Job ID = 9029500 sra ファイルのダウンロード中... Completed: 244356K bytes transferred in 4 seconds (418845K bits/sec), in 1 file, 2 directories. % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- 0:00:06 --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:06 --:--:-- 0 100 30318 0 30318 0 0 3739 0 --:--:-- 0:00:08 --:--:-- 20078 100 55220 0 55220 0 0 6417 0 --:--:-- 0:00:08 --:--:-- 27513 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 9544827 spots for /home/okishinya/chipatlas/results/dm3/SRX1794253/SRR3575297.sra Written 9544827 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: 00:03:52 9544827 reads; of these: 9544827 (100.00%) were unpaired; of these: 314402 (3.29%) aligned 0 times 6669194 (69.87%) aligned exactly 1 time 2561231 (26.83%) aligned >1 times 96.71% overall alignment rate Time searching: 00:03:52 Overall time: 00:03:52 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 411424 / 9230425 = 0.0446 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, 03 Jun 2017 14:04:04: # Command line: callpeak -t SRX1794253.bam -f BAM -g dm -n SRX1794253.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1794253.05 # format = BAM # ChIP-seq file = ['SRX1794253.bam'] # control file = None # effective genome size = 1.20e+08 # 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 INFO @ Sat, 03 Jun 2017 14:04:04: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:04:04: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:04:04: # Command line: callpeak -t SRX1794253.bam -f BAM -g dm -n SRX1794253.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1794253.20 # format = BAM # ChIP-seq file = ['SRX1794253.bam'] # control file = None # effective genome size = 1.20e+08 # 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 INFO @ Sat, 03 Jun 2017 14:04:04: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:04:04: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:04:04: # Command line: callpeak -t SRX1794253.bam -f BAM -g dm -n SRX1794253.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1794253.10 # format = BAM # ChIP-seq file = ['SRX1794253.bam'] # control file = None # effective genome size = 1.20e+08 # 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 INFO @ Sat, 03 Jun 2017 14:04:04: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:04:04: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:04:10: 1000000 INFO @ Sat, 03 Jun 2017 14:04:10: 1000000 INFO @ Sat, 03 Jun 2017 14:04:10: 1000000 INFO @ Sat, 03 Jun 2017 14:04:16: 2000000 INFO @ Sat, 03 Jun 2017 14:04:17: 2000000 INFO @ Sat, 03 Jun 2017 14:04:17: 2000000 INFO @ Sat, 03 Jun 2017 14:04:22: 3000000 INFO @ Sat, 03 Jun 2017 14:04:23: 3000000 INFO @ Sat, 03 Jun 2017 14:04:23: 3000000 INFO @ Sat, 03 Jun 2017 14:04:28: 4000000 INFO @ Sat, 03 Jun 2017 14:04:29: 4000000 INFO @ Sat, 03 Jun 2017 14:04:29: 4000000 INFO @ Sat, 03 Jun 2017 14:04:34: 5000000 INFO @ Sat, 03 Jun 2017 14:04:35: 5000000 INFO @ Sat, 03 Jun 2017 14:04:35: 5000000 INFO @ Sat, 03 Jun 2017 14:04:40: 6000000 INFO @ Sat, 03 Jun 2017 14:04:42: 6000000 INFO @ Sat, 03 Jun 2017 14:04:42: 6000000 INFO @ Sat, 03 Jun 2017 14:04:46: 7000000 INFO @ Sat, 03 Jun 2017 14:04:48: 7000000 INFO @ Sat, 03 Jun 2017 14:04:48: 7000000 INFO @ Sat, 03 Jun 2017 14:04:52: 8000000 INFO @ Sat, 03 Jun 2017 14:04:54: 8000000 INFO @ Sat, 03 Jun 2017 14:04:54: 8000000 INFO @ Sat, 03 Jun 2017 14:04:57: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 14:04:57: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 14:04:57: #1 total tags in treatment: 8819001 INFO @ Sat, 03 Jun 2017 14:04:57: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:04:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 14:04:59: #1 tags after filtering in treatment: 8817964 INFO @ Sat, 03 Jun 2017 14:04:59: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:04:59: #1 finished! INFO @ Sat, 03 Jun 2017 14:04:59: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:05:00: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 14:05:00: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 14:05:00: #1 total tags in treatment: 8819001 INFO @ Sat, 03 Jun 2017 14:05:00: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:05:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 14:05:00: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 14:05:00: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 14:05:00: #1 total tags in treatment: 8819001 INFO @ Sat, 03 Jun 2017 14:05:00: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:05:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 14:05:01: #2 number of paired peaks: 614 WARNING @ Sat, 03 Jun 2017 14:05:01: Fewer paired peaks (614) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 614 pairs to build model! INFO @ Sat, 03 Jun 2017 14:05:01: start model_add_line... INFO @ Sat, 03 Jun 2017 14:05:01: #1 tags after filtering in treatment: 8817964 INFO @ Sat, 03 Jun 2017 14:05:01: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:05:01: #1 finished! INFO @ Sat, 03 Jun 2017 14:05:01: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:05:01: #1 tags after filtering in treatment: 8817964 INFO @ Sat, 03 Jun 2017 14:05:01: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:05:01: #1 finished! INFO @ Sat, 03 Jun 2017 14:05:01: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:05:03: #2 number of paired peaks: 614 WARNING @ Sat, 03 Jun 2017 14:05:03: Fewer paired peaks (614) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 614 pairs to build model! INFO @ Sat, 03 Jun 2017 14:05:03: start model_add_line... INFO @ Sat, 03 Jun 2017 14:05:03: #2 number of paired peaks: 614 WARNING @ Sat, 03 Jun 2017 14:05:03: Fewer paired peaks (614) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 614 pairs to build model! INFO @ Sat, 03 Jun 2017 14:05:03: start model_add_line... INFO @ Sat, 03 Jun 2017 14:05:05: start X-correlation... INFO @ Sat, 03 Jun 2017 14:05:05: end of X-cor INFO @ Sat, 03 Jun 2017 14:05:05: #2 finished! INFO @ Sat, 03 Jun 2017 14:05:05: #2 predicted fragment length is 56 bps INFO @ Sat, 03 Jun 2017 14:05:05: #2 alternative fragment length(s) may be 3,56,582,597 bps INFO @ Sat, 03 Jun 2017 14:05:05: #2.2 Generate R script for model : SRX1794253.05_model.r WARNING @ Sat, 03 Jun 2017 14:05:05: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 14:05:05: #2 You may need to consider one of the other alternative d(s): 3,56,582,597 WARNING @ Sat, 03 Jun 2017 14:05:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 14:05:05: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:05:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:05:07: start X-correlation... INFO @ Sat, 03 Jun 2017 14:05:07: end of X-cor INFO @ Sat, 03 Jun 2017 14:05:07: #2 finished! INFO @ Sat, 03 Jun 2017 14:05:07: #2 predicted fragment length is 56 bps INFO @ Sat, 03 Jun 2017 14:05:07: #2 alternative fragment length(s) may be 3,56,582,597 bps INFO @ Sat, 03 Jun 2017 14:05:07: #2.2 Generate R script for model : SRX1794253.20_model.r WARNING @ Sat, 03 Jun 2017 14:05:07: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 14:05:07: #2 You may need to consider one of the other alternative d(s): 3,56,582,597 WARNING @ Sat, 03 Jun 2017 14:05:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 14:05:07: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:05:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:05:07: start X-correlation... INFO @ Sat, 03 Jun 2017 14:05:07: end of X-cor INFO @ Sat, 03 Jun 2017 14:05:07: #2 finished! INFO @ Sat, 03 Jun 2017 14:05:07: #2 predicted fragment length is 56 bps INFO @ Sat, 03 Jun 2017 14:05:07: #2 alternative fragment length(s) may be 3,56,582,597 bps INFO @ Sat, 03 Jun 2017 14:05:07: #2.2 Generate R script for model : SRX1794253.10_model.r WARNING @ Sat, 03 Jun 2017 14:05:07: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 14:05:07: #2 You may need to consider one of the other alternative d(s): 3,56,582,597 WARNING @ Sat, 03 Jun 2017 14:05:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 14:05:07: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:05:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:05:52: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:05:59: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:06:00: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:06:27: #4 Write output xls file... SRX1794253.05_peaks.xls INFO @ Sat, 03 Jun 2017 14:06:27: #4 Write peak in narrowPeak format file... SRX1794253.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:06:27: #4 Write summits bed file... SRX1794253.05_summits.bed INFO @ Sat, 03 Jun 2017 14:06:27: Done! pass1 - making usageList (15 chroms): 10 millis pass2 - checking and writing primary data (1846 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 14:06:36: #4 Write output xls file... SRX1794253.20_peaks.xls INFO @ Sat, 03 Jun 2017 14:06:36: #4 Write peak in narrowPeak format file... SRX1794253.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:06:36: #4 Write summits bed file... SRX1794253.20_summits.bed INFO @ Sat, 03 Jun 2017 14:06:36: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (214 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 14:06:39: #4 Write output xls file... SRX1794253.10_peaks.xls INFO @ Sat, 03 Jun 2017 14:06:39: #4 Write peak in narrowPeak format file... SRX1794253.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:06:39: #4 Write summits bed file... SRX1794253.10_summits.bed INFO @ Sat, 03 Jun 2017 14:06:39: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (837 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。