Job ID = 9157178 sra ファイルのダウンロード中... Completed: 500752K bytes transferred in 5 seconds (691827K 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 28110258 spots for /home/okishinya/chipatlas/results/ce10/SRX2228898/SRR4380354.sra Written 28110258 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: 00:05:22 28110258 reads; of these: 28110258 (100.00%) were unpaired; of these: 350063 (1.25%) aligned 0 times 22849306 (81.28%) aligned exactly 1 time 4910889 (17.47%) aligned >1 times 98.75% overall alignment rate Time searching: 00:05:22 Overall time: 00:05:22 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] 5006081 / 27760195 = 0.1803 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 11:05:19: # Command line: callpeak -t SRX2228898.bam -f BAM -g ce -n SRX2228898.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2228898.20 # format = BAM # ChIP-seq file = ['SRX2228898.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 11:05:19: # Command line: callpeak -t SRX2228898.bam -f BAM -g ce -n SRX2228898.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2228898.10 # format = BAM # ChIP-seq file = ['SRX2228898.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 11:05:19: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:05:19: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:05:19: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:05:19: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:05:19: # Command line: callpeak -t SRX2228898.bam -f BAM -g ce -n SRX2228898.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2228898.05 # format = BAM # ChIP-seq file = ['SRX2228898.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 11:05:19: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:05:19: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:05:24: 1000000 INFO @ Tue, 27 Jun 2017 11:05:25: 1000000 INFO @ Tue, 27 Jun 2017 11:05:25: 1000000 INFO @ Tue, 27 Jun 2017 11:05:30: 2000000 INFO @ Tue, 27 Jun 2017 11:05:31: 2000000 INFO @ Tue, 27 Jun 2017 11:05:31: 2000000 INFO @ Tue, 27 Jun 2017 11:05:36: 3000000 INFO @ Tue, 27 Jun 2017 11:05:37: 3000000 INFO @ Tue, 27 Jun 2017 11:05:37: 3000000 INFO @ Tue, 27 Jun 2017 11:05:42: 4000000 INFO @ Tue, 27 Jun 2017 11:05:43: 4000000 INFO @ Tue, 27 Jun 2017 11:05:43: 4000000 INFO @ Tue, 27 Jun 2017 11:05:47: 5000000 INFO @ Tue, 27 Jun 2017 11:05:50: 5000000 INFO @ Tue, 27 Jun 2017 11:05:50: 5000000 INFO @ Tue, 27 Jun 2017 11:05:53: 6000000 INFO @ Tue, 27 Jun 2017 11:05:55: 6000000 INFO @ Tue, 27 Jun 2017 11:05:56: 6000000 INFO @ Tue, 27 Jun 2017 11:05:59: 7000000 INFO @ Tue, 27 Jun 2017 11:06:01: 7000000 INFO @ Tue, 27 Jun 2017 11:06:02: 7000000 INFO @ Tue, 27 Jun 2017 11:06:05: 8000000 INFO @ Tue, 27 Jun 2017 11:06:08: 8000000 INFO @ Tue, 27 Jun 2017 11:06:08: 8000000 INFO @ Tue, 27 Jun 2017 11:06:11: 9000000 INFO @ Tue, 27 Jun 2017 11:06:14: 9000000 INFO @ Tue, 27 Jun 2017 11:06:14: 9000000 INFO @ Tue, 27 Jun 2017 11:06:16: 10000000 INFO @ Tue, 27 Jun 2017 11:06:20: 10000000 INFO @ Tue, 27 Jun 2017 11:06:20: 10000000 INFO @ Tue, 27 Jun 2017 11:06:22: 11000000 INFO @ Tue, 27 Jun 2017 11:06:26: 11000000 INFO @ Tue, 27 Jun 2017 11:06:26: 11000000 INFO @ Tue, 27 Jun 2017 11:06:28: 12000000 INFO @ Tue, 27 Jun 2017 11:06:32: 12000000 INFO @ Tue, 27 Jun 2017 11:06:32: 12000000 INFO @ Tue, 27 Jun 2017 11:06:33: 13000000 INFO @ Tue, 27 Jun 2017 11:06:38: 13000000 INFO @ Tue, 27 Jun 2017 11:06:38: 13000000 INFO @ Tue, 27 Jun 2017 11:06:39: 14000000 INFO @ Tue, 27 Jun 2017 11:06:44: 14000000 INFO @ Tue, 27 Jun 2017 11:06:44: 14000000 INFO @ Tue, 27 Jun 2017 11:06:45: 15000000 INFO @ Tue, 27 Jun 2017 11:06:50: 15000000 INFO @ Tue, 27 Jun 2017 11:06:50: 16000000 INFO @ Tue, 27 Jun 2017 11:06:50: 15000000 INFO @ Tue, 27 Jun 2017 11:06:56: 17000000 INFO @ Tue, 27 Jun 2017 11:06:57: 16000000 INFO @ Tue, 27 Jun 2017 11:06:57: 16000000 INFO @ Tue, 27 Jun 2017 11:07:02: 18000000 INFO @ Tue, 27 Jun 2017 11:07:03: 17000000 INFO @ Tue, 27 Jun 2017 11:07:03: 17000000 INFO @ Tue, 27 Jun 2017 11:07:07: 19000000 INFO @ Tue, 27 Jun 2017 11:07:09: 18000000 INFO @ Tue, 27 Jun 2017 11:07:09: 18000000 INFO @ Tue, 27 Jun 2017 11:07:13: 20000000 INFO @ Tue, 27 Jun 2017 11:07:15: 19000000 INFO @ Tue, 27 Jun 2017 11:07:16: 19000000 INFO @ Tue, 27 Jun 2017 11:07:18: 21000000 INFO @ Tue, 27 Jun 2017 11:07:22: 20000000 INFO @ Tue, 27 Jun 2017 11:07:22: 20000000 INFO @ Tue, 27 Jun 2017 11:07:24: 22000000 INFO @ Tue, 27 Jun 2017 11:07:28: 21000000 INFO @ Tue, 27 Jun 2017 11:07:28: 21000000 INFO @ Tue, 27 Jun 2017 11:07:28: #1 tag size is determined as 35 bps INFO @ Tue, 27 Jun 2017 11:07:28: #1 tag size = 35 INFO @ Tue, 27 Jun 2017 11:07:28: #1 total tags in treatment: 22754114 INFO @ Tue, 27 Jun 2017 11:07:28: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:07:28: #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 11:07:29: #1 tags after filtering in treatment: 22754114 INFO @ Tue, 27 Jun 2017 11:07:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:07:29: #1 finished! INFO @ Tue, 27 Jun 2017 11:07:29: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:07:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:07:30: #2 number of paired peaks: 196 WARNING @ Tue, 27 Jun 2017 11:07:30: Fewer paired peaks (196) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 196 pairs to build model! INFO @ Tue, 27 Jun 2017 11:07:30: start model_add_line... INFO @ Tue, 27 Jun 2017 11:07:31: start X-correlation... INFO @ Tue, 27 Jun 2017 11:07:31: end of X-cor INFO @ Tue, 27 Jun 2017 11:07:31: #2 finished! INFO @ Tue, 27 Jun 2017 11:07:31: #2 predicted fragment length is 1 bps INFO @ Tue, 27 Jun 2017 11:07:31: #2 alternative fragment length(s) may be 1,32,494,566 bps INFO @ Tue, 27 Jun 2017 11:07:31: #2.2 Generate R script for model : SRX2228898.20_model.r WARNING @ Tue, 27 Jun 2017 11:07:31: #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 11:07:31: #2 You may need to consider one of the other alternative d(s): 1,32,494,566 WARNING @ Tue, 27 Jun 2017 11:07:31: #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 11:07:31: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:07:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:07:34: 22000000 INFO @ Tue, 27 Jun 2017 11:07:34: 22000000 INFO @ Tue, 27 Jun 2017 11:07:39: #1 tag size is determined as 35 bps INFO @ Tue, 27 Jun 2017 11:07:39: #1 tag size = 35 INFO @ Tue, 27 Jun 2017 11:07:39: #1 total tags in treatment: 22754114 INFO @ Tue, 27 Jun 2017 11:07:39: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:07:39: #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 11:07:39: #1 tag size is determined as 35 bps INFO @ Tue, 27 Jun 2017 11:07:39: #1 tag size = 35 INFO @ Tue, 27 Jun 2017 11:07:39: #1 total tags in treatment: 22754114 INFO @ Tue, 27 Jun 2017 11:07:39: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:07:39: #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 11:07:39: #1 tags after filtering in treatment: 22754114 INFO @ Tue, 27 Jun 2017 11:07:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:07:39: #1 finished! INFO @ Tue, 27 Jun 2017 11:07:39: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:07:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:07:40: #1 tags after filtering in treatment: 22754114 INFO @ Tue, 27 Jun 2017 11:07:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:07:40: #1 finished! INFO @ Tue, 27 Jun 2017 11:07:40: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:07:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:07:41: #2 number of paired peaks: 196 WARNING @ Tue, 27 Jun 2017 11:07:41: Fewer paired peaks (196) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 196 pairs to build model! INFO @ Tue, 27 Jun 2017 11:07:41: start model_add_line... INFO @ Tue, 27 Jun 2017 11:07:41: start X-correlation... INFO @ Tue, 27 Jun 2017 11:07:41: end of X-cor INFO @ Tue, 27 Jun 2017 11:07:41: #2 finished! INFO @ Tue, 27 Jun 2017 11:07:41: #2 predicted fragment length is 1 bps INFO @ Tue, 27 Jun 2017 11:07:41: #2 alternative fragment length(s) may be 1,32,494,566 bps INFO @ Tue, 27 Jun 2017 11:07:41: #2.2 Generate R script for model : SRX2228898.05_model.r WARNING @ Tue, 27 Jun 2017 11:07:41: #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 11:07:41: #2 You may need to consider one of the other alternative d(s): 1,32,494,566 WARNING @ Tue, 27 Jun 2017 11:07:41: #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 11:07:41: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:07:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:07:41: #2 number of paired peaks: 196 WARNING @ Tue, 27 Jun 2017 11:07:41: Fewer paired peaks (196) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 196 pairs to build model! INFO @ Tue, 27 Jun 2017 11:07:41: start model_add_line... INFO @ Tue, 27 Jun 2017 11:07:41: start X-correlation... INFO @ Tue, 27 Jun 2017 11:07:41: end of X-cor INFO @ Tue, 27 Jun 2017 11:07:41: #2 finished! INFO @ Tue, 27 Jun 2017 11:07:41: #2 predicted fragment length is 1 bps INFO @ Tue, 27 Jun 2017 11:07:41: #2 alternative fragment length(s) may be 1,32,494,566 bps INFO @ Tue, 27 Jun 2017 11:07:41: #2.2 Generate R script for model : SRX2228898.10_model.r WARNING @ Tue, 27 Jun 2017 11:07:41: #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 11:07:41: #2 You may need to consider one of the other alternative d(s): 1,32,494,566 WARNING @ Tue, 27 Jun 2017 11:07:41: #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 11:07:41: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:07:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:08:05: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:08:15: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:08:18: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:08:24: #4 Write output xls file... SRX2228898.20_peaks.xls INFO @ Tue, 27 Jun 2017 11:08:24: #4 Write peak in narrowPeak format file... SRX2228898.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:08:24: #4 Write summits bed file... SRX2228898.20_summits.bed INFO @ Tue, 27 Jun 2017 11:08:24: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:08:37: #4 Write output xls file... SRX2228898.10_peaks.xls INFO @ Tue, 27 Jun 2017 11:08:37: #4 Write peak in narrowPeak format file... SRX2228898.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:08:37: #4 Write summits bed file... SRX2228898.10_summits.bed INFO @ Tue, 27 Jun 2017 11:08:37: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:08:37: #4 Write output xls file... SRX2228898.05_peaks.xls INFO @ Tue, 27 Jun 2017 11:08:37: #4 Write peak in narrowPeak format file... SRX2228898.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:08:37: #4 Write summits bed file... SRX2228898.05_summits.bed INFO @ Tue, 27 Jun 2017 11:08:37: 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。