Job ID = 9157343 sra ファイルのダウンロード中... Completed: 591911K bytes transferred in 8 seconds (555055K 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 19874451 spots for /home/okishinya/chipatlas/results/ce10/SRX059221/SRR190661.sra Written 19874451 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: 00:05:27 19874451 reads; of these: 19874451 (100.00%) were unpaired; of these: 312752 (1.57%) aligned 0 times 16204284 (81.53%) aligned exactly 1 time 3357415 (16.89%) aligned >1 times 98.43% overall alignment rate Time searching: 00:05:27 Overall time: 00:05:27 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] 2055200 / 19561699 = 0.1051 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 11:36:17: # Command line: callpeak -t SRX059221.bam -f BAM -g ce -n SRX059221.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX059221.10 # format = BAM # ChIP-seq file = ['SRX059221.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 11:36:17: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:36:17: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:36:17: # Command line: callpeak -t SRX059221.bam -f BAM -g ce -n SRX059221.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX059221.05 # format = BAM # ChIP-seq file = ['SRX059221.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 11:36:17: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:36:17: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:36:17: # Command line: callpeak -t SRX059221.bam -f BAM -g ce -n SRX059221.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX059221.20 # format = BAM # ChIP-seq file = ['SRX059221.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 11:36:17: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:36:17: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:36:24: 1000000 INFO @ Tue, 27 Jun 2017 11:36:24: 1000000 INFO @ Tue, 27 Jun 2017 11:36:24: 1000000 INFO @ Tue, 27 Jun 2017 11:36:31: 2000000 INFO @ Tue, 27 Jun 2017 11:36:31: 2000000 INFO @ Tue, 27 Jun 2017 11:36:31: 2000000 INFO @ Tue, 27 Jun 2017 11:36:38: 3000000 INFO @ Tue, 27 Jun 2017 11:36:38: 3000000 INFO @ Tue, 27 Jun 2017 11:36:39: 3000000 INFO @ Tue, 27 Jun 2017 11:36:45: 4000000 INFO @ Tue, 27 Jun 2017 11:36:45: 4000000 INFO @ Tue, 27 Jun 2017 11:36:46: 4000000 INFO @ Tue, 27 Jun 2017 11:36:52: 5000000 INFO @ Tue, 27 Jun 2017 11:36:52: 5000000 INFO @ Tue, 27 Jun 2017 11:36:54: 5000000 INFO @ Tue, 27 Jun 2017 11:36:59: 6000000 INFO @ Tue, 27 Jun 2017 11:36:59: 6000000 INFO @ Tue, 27 Jun 2017 11:37:01: 6000000 INFO @ Tue, 27 Jun 2017 11:37:06: 7000000 INFO @ Tue, 27 Jun 2017 11:37:06: 7000000 INFO @ Tue, 27 Jun 2017 11:37:08: 7000000 INFO @ Tue, 27 Jun 2017 11:37:13: 8000000 INFO @ Tue, 27 Jun 2017 11:37:14: 8000000 INFO @ Tue, 27 Jun 2017 11:37:16: 8000000 INFO @ Tue, 27 Jun 2017 11:37:21: 9000000 INFO @ Tue, 27 Jun 2017 11:37:21: 9000000 INFO @ Tue, 27 Jun 2017 11:37:23: 9000000 INFO @ Tue, 27 Jun 2017 11:37:28: 10000000 INFO @ Tue, 27 Jun 2017 11:37:28: 10000000 INFO @ Tue, 27 Jun 2017 11:37:31: 10000000 INFO @ Tue, 27 Jun 2017 11:37:35: 11000000 INFO @ Tue, 27 Jun 2017 11:37:35: 11000000 INFO @ Tue, 27 Jun 2017 11:37:38: 11000000 INFO @ Tue, 27 Jun 2017 11:37:42: 12000000 INFO @ Tue, 27 Jun 2017 11:37:42: 12000000 INFO @ Tue, 27 Jun 2017 11:37:46: 12000000 INFO @ Tue, 27 Jun 2017 11:37:49: 13000000 INFO @ Tue, 27 Jun 2017 11:37:49: 13000000 INFO @ Tue, 27 Jun 2017 11:37:53: 13000000 INFO @ Tue, 27 Jun 2017 11:37:57: 14000000 INFO @ Tue, 27 Jun 2017 11:37:57: 14000000 INFO @ Tue, 27 Jun 2017 11:38:01: 14000000 INFO @ Tue, 27 Jun 2017 11:38:04: 15000000 INFO @ Tue, 27 Jun 2017 11:38:04: 15000000 INFO @ Tue, 27 Jun 2017 11:38:08: 15000000 INFO @ Tue, 27 Jun 2017 11:38:11: 16000000 INFO @ Tue, 27 Jun 2017 11:38:11: 16000000 INFO @ Tue, 27 Jun 2017 11:38:16: 16000000 INFO @ Tue, 27 Jun 2017 11:38:18: 17000000 INFO @ Tue, 27 Jun 2017 11:38:18: 17000000 INFO @ Tue, 27 Jun 2017 11:38:22: #1 tag size is determined as 42 bps INFO @ Tue, 27 Jun 2017 11:38:22: #1 tag size = 42 INFO @ Tue, 27 Jun 2017 11:38:22: #1 total tags in treatment: 17506499 INFO @ Tue, 27 Jun 2017 11:38:22: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:38:22: #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 11:38:22: #1 tag size is determined as 42 bps INFO @ Tue, 27 Jun 2017 11:38:22: #1 tag size = 42 INFO @ Tue, 27 Jun 2017 11:38:22: #1 total tags in treatment: 17506499 INFO @ Tue, 27 Jun 2017 11:38:22: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:38:22: #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 11:38:22: #1 tags after filtering in treatment: 17506499 INFO @ Tue, 27 Jun 2017 11:38:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:38:22: #1 finished! INFO @ Tue, 27 Jun 2017 11:38:22: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:38:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:38:22: #1 tags after filtering in treatment: 17506499 INFO @ Tue, 27 Jun 2017 11:38:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:38:22: #1 finished! INFO @ Tue, 27 Jun 2017 11:38:22: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:38:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:38:23: 17000000 INFO @ Tue, 27 Jun 2017 11:38:23: #2 number of paired peaks: 166 WARNING @ Tue, 27 Jun 2017 11:38:23: Fewer paired peaks (166) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 166 pairs to build model! INFO @ Tue, 27 Jun 2017 11:38:23: start model_add_line... INFO @ Tue, 27 Jun 2017 11:38:23: #2 number of paired peaks: 166 WARNING @ Tue, 27 Jun 2017 11:38:23: Fewer paired peaks (166) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 166 pairs to build model! INFO @ Tue, 27 Jun 2017 11:38:23: start model_add_line... INFO @ Tue, 27 Jun 2017 11:38:24: start X-correlation... INFO @ Tue, 27 Jun 2017 11:38:24: end of X-cor INFO @ Tue, 27 Jun 2017 11:38:24: #2 finished! INFO @ Tue, 27 Jun 2017 11:38:24: #2 predicted fragment length is 1 bps INFO @ Tue, 27 Jun 2017 11:38:24: #2 alternative fragment length(s) may be 1,25,497,518,533,596 bps INFO @ Tue, 27 Jun 2017 11:38:24: #2.2 Generate R script for model : SRX059221.10_model.r WARNING @ Tue, 27 Jun 2017 11:38:24: #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 11:38:24: #2 You may need to consider one of the other alternative d(s): 1,25,497,518,533,596 WARNING @ Tue, 27 Jun 2017 11:38:24: #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 11:38:24: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:38:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:38:24: start X-correlation... INFO @ Tue, 27 Jun 2017 11:38:24: end of X-cor INFO @ Tue, 27 Jun 2017 11:38:24: #2 finished! INFO @ Tue, 27 Jun 2017 11:38:24: #2 predicted fragment length is 1 bps INFO @ Tue, 27 Jun 2017 11:38:24: #2 alternative fragment length(s) may be 1,25,497,518,533,596 bps INFO @ Tue, 27 Jun 2017 11:38:24: #2.2 Generate R script for model : SRX059221.05_model.r WARNING @ Tue, 27 Jun 2017 11:38:24: #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 11:38:24: #2 You may need to consider one of the other alternative d(s): 1,25,497,518,533,596 WARNING @ Tue, 27 Jun 2017 11:38:24: #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 11:38:24: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:38:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:38:27: #1 tag size is determined as 42 bps INFO @ Tue, 27 Jun 2017 11:38:27: #1 tag size = 42 INFO @ Tue, 27 Jun 2017 11:38:27: #1 total tags in treatment: 17506499 INFO @ Tue, 27 Jun 2017 11:38:27: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:38:27: #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 11:38:27: #1 tags after filtering in treatment: 17506499 INFO @ Tue, 27 Jun 2017 11:38:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:38:27: #1 finished! INFO @ Tue, 27 Jun 2017 11:38:27: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:38:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:38:28: #2 number of paired peaks: 166 WARNING @ Tue, 27 Jun 2017 11:38:28: Fewer paired peaks (166) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 166 pairs to build model! INFO @ Tue, 27 Jun 2017 11:38:28: start model_add_line... INFO @ Tue, 27 Jun 2017 11:38:29: start X-correlation... INFO @ Tue, 27 Jun 2017 11:38:29: end of X-cor INFO @ Tue, 27 Jun 2017 11:38:29: #2 finished! INFO @ Tue, 27 Jun 2017 11:38:29: #2 predicted fragment length is 1 bps INFO @ Tue, 27 Jun 2017 11:38:29: #2 alternative fragment length(s) may be 1,25,497,518,533,596 bps INFO @ Tue, 27 Jun 2017 11:38:29: #2.2 Generate R script for model : SRX059221.20_model.r WARNING @ Tue, 27 Jun 2017 11:38:29: #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 11:38:29: #2 You may need to consider one of the other alternative d(s): 1,25,497,518,533,596 WARNING @ Tue, 27 Jun 2017 11:38:29: #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 11:38:29: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:38:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:38:54: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:38:55: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:38:58: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:39:12: #4 Write output xls file... SRX059221.05_peaks.xls INFO @ Tue, 27 Jun 2017 11:39:12: #4 Write peak in narrowPeak format file... SRX059221.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:39:12: #4 Write summits bed file... SRX059221.05_summits.bed INFO @ Tue, 27 Jun 2017 11:39:12: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:39:12: #4 Write output xls file... SRX059221.10_peaks.xls INFO @ Tue, 27 Jun 2017 11:39:12: #4 Write peak in narrowPeak format file... SRX059221.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:39:12: #4 Write summits bed file... SRX059221.10_summits.bed INFO @ Tue, 27 Jun 2017 11:39:12: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:39:15: #4 Write output xls file... SRX059221.20_peaks.xls INFO @ Tue, 27 Jun 2017 11:39:15: #4 Write peak in narrowPeak format file... SRX059221.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:39:15: #4 Write summits bed file... SRX059221.20_summits.bed INFO @ Tue, 27 Jun 2017 11:39:15: 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。