Job ID = 9157298 sra ファイルのダウンロード中... Completed: 875422K bytes transferred in 17 seconds (410099K 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 17943886 spots for /home/okishinya/chipatlas/results/ce10/SRX2761387/SRR5476961.sra Written 17943886 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: 00:05:01 17943886 reads; of these: 17943886 (100.00%) were unpaired; of these: 841356 (4.69%) aligned 0 times 13797644 (76.89%) aligned exactly 1 time 3304886 (18.42%) aligned >1 times 95.31% overall alignment rate Time searching: 00:05:01 Overall time: 00:05:01 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] 1629191 / 17102530 = 0.0953 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 11:31:16: # Command line: callpeak -t SRX2761387.bam -f BAM -g ce -n SRX2761387.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2761387.10 # format = BAM # ChIP-seq file = ['SRX2761387.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 11:31:16: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:31:16: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:31:16: # Command line: callpeak -t SRX2761387.bam -f BAM -g ce -n SRX2761387.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2761387.20 # format = BAM # ChIP-seq file = ['SRX2761387.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 11:31:16: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:31:16: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:31:16: # Command line: callpeak -t SRX2761387.bam -f BAM -g ce -n SRX2761387.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2761387.05 # format = BAM # ChIP-seq file = ['SRX2761387.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 11:31:16: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:31:16: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:31:23: 1000000 INFO @ Tue, 27 Jun 2017 11:31:23: 1000000 INFO @ Tue, 27 Jun 2017 11:31:23: 1000000 INFO @ Tue, 27 Jun 2017 11:31:30: 2000000 INFO @ Tue, 27 Jun 2017 11:31:30: 2000000 INFO @ Tue, 27 Jun 2017 11:31:31: 2000000 INFO @ Tue, 27 Jun 2017 11:31:36: 3000000 INFO @ Tue, 27 Jun 2017 11:31:37: 3000000 INFO @ Tue, 27 Jun 2017 11:31:38: 3000000 INFO @ Tue, 27 Jun 2017 11:31:43: 4000000 INFO @ Tue, 27 Jun 2017 11:31:45: 4000000 INFO @ Tue, 27 Jun 2017 11:31:45: 4000000 INFO @ Tue, 27 Jun 2017 11:31:49: 5000000 INFO @ Tue, 27 Jun 2017 11:31:52: 5000000 INFO @ Tue, 27 Jun 2017 11:31:53: 5000000 INFO @ Tue, 27 Jun 2017 11:31:56: 6000000 INFO @ Tue, 27 Jun 2017 11:31:59: 6000000 INFO @ Tue, 27 Jun 2017 11:32:01: 6000000 INFO @ Tue, 27 Jun 2017 11:32:02: 7000000 INFO @ Tue, 27 Jun 2017 11:32:07: 7000000 INFO @ Tue, 27 Jun 2017 11:32:08: 7000000 INFO @ Tue, 27 Jun 2017 11:32:09: 8000000 INFO @ Tue, 27 Jun 2017 11:32:14: 8000000 INFO @ Tue, 27 Jun 2017 11:32:15: 9000000 INFO @ Tue, 27 Jun 2017 11:32:16: 8000000 INFO @ Tue, 27 Jun 2017 11:32:21: 9000000 INFO @ Tue, 27 Jun 2017 11:32:22: 10000000 INFO @ Tue, 27 Jun 2017 11:32:23: 9000000 INFO @ Tue, 27 Jun 2017 11:32:28: 11000000 INFO @ Tue, 27 Jun 2017 11:32:29: 10000000 INFO @ Tue, 27 Jun 2017 11:32:31: 10000000 INFO @ Tue, 27 Jun 2017 11:32:35: 12000000 INFO @ Tue, 27 Jun 2017 11:32:36: 11000000 INFO @ Tue, 27 Jun 2017 11:32:38: 11000000 INFO @ Tue, 27 Jun 2017 11:32:42: 13000000 INFO @ Tue, 27 Jun 2017 11:32:43: 12000000 INFO @ Tue, 27 Jun 2017 11:32:46: 12000000 INFO @ Tue, 27 Jun 2017 11:32:48: 14000000 INFO @ Tue, 27 Jun 2017 11:32:51: 13000000 INFO @ Tue, 27 Jun 2017 11:32:54: 13000000 INFO @ Tue, 27 Jun 2017 11:32:55: 15000000 INFO @ Tue, 27 Jun 2017 11:32:58: 14000000 INFO @ Tue, 27 Jun 2017 11:32:58: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:32:58: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:32:58: #1 total tags in treatment: 15473339 INFO @ Tue, 27 Jun 2017 11:32:58: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:32:58: #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 11:32:58: #1 tags after filtering in treatment: 15473339 INFO @ Tue, 27 Jun 2017 11:32:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:32:58: #1 finished! INFO @ Tue, 27 Jun 2017 11:32:58: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:32:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:32:59: #2 number of paired peaks: 386 WARNING @ Tue, 27 Jun 2017 11:32:59: Fewer paired peaks (386) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 386 pairs to build model! INFO @ Tue, 27 Jun 2017 11:32:59: start model_add_line... INFO @ Tue, 27 Jun 2017 11:32:59: start X-correlation... INFO @ Tue, 27 Jun 2017 11:32:59: end of X-cor INFO @ Tue, 27 Jun 2017 11:32:59: #2 finished! INFO @ Tue, 27 Jun 2017 11:32:59: #2 predicted fragment length is 1 bps INFO @ Tue, 27 Jun 2017 11:32:59: #2 alternative fragment length(s) may be 1,21,45 bps INFO @ Tue, 27 Jun 2017 11:32:59: #2.2 Generate R script for model : SRX2761387.20_model.r WARNING @ Tue, 27 Jun 2017 11:32:59: #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 11:32:59: #2 You may need to consider one of the other alternative d(s): 1,21,45 WARNING @ Tue, 27 Jun 2017 11:32:59: #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 11:32:59: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:32:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:33:01: 14000000 INFO @ Tue, 27 Jun 2017 11:33:05: 15000000 INFO @ Tue, 27 Jun 2017 11:33:08: 15000000 INFO @ Tue, 27 Jun 2017 11:33:09: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:33:09: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:33:09: #1 total tags in treatment: 15473339 INFO @ Tue, 27 Jun 2017 11:33:09: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:33:09: #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 11:33:09: #1 tags after filtering in treatment: 15473339 INFO @ Tue, 27 Jun 2017 11:33:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:33:09: #1 finished! INFO @ Tue, 27 Jun 2017 11:33:09: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:33:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:33:10: #2 number of paired peaks: 386 WARNING @ Tue, 27 Jun 2017 11:33:10: Fewer paired peaks (386) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 386 pairs to build model! INFO @ Tue, 27 Jun 2017 11:33:10: start model_add_line... INFO @ Tue, 27 Jun 2017 11:33:10: start X-correlation... INFO @ Tue, 27 Jun 2017 11:33:10: end of X-cor INFO @ Tue, 27 Jun 2017 11:33:10: #2 finished! INFO @ Tue, 27 Jun 2017 11:33:10: #2 predicted fragment length is 1 bps INFO @ Tue, 27 Jun 2017 11:33:10: #2 alternative fragment length(s) may be 1,21,45 bps INFO @ Tue, 27 Jun 2017 11:33:10: #2.2 Generate R script for model : SRX2761387.10_model.r WARNING @ Tue, 27 Jun 2017 11:33:10: #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 11:33:10: #2 You may need to consider one of the other alternative d(s): 1,21,45 WARNING @ Tue, 27 Jun 2017 11:33:10: #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 11:33:10: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:33:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:33:12: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:33:12: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:33:12: #1 total tags in treatment: 15473339 INFO @ Tue, 27 Jun 2017 11:33:12: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:33:12: #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 11:33:12: #1 tags after filtering in treatment: 15473339 INFO @ Tue, 27 Jun 2017 11:33:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:33:12: #1 finished! INFO @ Tue, 27 Jun 2017 11:33:12: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:33:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:33:13: #2 number of paired peaks: 386 WARNING @ Tue, 27 Jun 2017 11:33:13: Fewer paired peaks (386) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 386 pairs to build model! INFO @ Tue, 27 Jun 2017 11:33:13: start model_add_line... INFO @ Tue, 27 Jun 2017 11:33:13: start X-correlation... INFO @ Tue, 27 Jun 2017 11:33:13: end of X-cor INFO @ Tue, 27 Jun 2017 11:33:13: #2 finished! INFO @ Tue, 27 Jun 2017 11:33:13: #2 predicted fragment length is 1 bps INFO @ Tue, 27 Jun 2017 11:33:13: #2 alternative fragment length(s) may be 1,21,45 bps INFO @ Tue, 27 Jun 2017 11:33:13: #2.2 Generate R script for model : SRX2761387.05_model.r WARNING @ Tue, 27 Jun 2017 11:33:13: #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 11:33:13: #2 You may need to consider one of the other alternative d(s): 1,21,45 WARNING @ Tue, 27 Jun 2017 11:33:13: #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 11:33:13: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:33:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:33:29: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:33:39: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:33:39: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:33:43: #4 Write output xls file... SRX2761387.20_peaks.xls INFO @ Tue, 27 Jun 2017 11:33:43: #4 Write peak in narrowPeak format file... SRX2761387.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:33:43: #4 Write summits bed file... SRX2761387.20_summits.bed INFO @ Tue, 27 Jun 2017 11:33:43: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:33:56: #4 Write output xls file... SRX2761387.05_peaks.xls INFO @ Tue, 27 Jun 2017 11:33:56: #4 Write peak in narrowPeak format file... SRX2761387.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:33:56: #4 Write summits bed file... SRX2761387.05_summits.bed INFO @ Tue, 27 Jun 2017 11:33:56: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:33:56: #4 Write output xls file... SRX2761387.10_peaks.xls INFO @ Tue, 27 Jun 2017 11:33:56: #4 Write peak in narrowPeak format file... SRX2761387.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:33:56: #4 Write summits bed file... SRX2761387.10_summits.bed INFO @ Tue, 27 Jun 2017 11:33:56: 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。