Job ID = 9157381 sra ファイルのダウンロード中... Completed: 2939848K bytes transferred in 25 seconds (936598K 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 85546882 spots for /home/okishinya/chipatlas/results/ce10/SRX1674095/SRR3320141.sra Written 85546882 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: 00:21:35 85546882 reads; of these: 85546882 (100.00%) were unpaired; of these: 12028739 (14.06%) aligned 0 times 60960496 (71.26%) aligned exactly 1 time 12557647 (14.68%) aligned >1 times 85.94% overall alignment rate Time searching: 00:21:35 Overall time: 00:21:35 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 32 files... [bam_rmdupse_core] 52628933 / 73518143 = 0.7159 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 12:12:00: # Command line: callpeak -t SRX1674095.bam -f BAM -g ce -n SRX1674095.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1674095.10 # format = BAM # ChIP-seq file = ['SRX1674095.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 12:12:00: #1 read tag files... INFO @ Tue, 27 Jun 2017 12:12:00: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 12:12:00: # Command line: callpeak -t SRX1674095.bam -f BAM -g ce -n SRX1674095.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1674095.20 # format = BAM # ChIP-seq file = ['SRX1674095.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 12:12:00: #1 read tag files... INFO @ Tue, 27 Jun 2017 12:12:00: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 12:12:00: # Command line: callpeak -t SRX1674095.bam -f BAM -g ce -n SRX1674095.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1674095.05 # format = BAM # ChIP-seq file = ['SRX1674095.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 12:12:00: #1 read tag files... INFO @ Tue, 27 Jun 2017 12:12:00: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 12:12:06: 1000000 INFO @ Tue, 27 Jun 2017 12:12:06: 1000000 INFO @ Tue, 27 Jun 2017 12:12:08: 1000000 INFO @ Tue, 27 Jun 2017 12:12:13: 2000000 INFO @ Tue, 27 Jun 2017 12:12:13: 2000000 INFO @ Tue, 27 Jun 2017 12:12:16: 2000000 INFO @ Tue, 27 Jun 2017 12:12:20: 3000000 INFO @ Tue, 27 Jun 2017 12:12:20: 3000000 INFO @ Tue, 27 Jun 2017 12:12:25: 3000000 INFO @ Tue, 27 Jun 2017 12:12:26: 4000000 INFO @ Tue, 27 Jun 2017 12:12:26: 4000000 INFO @ Tue, 27 Jun 2017 12:12:32: 5000000 INFO @ Tue, 27 Jun 2017 12:12:32: 5000000 INFO @ Tue, 27 Jun 2017 12:12:33: 4000000 INFO @ Tue, 27 Jun 2017 12:12:39: 6000000 INFO @ Tue, 27 Jun 2017 12:12:39: 6000000 INFO @ Tue, 27 Jun 2017 12:12:41: 5000000 INFO @ Tue, 27 Jun 2017 12:12:45: 7000000 INFO @ Tue, 27 Jun 2017 12:12:45: 7000000 INFO @ Tue, 27 Jun 2017 12:12:49: 6000000 INFO @ Tue, 27 Jun 2017 12:12:51: 8000000 INFO @ Tue, 27 Jun 2017 12:12:52: 8000000 INFO @ Tue, 27 Jun 2017 12:12:57: 7000000 INFO @ Tue, 27 Jun 2017 12:12:58: 9000000 INFO @ Tue, 27 Jun 2017 12:12:58: 9000000 INFO @ Tue, 27 Jun 2017 12:13:04: 10000000 INFO @ Tue, 27 Jun 2017 12:13:05: 10000000 INFO @ Tue, 27 Jun 2017 12:13:05: 8000000 INFO @ Tue, 27 Jun 2017 12:13:11: 11000000 INFO @ Tue, 27 Jun 2017 12:13:11: 11000000 INFO @ Tue, 27 Jun 2017 12:13:13: 9000000 INFO @ Tue, 27 Jun 2017 12:13:17: 12000000 INFO @ Tue, 27 Jun 2017 12:13:18: 12000000 INFO @ Tue, 27 Jun 2017 12:13:21: 10000000 INFO @ Tue, 27 Jun 2017 12:13:24: 13000000 INFO @ Tue, 27 Jun 2017 12:13:24: 13000000 INFO @ Tue, 27 Jun 2017 12:13:29: 11000000 INFO @ Tue, 27 Jun 2017 12:13:30: 14000000 INFO @ Tue, 27 Jun 2017 12:13:31: 14000000 INFO @ Tue, 27 Jun 2017 12:13:37: 15000000 INFO @ Tue, 27 Jun 2017 12:13:37: 12000000 INFO @ Tue, 27 Jun 2017 12:13:37: 15000000 INFO @ Tue, 27 Jun 2017 12:13:43: 16000000 INFO @ Tue, 27 Jun 2017 12:13:44: 16000000 INFO @ Tue, 27 Jun 2017 12:13:45: 13000000 INFO @ Tue, 27 Jun 2017 12:13:50: 17000000 INFO @ Tue, 27 Jun 2017 12:13:51: 17000000 INFO @ Tue, 27 Jun 2017 12:13:53: 14000000 INFO @ Tue, 27 Jun 2017 12:13:57: 18000000 INFO @ Tue, 27 Jun 2017 12:13:57: 18000000 INFO @ Tue, 27 Jun 2017 12:14:01: 15000000 INFO @ Tue, 27 Jun 2017 12:14:03: 19000000 INFO @ Tue, 27 Jun 2017 12:14:04: 19000000 INFO @ Tue, 27 Jun 2017 12:14:09: 16000000 INFO @ Tue, 27 Jun 2017 12:14:10: 20000000 INFO @ Tue, 27 Jun 2017 12:14:11: 20000000 INFO @ Tue, 27 Jun 2017 12:14:16: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 12:14:16: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 12:14:16: #1 total tags in treatment: 20889210 INFO @ Tue, 27 Jun 2017 12:14:16: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 12:14:16: #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 12:14:17: #1 tags after filtering in treatment: 20889210 INFO @ Tue, 27 Jun 2017 12:14:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 12:14:17: #1 finished! INFO @ Tue, 27 Jun 2017 12:14:17: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 12:14:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 12:14:17: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 12:14:17: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 12:14:17: #1 total tags in treatment: 20889210 INFO @ Tue, 27 Jun 2017 12:14:17: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 12:14:17: #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 12:14:17: 17000000 INFO @ Tue, 27 Jun 2017 12:14:17: #1 tags after filtering in treatment: 20889210 INFO @ Tue, 27 Jun 2017 12:14:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 12:14:17: #1 finished! INFO @ Tue, 27 Jun 2017 12:14:17: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 12:14:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 12:14:18: #2 number of paired peaks: 372 WARNING @ Tue, 27 Jun 2017 12:14:18: Fewer paired peaks (372) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 372 pairs to build model! INFO @ Tue, 27 Jun 2017 12:14:18: start model_add_line... INFO @ Tue, 27 Jun 2017 12:14:18: start X-correlation... INFO @ Tue, 27 Jun 2017 12:14:18: end of X-cor INFO @ Tue, 27 Jun 2017 12:14:18: #2 finished! INFO @ Tue, 27 Jun 2017 12:14:18: #2 predicted fragment length is 1 bps INFO @ Tue, 27 Jun 2017 12:14:18: #2 alternative fragment length(s) may be 1,596 bps INFO @ Tue, 27 Jun 2017 12:14:18: #2.2 Generate R script for model : SRX1674095.10_model.r WARNING @ Tue, 27 Jun 2017 12:14:18: #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 12:14:18: #2 You may need to consider one of the other alternative d(s): 1,596 WARNING @ Tue, 27 Jun 2017 12:14:18: #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 12:14:18: #3 Call peaks... INFO @ Tue, 27 Jun 2017 12:14:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 12:14:19: #2 number of paired peaks: 372 WARNING @ Tue, 27 Jun 2017 12:14:19: Fewer paired peaks (372) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 372 pairs to build model! INFO @ Tue, 27 Jun 2017 12:14:19: start model_add_line... INFO @ Tue, 27 Jun 2017 12:14:19: start X-correlation... INFO @ Tue, 27 Jun 2017 12:14:19: end of X-cor INFO @ Tue, 27 Jun 2017 12:14:19: #2 finished! INFO @ Tue, 27 Jun 2017 12:14:19: #2 predicted fragment length is 1 bps INFO @ Tue, 27 Jun 2017 12:14:19: #2 alternative fragment length(s) may be 1,596 bps INFO @ Tue, 27 Jun 2017 12:14:19: #2.2 Generate R script for model : SRX1674095.20_model.r WARNING @ Tue, 27 Jun 2017 12:14:19: #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 12:14:19: #2 You may need to consider one of the other alternative d(s): 1,596 WARNING @ Tue, 27 Jun 2017 12:14:19: #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 12:14:19: #3 Call peaks... INFO @ Tue, 27 Jun 2017 12:14:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 12:14:25: 18000000 INFO @ Tue, 27 Jun 2017 12:14:33: 19000000 INFO @ Tue, 27 Jun 2017 12:14:41: 20000000 INFO @ Tue, 27 Jun 2017 12:14:47: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 12:14:47: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 12:14:47: #1 total tags in treatment: 20889210 INFO @ Tue, 27 Jun 2017 12:14:47: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 12:14:47: #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 12:14:48: #1 tags after filtering in treatment: 20889210 INFO @ Tue, 27 Jun 2017 12:14:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 12:14:48: #1 finished! INFO @ Tue, 27 Jun 2017 12:14:48: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 12:14:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 12:14:49: #2 number of paired peaks: 372 WARNING @ Tue, 27 Jun 2017 12:14:49: Fewer paired peaks (372) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 372 pairs to build model! INFO @ Tue, 27 Jun 2017 12:14:49: start model_add_line... INFO @ Tue, 27 Jun 2017 12:14:50: start X-correlation... INFO @ Tue, 27 Jun 2017 12:14:50: end of X-cor INFO @ Tue, 27 Jun 2017 12:14:50: #2 finished! INFO @ Tue, 27 Jun 2017 12:14:50: #2 predicted fragment length is 1 bps INFO @ Tue, 27 Jun 2017 12:14:50: #2 alternative fragment length(s) may be 1,596 bps INFO @ Tue, 27 Jun 2017 12:14:50: #2.2 Generate R script for model : SRX1674095.05_model.r WARNING @ Tue, 27 Jun 2017 12:14:50: #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 12:14:50: #2 You may need to consider one of the other alternative d(s): 1,596 WARNING @ Tue, 27 Jun 2017 12:14:50: #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 12:14:50: #3 Call peaks... INFO @ Tue, 27 Jun 2017 12:14:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 12:14:53: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 12:14:53: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 12:15:11: #4 Write output xls file... SRX1674095.20_peaks.xls INFO @ Tue, 27 Jun 2017 12:15:11: #4 Write peak in narrowPeak format file... SRX1674095.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 12:15:11: #4 Write summits bed file... SRX1674095.20_summits.bed INFO @ Tue, 27 Jun 2017 12:15:11: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 12:15:11: #4 Write output xls file... SRX1674095.10_peaks.xls INFO @ Tue, 27 Jun 2017 12:15:11: #4 Write peak in narrowPeak format file... SRX1674095.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 12:15:11: #4 Write summits bed file... SRX1674095.10_summits.bed INFO @ Tue, 27 Jun 2017 12:15:11: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 12:15:22: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 12:15:39: #4 Write output xls file... SRX1674095.05_peaks.xls INFO @ Tue, 27 Jun 2017 12:15:39: #4 Write peak in narrowPeak format file... SRX1674095.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 12:15:39: #4 Write summits bed file... SRX1674095.05_summits.bed INFO @ Tue, 27 Jun 2017 12:15:39: 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。