Job ID = 9041300 sra ファイルのダウンロード中... Completed: 218363K bytes transferred in 5 seconds (342541K 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 14324 0 14324 0 0 1865 0 --:--:-- 0:00:07 --:--:-- 12986 100 46208 0 46208 0 0 5429 0 --:--:-- 0:00:08 --:--:-- 23917 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 22122681 spots for /home/okishinya/chipatlas/results/dm3/SRX1167591/SRR2192666.sra Written 22122681 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: 00:03:21 22122681 reads; of these: 22122681 (100.00%) were unpaired; of these: 451371 (2.04%) aligned 0 times 17518901 (79.19%) aligned exactly 1 time 4152409 (18.77%) aligned >1 times 97.96% overall alignment rate Time searching: 00:03:21 Overall time: 00:03:21 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_sort_core] merging from 16 files... [bam_rmdupse_core] 8749765 / 21671310 = 0.4037 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 @ Mon, 05 Jun 2017 00:52:09: # Command line: callpeak -t SRX1167591.bam -f BAM -g dm -n SRX1167591.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1167591.05 # format = BAM # ChIP-seq file = ['SRX1167591.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 @ Mon, 05 Jun 2017 00:52:09: #1 read tag files... INFO @ Mon, 05 Jun 2017 00:52:09: #1 read treatment tags... INFO @ Mon, 05 Jun 2017 00:52:09: # Command line: callpeak -t SRX1167591.bam -f BAM -g dm -n SRX1167591.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1167591.10 # format = BAM # ChIP-seq file = ['SRX1167591.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 @ Mon, 05 Jun 2017 00:52:09: #1 read tag files... INFO @ Mon, 05 Jun 2017 00:52:09: #1 read treatment tags... INFO @ Mon, 05 Jun 2017 00:52:09: # Command line: callpeak -t SRX1167591.bam -f BAM -g dm -n SRX1167591.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1167591.20 # format = BAM # ChIP-seq file = ['SRX1167591.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 @ Mon, 05 Jun 2017 00:52:09: #1 read tag files... INFO @ Mon, 05 Jun 2017 00:52:09: #1 read treatment tags... INFO @ Mon, 05 Jun 2017 00:52:15: 1000000 INFO @ Mon, 05 Jun 2017 00:52:15: 1000000 INFO @ Mon, 05 Jun 2017 00:52:15: 1000000 INFO @ Mon, 05 Jun 2017 00:52:21: 2000000 INFO @ Mon, 05 Jun 2017 00:52:21: 2000000 INFO @ Mon, 05 Jun 2017 00:52:21: 2000000 INFO @ Mon, 05 Jun 2017 00:52:27: 3000000 INFO @ Mon, 05 Jun 2017 00:52:27: 3000000 INFO @ Mon, 05 Jun 2017 00:52:27: 3000000 INFO @ Mon, 05 Jun 2017 00:52:33: 4000000 INFO @ Mon, 05 Jun 2017 00:52:33: 4000000 INFO @ Mon, 05 Jun 2017 00:52:33: 4000000 INFO @ Mon, 05 Jun 2017 00:52:39: 5000000 INFO @ Mon, 05 Jun 2017 00:52:39: 5000000 INFO @ Mon, 05 Jun 2017 00:52:39: 5000000 INFO @ Mon, 05 Jun 2017 00:52:45: 6000000 INFO @ Mon, 05 Jun 2017 00:52:46: 6000000 INFO @ Mon, 05 Jun 2017 00:52:46: 6000000 INFO @ Mon, 05 Jun 2017 00:52:52: 7000000 INFO @ Mon, 05 Jun 2017 00:52:52: 7000000 INFO @ Mon, 05 Jun 2017 00:52:52: 7000000 INFO @ Mon, 05 Jun 2017 00:52:58: 8000000 INFO @ Mon, 05 Jun 2017 00:52:58: 8000000 INFO @ Mon, 05 Jun 2017 00:52:58: 8000000 INFO @ Mon, 05 Jun 2017 00:53:04: 9000000 INFO @ Mon, 05 Jun 2017 00:53:04: 9000000 INFO @ Mon, 05 Jun 2017 00:53:04: 9000000 INFO @ Mon, 05 Jun 2017 00:53:10: 10000000 INFO @ Mon, 05 Jun 2017 00:53:10: 10000000 INFO @ Mon, 05 Jun 2017 00:53:10: 10000000 INFO @ Mon, 05 Jun 2017 00:53:15: 11000000 INFO @ Mon, 05 Jun 2017 00:53:16: 11000000 INFO @ Mon, 05 Jun 2017 00:53:16: 11000000 INFO @ Mon, 05 Jun 2017 00:53:21: 12000000 INFO @ Mon, 05 Jun 2017 00:53:22: 12000000 INFO @ Mon, 05 Jun 2017 00:53:22: 12000000 INFO @ Mon, 05 Jun 2017 00:53:26: #1 tag size is determined as 50 bps INFO @ Mon, 05 Jun 2017 00:53:26: #1 tag size = 50 INFO @ Mon, 05 Jun 2017 00:53:26: #1 total tags in treatment: 12921545 INFO @ Mon, 05 Jun 2017 00:53:26: #1 user defined the maximum tags... INFO @ Mon, 05 Jun 2017 00:53:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 05 Jun 2017 00:53:27: #1 tag size is determined as 50 bps INFO @ Mon, 05 Jun 2017 00:53:27: #1 tag size = 50 INFO @ Mon, 05 Jun 2017 00:53:27: #1 total tags in treatment: 12921545 INFO @ Mon, 05 Jun 2017 00:53:27: #1 user defined the maximum tags... INFO @ Mon, 05 Jun 2017 00:53:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 05 Jun 2017 00:53:27: #1 tag size is determined as 50 bps INFO @ Mon, 05 Jun 2017 00:53:27: #1 tag size = 50 INFO @ Mon, 05 Jun 2017 00:53:27: #1 total tags in treatment: 12921545 INFO @ Mon, 05 Jun 2017 00:53:27: #1 user defined the maximum tags... INFO @ Mon, 05 Jun 2017 00:53:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 05 Jun 2017 00:53:28: #1 tags after filtering in treatment: 12919142 INFO @ Mon, 05 Jun 2017 00:53:28: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Jun 2017 00:53:28: #1 finished! INFO @ Mon, 05 Jun 2017 00:53:28: #2 Build Peak Model... INFO @ Mon, 05 Jun 2017 00:53:30: #1 tags after filtering in treatment: 12919142 INFO @ Mon, 05 Jun 2017 00:53:30: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Jun 2017 00:53:30: #1 finished! INFO @ Mon, 05 Jun 2017 00:53:30: #2 Build Peak Model... INFO @ Mon, 05 Jun 2017 00:53:30: #1 tags after filtering in treatment: 12919142 INFO @ Mon, 05 Jun 2017 00:53:30: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Jun 2017 00:53:30: #1 finished! INFO @ Mon, 05 Jun 2017 00:53:30: #2 Build Peak Model... INFO @ Mon, 05 Jun 2017 00:53:30: #2 number of paired peaks: 114 WARNING @ Mon, 05 Jun 2017 00:53:30: Fewer paired peaks (114) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 114 pairs to build model! INFO @ Mon, 05 Jun 2017 00:53:30: start model_add_line... INFO @ Mon, 05 Jun 2017 00:53:31: start X-correlation... INFO @ Mon, 05 Jun 2017 00:53:31: end of X-cor INFO @ Mon, 05 Jun 2017 00:53:31: #2 finished! INFO @ Mon, 05 Jun 2017 00:53:31: #2 predicted fragment length is 50 bps INFO @ Mon, 05 Jun 2017 00:53:31: #2 alternative fragment length(s) may be 50 bps INFO @ Mon, 05 Jun 2017 00:53:31: #2.2 Generate R script for model : SRX1167591.05_model.r WARNING @ Mon, 05 Jun 2017 00:53:31: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 05 Jun 2017 00:53:31: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Mon, 05 Jun 2017 00:53:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 05 Jun 2017 00:53:31: #3 Call peaks... INFO @ Mon, 05 Jun 2017 00:53:31: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 05 Jun 2017 00:53:32: #2 number of paired peaks: 114 WARNING @ Mon, 05 Jun 2017 00:53:32: Fewer paired peaks (114) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 114 pairs to build model! INFO @ Mon, 05 Jun 2017 00:53:32: start model_add_line... INFO @ Mon, 05 Jun 2017 00:53:32: #2 number of paired peaks: 114 WARNING @ Mon, 05 Jun 2017 00:53:32: Fewer paired peaks (114) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 114 pairs to build model! INFO @ Mon, 05 Jun 2017 00:53:32: start model_add_line... INFO @ Mon, 05 Jun 2017 00:53:33: start X-correlation... INFO @ Mon, 05 Jun 2017 00:53:33: end of X-cor INFO @ Mon, 05 Jun 2017 00:53:33: #2 finished! INFO @ Mon, 05 Jun 2017 00:53:33: #2 predicted fragment length is 50 bps INFO @ Mon, 05 Jun 2017 00:53:33: #2 alternative fragment length(s) may be 50 bps INFO @ Mon, 05 Jun 2017 00:53:33: #2.2 Generate R script for model : SRX1167591.20_model.r WARNING @ Mon, 05 Jun 2017 00:53:33: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 05 Jun 2017 00:53:33: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Mon, 05 Jun 2017 00:53:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 05 Jun 2017 00:53:33: #3 Call peaks... INFO @ Mon, 05 Jun 2017 00:53:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 05 Jun 2017 00:53:34: start X-correlation... INFO @ Mon, 05 Jun 2017 00:53:34: end of X-cor INFO @ Mon, 05 Jun 2017 00:53:34: #2 finished! INFO @ Mon, 05 Jun 2017 00:53:34: #2 predicted fragment length is 50 bps INFO @ Mon, 05 Jun 2017 00:53:34: #2 alternative fragment length(s) may be 50 bps INFO @ Mon, 05 Jun 2017 00:53:34: #2.2 Generate R script for model : SRX1167591.10_model.r WARNING @ Mon, 05 Jun 2017 00:53:34: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 05 Jun 2017 00:53:34: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Mon, 05 Jun 2017 00:53:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 05 Jun 2017 00:53:34: #3 Call peaks... INFO @ Mon, 05 Jun 2017 00:53:34: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 05 Jun 2017 00:54:38: #3 Call peaks for each chromosome... INFO @ Mon, 05 Jun 2017 00:54:39: #3 Call peaks for each chromosome... INFO @ Mon, 05 Jun 2017 00:54:46: #3 Call peaks for each chromosome... INFO @ Mon, 05 Jun 2017 00:55:26: #4 Write output xls file... SRX1167591.20_peaks.xls INFO @ Mon, 05 Jun 2017 00:55:26: #4 Write peak in narrowPeak format file... SRX1167591.20_peaks.narrowPeak INFO @ Mon, 05 Jun 2017 00:55:26: #4 Write summits bed file... SRX1167591.20_summits.bed INFO @ Mon, 05 Jun 2017 00:55:26: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (675 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 05 Jun 2017 00:55:27: #4 Write output xls file... SRX1167591.05_peaks.xls INFO @ Mon, 05 Jun 2017 00:55:27: #4 Write peak in narrowPeak format file... SRX1167591.05_peaks.narrowPeak INFO @ Mon, 05 Jun 2017 00:55:27: #4 Write summits bed file... SRX1167591.05_summits.bed INFO @ Mon, 05 Jun 2017 00:55:27: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1462 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 05 Jun 2017 00:55:35: #4 Write output xls file... SRX1167591.10_peaks.xls INFO @ Mon, 05 Jun 2017 00:55:35: #4 Write peak in narrowPeak format file... SRX1167591.10_peaks.narrowPeak INFO @ Mon, 05 Jun 2017 00:55:35: #4 Write summits bed file... SRX1167591.10_summits.bed INFO @ Mon, 05 Jun 2017 00:55:35: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (969 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。