Job ID = 9157228 sra ファイルのダウンロード中... Completed: 630195K bytes transferred in 8 seconds (625663K 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 13822311 spots for /home/okishinya/chipatlas/results/ce10/SRX2350731/SRR5024040.sra Written 13822311 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: 00:04:30 13822311 reads; of these: 13822311 (100.00%) were unpaired; of these: 630779 (4.56%) aligned 0 times 10466183 (75.72%) aligned exactly 1 time 2725349 (19.72%) aligned >1 times 95.44% overall alignment rate Time searching: 00:04:30 Overall time: 00:04:30 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] 1656935 / 13191532 = 0.1256 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 11:15:10: # Command line: callpeak -t SRX2350731.bam -f BAM -g ce -n SRX2350731.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2350731.10 # format = BAM # ChIP-seq file = ['SRX2350731.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 11:15:10: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:15:10: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:15:10: # Command line: callpeak -t SRX2350731.bam -f BAM -g ce -n SRX2350731.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2350731.20 # format = BAM # ChIP-seq file = ['SRX2350731.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 11:15:10: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:15:10: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:15:10: # Command line: callpeak -t SRX2350731.bam -f BAM -g ce -n SRX2350731.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2350731.05 # format = BAM # ChIP-seq file = ['SRX2350731.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 11:15:10: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:15:10: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:15:18: 1000000 INFO @ Tue, 27 Jun 2017 11:15:18: 1000000 INFO @ Tue, 27 Jun 2017 11:15:18: 1000000 INFO @ Tue, 27 Jun 2017 11:15:25: 2000000 INFO @ Tue, 27 Jun 2017 11:15:26: 2000000 INFO @ Tue, 27 Jun 2017 11:15:28: 2000000 INFO @ Tue, 27 Jun 2017 11:15:32: 3000000 INFO @ Tue, 27 Jun 2017 11:15:35: 3000000 INFO @ Tue, 27 Jun 2017 11:15:37: 3000000 INFO @ Tue, 27 Jun 2017 11:15:40: 4000000 INFO @ Tue, 27 Jun 2017 11:15:43: 4000000 INFO @ Tue, 27 Jun 2017 11:15:45: 4000000 INFO @ Tue, 27 Jun 2017 11:15:49: 5000000 INFO @ Tue, 27 Jun 2017 11:15:51: 5000000 INFO @ Tue, 27 Jun 2017 11:15:53: 5000000 INFO @ Tue, 27 Jun 2017 11:15:57: 6000000 INFO @ Tue, 27 Jun 2017 11:15:58: 6000000 INFO @ Tue, 27 Jun 2017 11:16:02: 6000000 INFO @ Tue, 27 Jun 2017 11:16:05: 7000000 INFO @ Tue, 27 Jun 2017 11:16:06: 7000000 INFO @ Tue, 27 Jun 2017 11:16:10: 7000000 INFO @ Tue, 27 Jun 2017 11:16:14: 8000000 INFO @ Tue, 27 Jun 2017 11:16:14: 8000000 INFO @ Tue, 27 Jun 2017 11:16:18: 8000000 INFO @ Tue, 27 Jun 2017 11:16:22: 9000000 INFO @ Tue, 27 Jun 2017 11:16:22: 9000000 INFO @ Tue, 27 Jun 2017 11:16:26: 9000000 INFO @ Tue, 27 Jun 2017 11:16:30: 10000000 INFO @ Tue, 27 Jun 2017 11:16:30: 10000000 INFO @ Tue, 27 Jun 2017 11:16:35: 10000000 INFO @ Tue, 27 Jun 2017 11:16:38: 11000000 INFO @ Tue, 27 Jun 2017 11:16:38: 11000000 INFO @ Tue, 27 Jun 2017 11:16:42: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:16:42: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:16:42: #1 total tags in treatment: 11534597 INFO @ Tue, 27 Jun 2017 11:16:42: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:16:42: #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 11:16:42: #1 tags after filtering in treatment: 11534597 INFO @ Tue, 27 Jun 2017 11:16:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:16:42: #1 finished! INFO @ Tue, 27 Jun 2017 11:16:42: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:16:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:16:42: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:16:42: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:16:43: #1 total tags in treatment: 11534597 INFO @ Tue, 27 Jun 2017 11:16:43: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:16:43: #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 11:16:43: #1 tags after filtering in treatment: 11534597 INFO @ Tue, 27 Jun 2017 11:16:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:16:43: #1 finished! INFO @ Tue, 27 Jun 2017 11:16:43: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:16:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:16:43: 11000000 INFO @ Tue, 27 Jun 2017 11:16:43: #2 number of paired peaks: 330 WARNING @ Tue, 27 Jun 2017 11:16:43: Fewer paired peaks (330) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 330 pairs to build model! INFO @ Tue, 27 Jun 2017 11:16:43: start model_add_line... INFO @ Tue, 27 Jun 2017 11:16:43: start X-correlation... INFO @ Tue, 27 Jun 2017 11:16:43: end of X-cor INFO @ Tue, 27 Jun 2017 11:16:43: #2 finished! INFO @ Tue, 27 Jun 2017 11:16:43: #2 predicted fragment length is 39 bps INFO @ Tue, 27 Jun 2017 11:16:43: #2 alternative fragment length(s) may be 1,39 bps INFO @ Tue, 27 Jun 2017 11:16:43: #2.2 Generate R script for model : SRX2350731.05_model.r WARNING @ Tue, 27 Jun 2017 11:16:43: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:16:43: #2 You may need to consider one of the other alternative d(s): 1,39 WARNING @ Tue, 27 Jun 2017 11:16:43: #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 11:16:43: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:16:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:16:44: #2 number of paired peaks: 330 WARNING @ Tue, 27 Jun 2017 11:16:44: Fewer paired peaks (330) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 330 pairs to build model! INFO @ Tue, 27 Jun 2017 11:16:44: start model_add_line... INFO @ Tue, 27 Jun 2017 11:16:44: start X-correlation... INFO @ Tue, 27 Jun 2017 11:16:44: end of X-cor INFO @ Tue, 27 Jun 2017 11:16:44: #2 finished! INFO @ Tue, 27 Jun 2017 11:16:44: #2 predicted fragment length is 39 bps INFO @ Tue, 27 Jun 2017 11:16:44: #2 alternative fragment length(s) may be 1,39 bps INFO @ Tue, 27 Jun 2017 11:16:44: #2.2 Generate R script for model : SRX2350731.10_model.r WARNING @ Tue, 27 Jun 2017 11:16:44: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:16:44: #2 You may need to consider one of the other alternative d(s): 1,39 WARNING @ Tue, 27 Jun 2017 11:16:44: #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 11:16:44: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:16:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:16:47: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:16:47: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:16:47: #1 total tags in treatment: 11534597 INFO @ Tue, 27 Jun 2017 11:16:47: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:16:47: #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 11:16:47: #1 tags after filtering in treatment: 11534597 INFO @ Tue, 27 Jun 2017 11:16:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:16:47: #1 finished! INFO @ Tue, 27 Jun 2017 11:16:47: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:16:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:16:48: #2 number of paired peaks: 330 WARNING @ Tue, 27 Jun 2017 11:16:48: Fewer paired peaks (330) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 330 pairs to build model! INFO @ Tue, 27 Jun 2017 11:16:48: start model_add_line... INFO @ Tue, 27 Jun 2017 11:16:48: start X-correlation... INFO @ Tue, 27 Jun 2017 11:16:48: end of X-cor INFO @ Tue, 27 Jun 2017 11:16:48: #2 finished! INFO @ Tue, 27 Jun 2017 11:16:48: #2 predicted fragment length is 39 bps INFO @ Tue, 27 Jun 2017 11:16:48: #2 alternative fragment length(s) may be 1,39 bps INFO @ Tue, 27 Jun 2017 11:16:48: #2.2 Generate R script for model : SRX2350731.20_model.r WARNING @ Tue, 27 Jun 2017 11:16:48: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:16:48: #2 You may need to consider one of the other alternative d(s): 1,39 WARNING @ Tue, 27 Jun 2017 11:16:48: #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 11:16:48: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:16:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:17:07: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:17:07: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:17:12: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:17:20: #4 Write output xls file... SRX2350731.05_peaks.xls INFO @ Tue, 27 Jun 2017 11:17:20: #4 Write peak in narrowPeak format file... SRX2350731.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:17:20: #4 Write summits bed file... SRX2350731.05_summits.bed INFO @ Tue, 27 Jun 2017 11:17:20: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (741 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:17:20: #4 Write output xls file... SRX2350731.10_peaks.xls INFO @ Tue, 27 Jun 2017 11:17:20: #4 Write peak in narrowPeak format file... SRX2350731.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:17:20: #4 Write summits bed file... SRX2350731.10_summits.bed INFO @ Tue, 27 Jun 2017 11:17:20: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (412 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:17:24: #4 Write output xls file... SRX2350731.20_peaks.xls INFO @ Tue, 27 Jun 2017 11:17:24: #4 Write peak in narrowPeak format file... SRX2350731.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:17:24: #4 Write summits bed file... SRX2350731.20_summits.bed INFO @ Tue, 27 Jun 2017 11:17:24: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (142 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。