Job ID = 11170810 sra ファイルのダウンロード中... Completed: 1324722K bytes transferred in 110 seconds (98527K bits/sec), in 1 file. 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... Read 45844906 spots for /home/okishinya/chipatlas/results/ce10/SRX2965735/SRR5766320.sra Written 45844906 spots for /home/okishinya/chipatlas/results/ce10/SRX2965735/SRR5766320.sra rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません 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: 00:17:33 45844906 reads; of these: 45844906 (100.00%) were unpaired; of these: 5563012 (12.13%) aligned 0 times 33530229 (73.14%) aligned exactly 1 time 6751665 (14.73%) aligned >1 times 87.87% overall alignment rate Time searching: 00:17:33 Overall time: 00:17:33 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 20 files... [bam_rmdupse_core] 10512840 / 40281894 = 0.2610 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 @ Sat, 08 Sep 2018 11:57:16: # Command line: callpeak -t SRX2965735.bam -f BAM -g ce -n SRX2965735.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2965735.20 # format = BAM # ChIP-seq file = ['SRX2965735.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 @ Sat, 08 Sep 2018 11:57:16: # Command line: callpeak -t SRX2965735.bam -f BAM -g ce -n SRX2965735.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2965735.05 # format = BAM # ChIP-seq file = ['SRX2965735.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 @ Sat, 08 Sep 2018 11:57:16: #1 read tag files... INFO @ Sat, 08 Sep 2018 11:57:16: #1 read tag files... INFO @ Sat, 08 Sep 2018 11:57:16: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 11:57:16: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 11:57:16: # Command line: callpeak -t SRX2965735.bam -f BAM -g ce -n SRX2965735.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2965735.10 # format = BAM # ChIP-seq file = ['SRX2965735.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 @ Sat, 08 Sep 2018 11:57:16: #1 read tag files... INFO @ Sat, 08 Sep 2018 11:57:16: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 11:57:25: 1000000 INFO @ Sat, 08 Sep 2018 11:57:25: 1000000 INFO @ Sat, 08 Sep 2018 11:57:25: 1000000 INFO @ Sat, 08 Sep 2018 11:57:32: 2000000 INFO @ Sat, 08 Sep 2018 11:57:33: 2000000 INFO @ Sat, 08 Sep 2018 11:57:33: 2000000 INFO @ Sat, 08 Sep 2018 11:57:40: 3000000 INFO @ Sat, 08 Sep 2018 11:57:42: 3000000 INFO @ Sat, 08 Sep 2018 11:57:42: 3000000 INFO @ Sat, 08 Sep 2018 11:57:48: 4000000 INFO @ Sat, 08 Sep 2018 11:57:51: 4000000 INFO @ Sat, 08 Sep 2018 11:57:51: 4000000 INFO @ Sat, 08 Sep 2018 11:57:56: 5000000 INFO @ Sat, 08 Sep 2018 11:57:59: 5000000 INFO @ Sat, 08 Sep 2018 11:57:59: 5000000 INFO @ Sat, 08 Sep 2018 11:58:04: 6000000 INFO @ Sat, 08 Sep 2018 11:58:08: 6000000 INFO @ Sat, 08 Sep 2018 11:58:08: 6000000 INFO @ Sat, 08 Sep 2018 11:58:12: 7000000 INFO @ Sat, 08 Sep 2018 11:58:16: 7000000 INFO @ Sat, 08 Sep 2018 11:58:16: 7000000 INFO @ Sat, 08 Sep 2018 11:58:20: 8000000 INFO @ Sat, 08 Sep 2018 11:58:24: 8000000 INFO @ Sat, 08 Sep 2018 11:58:24: 8000000 INFO @ Sat, 08 Sep 2018 11:58:28: 9000000 INFO @ Sat, 08 Sep 2018 11:58:33: 9000000 INFO @ Sat, 08 Sep 2018 11:58:33: 9000000 INFO @ Sat, 08 Sep 2018 11:58:36: 10000000 INFO @ Sat, 08 Sep 2018 11:58:41: 10000000 INFO @ Sat, 08 Sep 2018 11:58:41: 10000000 INFO @ Sat, 08 Sep 2018 11:58:44: 11000000 INFO @ Sat, 08 Sep 2018 11:58:50: 11000000 INFO @ Sat, 08 Sep 2018 11:58:50: 11000000 INFO @ Sat, 08 Sep 2018 11:58:52: 12000000 INFO @ Sat, 08 Sep 2018 11:58:58: 12000000 INFO @ Sat, 08 Sep 2018 11:58:58: 12000000 INFO @ Sat, 08 Sep 2018 11:59:00: 13000000 INFO @ Sat, 08 Sep 2018 11:59:06: 13000000 INFO @ Sat, 08 Sep 2018 11:59:06: 13000000 INFO @ Sat, 08 Sep 2018 11:59:08: 14000000 INFO @ Sat, 08 Sep 2018 11:59:15: 14000000 INFO @ Sat, 08 Sep 2018 11:59:15: 14000000 INFO @ Sat, 08 Sep 2018 11:59:16: 15000000 INFO @ Sat, 08 Sep 2018 11:59:23: 15000000 INFO @ Sat, 08 Sep 2018 11:59:23: 15000000 INFO @ Sat, 08 Sep 2018 11:59:24: 16000000 INFO @ Sat, 08 Sep 2018 11:59:31: 16000000 INFO @ Sat, 08 Sep 2018 11:59:31: 16000000 INFO @ Sat, 08 Sep 2018 11:59:32: 17000000 INFO @ Sat, 08 Sep 2018 11:59:40: 17000000 INFO @ Sat, 08 Sep 2018 11:59:40: 17000000 INFO @ Sat, 08 Sep 2018 11:59:40: 18000000 INFO @ Sat, 08 Sep 2018 11:59:48: 19000000 INFO @ Sat, 08 Sep 2018 11:59:48: 18000000 INFO @ Sat, 08 Sep 2018 11:59:48: 18000000 INFO @ Sat, 08 Sep 2018 11:59:56: 20000000 INFO @ Sat, 08 Sep 2018 11:59:56: 19000000 INFO @ Sat, 08 Sep 2018 11:59:56: 19000000 INFO @ Sat, 08 Sep 2018 12:00:04: 21000000 INFO @ Sat, 08 Sep 2018 12:00:05: 20000000 INFO @ Sat, 08 Sep 2018 12:00:05: 20000000 INFO @ Sat, 08 Sep 2018 12:00:12: 22000000 INFO @ Sat, 08 Sep 2018 12:00:13: 21000000 INFO @ Sat, 08 Sep 2018 12:00:13: 21000000 INFO @ Sat, 08 Sep 2018 12:00:19: 23000000 INFO @ Sat, 08 Sep 2018 12:00:21: 22000000 INFO @ Sat, 08 Sep 2018 12:00:21: 22000000 INFO @ Sat, 08 Sep 2018 12:00:27: 24000000 INFO @ Sat, 08 Sep 2018 12:00:29: 23000000 INFO @ Sat, 08 Sep 2018 12:00:30: 23000000 INFO @ Sat, 08 Sep 2018 12:00:35: 25000000 INFO @ Sat, 08 Sep 2018 12:00:38: 24000000 INFO @ Sat, 08 Sep 2018 12:00:38: 24000000 INFO @ Sat, 08 Sep 2018 12:00:43: 26000000 INFO @ Sat, 08 Sep 2018 12:00:46: 25000000 INFO @ Sat, 08 Sep 2018 12:00:46: 25000000 INFO @ Sat, 08 Sep 2018 12:00:51: 27000000 INFO @ Sat, 08 Sep 2018 12:00:54: 26000000 INFO @ Sat, 08 Sep 2018 12:00:55: 26000000 INFO @ Sat, 08 Sep 2018 12:00:59: 28000000 INFO @ Sat, 08 Sep 2018 12:01:03: 27000000 INFO @ Sat, 08 Sep 2018 12:01:03: 27000000 INFO @ Sat, 08 Sep 2018 12:01:07: 29000000 INFO @ Sat, 08 Sep 2018 12:01:12: 28000000 INFO @ Sat, 08 Sep 2018 12:01:12: 28000000 INFO @ Sat, 08 Sep 2018 12:01:13: #1 tag size is determined as 76 bps INFO @ Sat, 08 Sep 2018 12:01:13: #1 tag size = 76 INFO @ Sat, 08 Sep 2018 12:01:13: #1 total tags in treatment: 29769054 INFO @ Sat, 08 Sep 2018 12:01:13: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 12:01:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 12:01:14: #1 tags after filtering in treatment: 29769054 INFO @ Sat, 08 Sep 2018 12:01:14: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 12:01:14: #1 finished! INFO @ Sat, 08 Sep 2018 12:01:14: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 12:01:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 12:01:15: #2 number of paired peaks: 106 WARNING @ Sat, 08 Sep 2018 12:01:15: Fewer paired peaks (106) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 106 pairs to build model! INFO @ Sat, 08 Sep 2018 12:01:15: start model_add_line... INFO @ Sat, 08 Sep 2018 12:01:16: start X-correlation... INFO @ Sat, 08 Sep 2018 12:01:16: end of X-cor INFO @ Sat, 08 Sep 2018 12:01:16: #2 finished! INFO @ Sat, 08 Sep 2018 12:01:16: #2 predicted fragment length is 1 bps INFO @ Sat, 08 Sep 2018 12:01:16: #2 alternative fragment length(s) may be 1,10,29,60,74 bps INFO @ Sat, 08 Sep 2018 12:01:16: #2.2 Generate R script for model : SRX2965735.10_model.r WARNING @ Sat, 08 Sep 2018 12:01:16: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 12:01:16: #2 You may need to consider one of the other alternative d(s): 1,10,29,60,74 WARNING @ Sat, 08 Sep 2018 12:01:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 12:01:16: #3 Call peaks... INFO @ Sat, 08 Sep 2018 12:01:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 12:01:20: 29000000 INFO @ Sat, 08 Sep 2018 12:01:20: 29000000 INFO @ Sat, 08 Sep 2018 12:01:27: #1 tag size is determined as 76 bps INFO @ Sat, 08 Sep 2018 12:01:27: #1 tag size = 76 INFO @ Sat, 08 Sep 2018 12:01:27: #1 total tags in treatment: 29769054 INFO @ Sat, 08 Sep 2018 12:01:27: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 12:01:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 12:01:27: #1 tag size is determined as 76 bps INFO @ Sat, 08 Sep 2018 12:01:27: #1 tag size = 76 INFO @ Sat, 08 Sep 2018 12:01:27: #1 total tags in treatment: 29769054 INFO @ Sat, 08 Sep 2018 12:01:27: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 12:01:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 12:01:27: #1 tags after filtering in treatment: 29769054 INFO @ Sat, 08 Sep 2018 12:01:27: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 12:01:27: #1 finished! INFO @ Sat, 08 Sep 2018 12:01:27: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 12:01:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 12:01:28: #1 tags after filtering in treatment: 29769054 INFO @ Sat, 08 Sep 2018 12:01:28: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 12:01:28: #1 finished! INFO @ Sat, 08 Sep 2018 12:01:28: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 12:01:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 12:01:29: #2 number of paired peaks: 106 WARNING @ Sat, 08 Sep 2018 12:01:29: Fewer paired peaks (106) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 106 pairs to build model! INFO @ Sat, 08 Sep 2018 12:01:29: start model_add_line... INFO @ Sat, 08 Sep 2018 12:01:29: start X-correlation... INFO @ Sat, 08 Sep 2018 12:01:29: end of X-cor INFO @ Sat, 08 Sep 2018 12:01:29: #2 finished! INFO @ Sat, 08 Sep 2018 12:01:29: #2 predicted fragment length is 1 bps INFO @ Sat, 08 Sep 2018 12:01:29: #2 alternative fragment length(s) may be 1,10,29,60,74 bps INFO @ Sat, 08 Sep 2018 12:01:29: #2.2 Generate R script for model : SRX2965735.20_model.r WARNING @ Sat, 08 Sep 2018 12:01:29: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 12:01:29: #2 You may need to consider one of the other alternative d(s): 1,10,29,60,74 WARNING @ Sat, 08 Sep 2018 12:01:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 12:01:29: #3 Call peaks... INFO @ Sat, 08 Sep 2018 12:01:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 12:01:30: #2 number of paired peaks: 106 WARNING @ Sat, 08 Sep 2018 12:01:30: Fewer paired peaks (106) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 106 pairs to build model! INFO @ Sat, 08 Sep 2018 12:01:30: start model_add_line... INFO @ Sat, 08 Sep 2018 12:01:30: start X-correlation... INFO @ Sat, 08 Sep 2018 12:01:30: end of X-cor INFO @ Sat, 08 Sep 2018 12:01:30: #2 finished! INFO @ Sat, 08 Sep 2018 12:01:30: #2 predicted fragment length is 1 bps INFO @ Sat, 08 Sep 2018 12:01:30: #2 alternative fragment length(s) may be 1,10,29,60,74 bps INFO @ Sat, 08 Sep 2018 12:01:30: #2.2 Generate R script for model : SRX2965735.05_model.r WARNING @ Sat, 08 Sep 2018 12:01:30: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 12:01:30: #2 You may need to consider one of the other alternative d(s): 1,10,29,60,74 WARNING @ Sat, 08 Sep 2018 12:01:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 12:01:30: #3 Call peaks... INFO @ Sat, 08 Sep 2018 12:01:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 12:02:04: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 12:02:12: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 12:02:17: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 12:02:29: #4 Write output xls file... SRX2965735.10_peaks.xls INFO @ Sat, 08 Sep 2018 12:02:29: #4 Write peak in narrowPeak format file... SRX2965735.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 12:02:29: #4 Write summits bed file... SRX2965735.10_summits.bed INFO @ Sat, 08 Sep 2018 12:02:29: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 12:02:34: #4 Write output xls file... SRX2965735.05_peaks.xls INFO @ Sat, 08 Sep 2018 12:02:34: #4 Write peak in narrowPeak format file... SRX2965735.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 12:02:34: #4 Write summits bed file... SRX2965735.05_summits.bed INFO @ Sat, 08 Sep 2018 12:02:34: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 12:02:37: #4 Write output xls file... SRX2965735.20_peaks.xls INFO @ Sat, 08 Sep 2018 12:02:37: #4 Write peak in narrowPeak format file... SRX2965735.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 12:02:37: #4 Write summits bed file... SRX2965735.20_summits.bed INFO @ Sat, 08 Sep 2018 12:02:37: 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。