Job ID = 9029473 sra ファイルのダウンロード中... Completed: 221728K bytes transferred in 4 seconds (384217K 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 --:--:-- 0 100 7663 0 7663 0 0 1056 0 --:--:-- 0:00:07 --:--:-- 11645 100 31694 0 31694 0 0 3840 0 --:--:-- 0:00:08 --:--:-- 19162 100 52385 0 52385 0 0 5986 0 --:--:-- 0:00:08 --:--:-- 24342 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 7110867 spots for /home/okishinya/chipatlas/results/dm3/SRX1794226/SRR3575262.sra Written 7110867 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: 00:02:51 7110867 reads; of these: 7110867 (100.00%) were unpaired; of these: 242562 (3.41%) aligned 0 times 4926754 (69.28%) aligned exactly 1 time 1941551 (27.30%) aligned >1 times 96.59% overall alignment rate Time searching: 00:02:51 Overall time: 00:02:51 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] 272184 / 6868305 = 0.0396 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 13:56:09: # Command line: callpeak -t SRX1794226.bam -f BAM -g dm -n SRX1794226.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1794226.10 # format = BAM # ChIP-seq file = ['SRX1794226.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 13:56:09: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:56:09: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:56:09: # Command line: callpeak -t SRX1794226.bam -f BAM -g dm -n SRX1794226.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1794226.05 # format = BAM # ChIP-seq file = ['SRX1794226.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 13:56:09: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:56:09: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:56:09: # Command line: callpeak -t SRX1794226.bam -f BAM -g dm -n SRX1794226.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1794226.20 # format = BAM # ChIP-seq file = ['SRX1794226.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 13:56:09: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:56:09: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:56:15: 1000000 INFO @ Sat, 03 Jun 2017 13:56:16: 1000000 INFO @ Sat, 03 Jun 2017 13:56:16: 1000000 INFO @ Sat, 03 Jun 2017 13:56:21: 2000000 INFO @ Sat, 03 Jun 2017 13:56:22: 2000000 INFO @ Sat, 03 Jun 2017 13:56:22: 2000000 INFO @ Sat, 03 Jun 2017 13:56:27: 3000000 INFO @ Sat, 03 Jun 2017 13:56:29: 3000000 INFO @ Sat, 03 Jun 2017 13:56:29: 3000000 INFO @ Sat, 03 Jun 2017 13:56:34: 4000000 INFO @ Sat, 03 Jun 2017 13:56:36: 4000000 INFO @ Sat, 03 Jun 2017 13:56:36: 4000000 INFO @ Sat, 03 Jun 2017 13:56:40: 5000000 INFO @ Sat, 03 Jun 2017 13:56:43: 5000000 INFO @ Sat, 03 Jun 2017 13:56:43: 5000000 INFO @ Sat, 03 Jun 2017 13:56:46: 6000000 INFO @ Sat, 03 Jun 2017 13:56:49: 6000000 INFO @ Sat, 03 Jun 2017 13:56:49: 6000000 INFO @ Sat, 03 Jun 2017 13:56:50: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 13:56:50: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 13:56:50: #1 total tags in treatment: 6596121 INFO @ Sat, 03 Jun 2017 13:56:50: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:56:50: #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 13:56:51: #1 tags after filtering in treatment: 6595493 INFO @ Sat, 03 Jun 2017 13:56:51: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:56:51: #1 finished! INFO @ Sat, 03 Jun 2017 13:56:51: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:56:52: #2 number of paired peaks: 697 WARNING @ Sat, 03 Jun 2017 13:56:52: Fewer paired peaks (697) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 697 pairs to build model! INFO @ Sat, 03 Jun 2017 13:56:52: start model_add_line... INFO @ Sat, 03 Jun 2017 13:56:53: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 13:56:53: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 13:56:53: #1 total tags in treatment: 6596121 INFO @ Sat, 03 Jun 2017 13:56:53: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:56:53: #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 13:56:53: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 13:56:53: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 13:56:53: #1 total tags in treatment: 6596121 INFO @ Sat, 03 Jun 2017 13:56:53: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:56:53: #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 13:56:54: #1 tags after filtering in treatment: 6595493 INFO @ Sat, 03 Jun 2017 13:56:54: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:56:54: #1 finished! INFO @ Sat, 03 Jun 2017 13:56:54: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:56:55: #1 tags after filtering in treatment: 6595493 INFO @ Sat, 03 Jun 2017 13:56:55: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:56:55: #1 finished! INFO @ Sat, 03 Jun 2017 13:56:55: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:56:56: #2 number of paired peaks: 697 WARNING @ Sat, 03 Jun 2017 13:56:56: Fewer paired peaks (697) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 697 pairs to build model! INFO @ Sat, 03 Jun 2017 13:56:56: start model_add_line... INFO @ Sat, 03 Jun 2017 13:56:56: start X-correlation... INFO @ Sat, 03 Jun 2017 13:56:56: end of X-cor INFO @ Sat, 03 Jun 2017 13:56:56: #2 finished! INFO @ Sat, 03 Jun 2017 13:56:56: #2 predicted fragment length is 52 bps INFO @ Sat, 03 Jun 2017 13:56:56: #2 alternative fragment length(s) may be 52,578 bps INFO @ Sat, 03 Jun 2017 13:56:56: #2.2 Generate R script for model : SRX1794226.05_model.r INFO @ Sat, 03 Jun 2017 13:56:56: #2 number of paired peaks: 697 WARNING @ Sat, 03 Jun 2017 13:56:56: Fewer paired peaks (697) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 697 pairs to build model! INFO @ Sat, 03 Jun 2017 13:56:56: start model_add_line... WARNING @ Sat, 03 Jun 2017 13:56:56: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:56:56: #2 You may need to consider one of the other alternative d(s): 52,578 WARNING @ Sat, 03 Jun 2017 13:56:56: #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 13:56:56: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:56:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:56:59: start X-correlation... INFO @ Sat, 03 Jun 2017 13:56:59: end of X-cor INFO @ Sat, 03 Jun 2017 13:56:59: #2 finished! INFO @ Sat, 03 Jun 2017 13:56:59: #2 predicted fragment length is 52 bps INFO @ Sat, 03 Jun 2017 13:56:59: #2 alternative fragment length(s) may be 52,578 bps INFO @ Sat, 03 Jun 2017 13:56:59: #2.2 Generate R script for model : SRX1794226.20_model.r WARNING @ Sat, 03 Jun 2017 13:56:59: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:56:59: #2 You may need to consider one of the other alternative d(s): 52,578 WARNING @ Sat, 03 Jun 2017 13:56:59: #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 13:56:59: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:56:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:56:59: start X-correlation... INFO @ Sat, 03 Jun 2017 13:56:59: end of X-cor INFO @ Sat, 03 Jun 2017 13:56:59: #2 finished! INFO @ Sat, 03 Jun 2017 13:56:59: #2 predicted fragment length is 52 bps INFO @ Sat, 03 Jun 2017 13:56:59: #2 alternative fragment length(s) may be 52,578 bps INFO @ Sat, 03 Jun 2017 13:56:59: #2.2 Generate R script for model : SRX1794226.10_model.r WARNING @ Sat, 03 Jun 2017 13:56:59: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:56:59: #2 You may need to consider one of the other alternative d(s): 52,578 WARNING @ Sat, 03 Jun 2017 13:56:59: #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 13:57:00: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:57:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:57:37: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:57:37: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:57:38: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:58:05: #4 Write output xls file... SRX1794226.20_peaks.xls INFO @ Sat, 03 Jun 2017 13:58:05: #4 Write peak in narrowPeak format file... SRX1794226.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:58:05: #4 Write summits bed file... SRX1794226.20_summits.bed INFO @ Sat, 03 Jun 2017 13:58:05: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (218 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:58:05: #4 Write output xls file... SRX1794226.10_peaks.xls INFO @ Sat, 03 Jun 2017 13:58:05: #4 Write peak in narrowPeak format file... SRX1794226.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:58:05: #4 Write summits bed file... SRX1794226.10_summits.bed INFO @ Sat, 03 Jun 2017 13:58:05: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (989 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:58:05: #4 Write output xls file... SRX1794226.05_peaks.xls INFO @ Sat, 03 Jun 2017 13:58:06: #4 Write peak in narrowPeak format file... SRX1794226.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:58:06: #4 Write summits bed file... SRX1794226.05_summits.bed INFO @ Sat, 03 Jun 2017 13:58:06: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1957 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。