Job ID = 9157404 sra ファイルのダウンロード中... Completed: 1177006K bytes transferred in 13 seconds (724932K 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: PAIRED fastq に変換中... Written 9344677 spots for /home/okishinya/chipatlas/results/ce10/SRX2011718/SRR4017960.sra Written 9344677 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: 00:17:09 9344677 reads; of these: 9344677 (100.00%) were paired; of these: 806091 (8.63%) aligned concordantly 0 times 7394950 (79.14%) aligned concordantly exactly 1 time 1143636 (12.24%) aligned concordantly >1 times ---- 806091 pairs aligned concordantly 0 times; of these: 580047 (71.96%) aligned discordantly 1 time ---- 226044 pairs aligned 0 times concordantly or discordantly; of these: 452088 mates make up the pairs; of these: 165901 (36.70%) aligned 0 times 130057 (28.77%) aligned exactly 1 time 156130 (34.54%) aligned >1 times 99.11% overall alignment rate Time searching: 00:17:09 Overall time: 00:17:09 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_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 396013 / 9009630 = 0.0440 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 12:12:20: # Command line: callpeak -t SRX2011718.bam -f BAM -g ce -n SRX2011718.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2011718.05 # format = BAM # ChIP-seq file = ['SRX2011718.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 12:12:20: #1 read tag files... INFO @ Tue, 27 Jun 2017 12:12:20: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 12:12:20: # Command line: callpeak -t SRX2011718.bam -f BAM -g ce -n SRX2011718.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2011718.20 # format = BAM # ChIP-seq file = ['SRX2011718.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 12:12:20: #1 read tag files... INFO @ Tue, 27 Jun 2017 12:12:20: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 12:12:20: # Command line: callpeak -t SRX2011718.bam -f BAM -g ce -n SRX2011718.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2011718.10 # format = BAM # ChIP-seq file = ['SRX2011718.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 12:12:20: #1 read tag files... INFO @ Tue, 27 Jun 2017 12:12:20: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 12:12:28: 1000000 INFO @ Tue, 27 Jun 2017 12:12:28: 1000000 INFO @ Tue, 27 Jun 2017 12:12:28: 1000000 INFO @ Tue, 27 Jun 2017 12:12:35: 2000000 INFO @ Tue, 27 Jun 2017 12:12:36: 2000000 INFO @ Tue, 27 Jun 2017 12:12:36: 2000000 INFO @ Tue, 27 Jun 2017 12:12:43: 3000000 INFO @ Tue, 27 Jun 2017 12:12:43: 3000000 INFO @ Tue, 27 Jun 2017 12:12:44: 3000000 INFO @ Tue, 27 Jun 2017 12:12:51: 4000000 INFO @ Tue, 27 Jun 2017 12:12:51: 4000000 INFO @ Tue, 27 Jun 2017 12:12:52: 4000000 INFO @ Tue, 27 Jun 2017 12:12:58: 5000000 INFO @ Tue, 27 Jun 2017 12:12:58: 5000000 INFO @ Tue, 27 Jun 2017 12:13:00: 5000000 INFO @ Tue, 27 Jun 2017 12:13:05: 6000000 INFO @ Tue, 27 Jun 2017 12:13:06: 6000000 INFO @ Tue, 27 Jun 2017 12:13:08: 6000000 INFO @ Tue, 27 Jun 2017 12:13:13: 7000000 INFO @ Tue, 27 Jun 2017 12:13:14: 7000000 INFO @ Tue, 27 Jun 2017 12:13:16: 7000000 INFO @ Tue, 27 Jun 2017 12:13:20: 8000000 INFO @ Tue, 27 Jun 2017 12:13:21: 8000000 INFO @ Tue, 27 Jun 2017 12:13:24: 8000000 INFO @ Tue, 27 Jun 2017 12:13:27: 9000000 INFO @ Tue, 27 Jun 2017 12:13:29: 9000000 INFO @ Tue, 27 Jun 2017 12:13:32: 9000000 INFO @ Tue, 27 Jun 2017 12:13:35: 10000000 INFO @ Tue, 27 Jun 2017 12:13:37: 10000000 INFO @ Tue, 27 Jun 2017 12:13:40: 10000000 INFO @ Tue, 27 Jun 2017 12:13:42: 11000000 INFO @ Tue, 27 Jun 2017 12:13:44: 11000000 INFO @ Tue, 27 Jun 2017 12:13:47: 11000000 INFO @ Tue, 27 Jun 2017 12:13:50: 12000000 INFO @ Tue, 27 Jun 2017 12:13:52: 12000000 INFO @ Tue, 27 Jun 2017 12:13:55: 12000000 INFO @ Tue, 27 Jun 2017 12:13:57: 13000000 INFO @ Tue, 27 Jun 2017 12:13:59: 13000000 INFO @ Tue, 27 Jun 2017 12:14:03: 13000000 INFO @ Tue, 27 Jun 2017 12:14:04: 14000000 INFO @ Tue, 27 Jun 2017 12:14:07: 14000000 INFO @ Tue, 27 Jun 2017 12:14:11: 14000000 INFO @ Tue, 27 Jun 2017 12:14:12: 15000000 INFO @ Tue, 27 Jun 2017 12:14:15: 15000000 INFO @ Tue, 27 Jun 2017 12:14:19: 16000000 INFO @ Tue, 27 Jun 2017 12:14:19: 15000000 INFO @ Tue, 27 Jun 2017 12:14:22: 16000000 INFO @ Tue, 27 Jun 2017 12:14:26: 17000000 INFO @ Tue, 27 Jun 2017 12:14:27: 16000000 INFO @ Tue, 27 Jun 2017 12:14:30: 17000000 INFO @ Tue, 27 Jun 2017 12:14:32: #1 tag size is determined as 101 bps INFO @ Tue, 27 Jun 2017 12:14:32: #1 tag size = 101 INFO @ Tue, 27 Jun 2017 12:14:32: #1 total tags in treatment: 8152818 INFO @ Tue, 27 Jun 2017 12:14:32: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 12:14:32: #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 12:14:32: #1 tags after filtering in treatment: 7648757 INFO @ Tue, 27 Jun 2017 12:14:32: #1 Redundant rate of treatment: 0.06 INFO @ Tue, 27 Jun 2017 12:14:32: #1 finished! INFO @ Tue, 27 Jun 2017 12:14:32: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 12:14:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 12:14:33: #2 number of paired peaks: 347 WARNING @ Tue, 27 Jun 2017 12:14:33: Fewer paired peaks (347) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 347 pairs to build model! INFO @ Tue, 27 Jun 2017 12:14:33: start model_add_line... INFO @ Tue, 27 Jun 2017 12:14:33: start X-correlation... INFO @ Tue, 27 Jun 2017 12:14:33: end of X-cor INFO @ Tue, 27 Jun 2017 12:14:33: #2 finished! INFO @ Tue, 27 Jun 2017 12:14:33: #2 predicted fragment length is 173 bps INFO @ Tue, 27 Jun 2017 12:14:33: #2 alternative fragment length(s) may be 173 bps INFO @ Tue, 27 Jun 2017 12:14:33: #2.2 Generate R script for model : SRX2011718.05_model.r WARNING @ Tue, 27 Jun 2017 12:14:33: #2 Since the d (173) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 12:14:33: #2 You may need to consider one of the other alternative d(s): 173 WARNING @ Tue, 27 Jun 2017 12:14:33: #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 12:14:33: #3 Call peaks... INFO @ Tue, 27 Jun 2017 12:14:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 12:14:35: 17000000 INFO @ Tue, 27 Jun 2017 12:14:35: #1 tag size is determined as 101 bps INFO @ Tue, 27 Jun 2017 12:14:35: #1 tag size = 101 INFO @ Tue, 27 Jun 2017 12:14:35: #1 total tags in treatment: 8152818 INFO @ Tue, 27 Jun 2017 12:14:35: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 12:14:35: #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 12:14:36: #1 tags after filtering in treatment: 7648757 INFO @ Tue, 27 Jun 2017 12:14:36: #1 Redundant rate of treatment: 0.06 INFO @ Tue, 27 Jun 2017 12:14:36: #1 finished! INFO @ Tue, 27 Jun 2017 12:14:36: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 12:14:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 12:14:36: #2 number of paired peaks: 347 WARNING @ Tue, 27 Jun 2017 12:14:36: Fewer paired peaks (347) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 347 pairs to build model! INFO @ Tue, 27 Jun 2017 12:14:36: start model_add_line... INFO @ Tue, 27 Jun 2017 12:14:36: start X-correlation... INFO @ Tue, 27 Jun 2017 12:14:36: end of X-cor INFO @ Tue, 27 Jun 2017 12:14:36: #2 finished! INFO @ Tue, 27 Jun 2017 12:14:36: #2 predicted fragment length is 173 bps INFO @ Tue, 27 Jun 2017 12:14:36: #2 alternative fragment length(s) may be 173 bps INFO @ Tue, 27 Jun 2017 12:14:36: #2.2 Generate R script for model : SRX2011718.10_model.r WARNING @ Tue, 27 Jun 2017 12:14:36: #2 Since the d (173) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 12:14:36: #2 You may need to consider one of the other alternative d(s): 173 WARNING @ Tue, 27 Jun 2017 12:14:36: #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 12:14:36: #3 Call peaks... INFO @ Tue, 27 Jun 2017 12:14:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 12:14:40: #1 tag size is determined as 101 bps INFO @ Tue, 27 Jun 2017 12:14:40: #1 tag size = 101 INFO @ Tue, 27 Jun 2017 12:14:40: #1 total tags in treatment: 8152818 INFO @ Tue, 27 Jun 2017 12:14:40: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 12:14:40: #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 12:14:40: #1 tags after filtering in treatment: 7648757 INFO @ Tue, 27 Jun 2017 12:14:40: #1 Redundant rate of treatment: 0.06 INFO @ Tue, 27 Jun 2017 12:14:40: #1 finished! INFO @ Tue, 27 Jun 2017 12:14:40: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 12:14:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 12:14:41: #2 number of paired peaks: 347 WARNING @ Tue, 27 Jun 2017 12:14:41: Fewer paired peaks (347) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 347 pairs to build model! INFO @ Tue, 27 Jun 2017 12:14:41: start model_add_line... INFO @ Tue, 27 Jun 2017 12:14:41: start X-correlation... INFO @ Tue, 27 Jun 2017 12:14:41: end of X-cor INFO @ Tue, 27 Jun 2017 12:14:41: #2 finished! INFO @ Tue, 27 Jun 2017 12:14:41: #2 predicted fragment length is 173 bps INFO @ Tue, 27 Jun 2017 12:14:41: #2 alternative fragment length(s) may be 173 bps INFO @ Tue, 27 Jun 2017 12:14:41: #2.2 Generate R script for model : SRX2011718.20_model.r WARNING @ Tue, 27 Jun 2017 12:14:41: #2 Since the d (173) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 12:14:41: #2 You may need to consider one of the other alternative d(s): 173 WARNING @ Tue, 27 Jun 2017 12:14:41: #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 12:14:41: #3 Call peaks... INFO @ Tue, 27 Jun 2017 12:14:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 12:14:51: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 12:14:56: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 12:14:58: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 12:14:59: #4 Write output xls file... SRX2011718.05_peaks.xls INFO @ Tue, 27 Jun 2017 12:14:59: #4 Write peak in narrowPeak format file... SRX2011718.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 12:14:59: #4 Write summits bed file... SRX2011718.05_summits.bed INFO @ Tue, 27 Jun 2017 12:14:59: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (349 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 12:15:06: #4 Write output xls file... SRX2011718.10_peaks.xls INFO @ Tue, 27 Jun 2017 12:15:06: #4 Write peak in narrowPeak format file... SRX2011718.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 12:15:06: #4 Write summits bed file... SRX2011718.10_summits.bed INFO @ Tue, 27 Jun 2017 12:15:06: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (262 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 12:15:08: #4 Write output xls file... SRX2011718.20_peaks.xls INFO @ Tue, 27 Jun 2017 12:15:08: #4 Write peak in narrowPeak format file... SRX2011718.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 12:15:08: #4 Write summits bed file... SRX2011718.20_summits.bed INFO @ Tue, 27 Jun 2017 12:15:08: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (177 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。