2017 11:35:53: #2.2 Generate R script for model : SRX059227.10_model.r WARNING @ Tue, 27 Jun 2017 11:35:53: #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 11:35:53: #2 You may need to consider one of the other alternative d(s): 1,35,554,557,560 WARNING @ Tue, 27 Jun 2017 11:35:53: #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 11:35:53: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:35:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:35:53: 14000000 INFO @ Tue, 27 Jun 2017 11:35:57: #1 tag size is determined as 36 bps INFO @ Tue, 27 Jun 2017 11:35:57: #1 tag size = 36 INFO @ Tue, 27 Jun 2017 11:35:57: #1 total tags in treatment: 14565804 INFO @ Tue, 27 Jun 2017 11:35:57: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:35:57: #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 11:35:57: #1 tags after filtering in treatment: 14565804 INFO @ Tue, 27 Jun 2017 11:35:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:35:57: #1 finished! INFO @ Tue, 27 Jun 2017 11:35:57: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:35:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:35:58: #2 number of paired peaks: 268 WARNING @ Tue, 27 Jun 2017 11:35:58: Fewer paired peaks (268) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 268 pairs to build model! INFO @ Tue, 27 Jun 2017 11:35:58: start model_add_line... INFO @ Tue, 27 Jun 2017 11:35:58: start X-correlation... INFO @ Tue, 27 Jun 2017 11:35:58: end of X-cor INFO @ Tue, 27 Jun 2017 11:35:58: #2 finished! INFO @ Tue, 27 Jun 2017 11:35:58: #2 predicted fragment length is 1 bps INFO @ Tue, 27 Jun 2017 11:35:58: #2 alternative fragment length(s) may be 1,35,554,557,560 bps INFO @ Tue, 27 Jun 2017 11:35:58: #2.2 Generate R script for model : SRX059227.05_model.r WARNING @ Tue, 27 Jun 2017 11:35:58: #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 11:35:58: #2 You may need to consider one of the other alternative d(s): 1,35,554,557,560 WARNING @ Tue, 27 Jun 2017 11:35:58: #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 11:35:58: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:35:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:36:15: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:36:21: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:36:25: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:36:28: #4 Write output xls file... SRX059227.20_peaks.xls INFO @ Tue, 27 Jun 2017 11:36:28: #4 Write peak in narrowPeak format file... SRX059227.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:36:28: #4 Write summits bed file... SRX059227.20_summits.bed INFO @ Tue, 27 Jun 2017 11:36:28: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:36:34: #4 Write output xls file... SRX059227.10_peaks.xls INFO @ Tue, 27 Jun 2017 11:36:34: #4 Write peak in narrowPeak format file... SRX059227.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:36:34: #4 Write summits bed file... SRX059227.10_summits.bed INFO @ Tue, 27 Jun 2017 11:36:34: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:36:38: #4 Write output xls file... SRX059227.05_peaks.xls INFO @ Tue, 27 Jun 2017 11:36:38: #4 Write peak in narrowPeak format file... SRX059227.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:36:38: #4 Write summits bed file... SRX059227.05_summits.bed INFO @ Tue, 27 Jun 2017 11:36:38: 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。