Job ID = 9029562 sra ファイルのダウンロード中... Completed: 1099675K bytes transferred in 18 seconds (494732K 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 22318 0 22318 0 0 2863 0 --:--:-- 0:00:07 --:--:-- 16219 100 54318 0 54318 0 0 6066 0 --:--:-- 0:00:08 --:--:-- 21410 100 80303 0 80303 0 0 8647 0 --:--:-- 0:00:09 --:--:-- 27989 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 16974732 spots for /home/okishinya/chipatlas/results/dm3/SRX1840075/SRR3661301.sra Written 16974732 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: 00:13:10 16974732 reads; of these: 16974732 (100.00%) were unpaired; of these: 703506 (4.14%) aligned 0 times 11517560 (67.85%) aligned exactly 1 time 4753666 (28.00%) aligned >1 times 95.86% overall alignment rate Time searching: 00:13:10 Overall time: 00:13:10 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 8 files... [bam_rmdupse_core] 4166408 / 16271226 = 0.2561 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 14:29:42: # Command line: callpeak -t SRX1840075.bam -f BAM -g dm -n SRX1840075.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1840075.05 # format = BAM # ChIP-seq file = ['SRX1840075.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 14:29:42: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:29:42: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:29:42: # Command line: callpeak -t SRX1840075.bam -f BAM -g dm -n SRX1840075.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1840075.20 # format = BAM # ChIP-seq file = ['SRX1840075.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 14:29:42: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:29:42: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:29:42: # Command line: callpeak -t SRX1840075.bam -f BAM -g dm -n SRX1840075.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1840075.10 # format = BAM # ChIP-seq file = ['SRX1840075.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 14:29:42: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:29:42: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:29:50: 1000000 INFO @ Sat, 03 Jun 2017 14:29:51: 1000000 INFO @ Sat, 03 Jun 2017 14:29:51: 1000000 INFO @ Sat, 03 Jun 2017 14:29:59: 2000000 INFO @ Sat, 03 Jun 2017 14:30:00: 2000000 INFO @ Sat, 03 Jun 2017 14:30:00: 2000000 INFO @ Sat, 03 Jun 2017 14:30:07: 3000000 INFO @ Sat, 03 Jun 2017 14:30:08: 3000000 INFO @ Sat, 03 Jun 2017 14:30:08: 3000000 INFO @ Sat, 03 Jun 2017 14:30:16: 4000000 INFO @ Sat, 03 Jun 2017 14:30:19: 4000000 INFO @ Sat, 03 Jun 2017 14:30:19: 4000000 INFO @ Sat, 03 Jun 2017 14:30:26: 5000000 INFO @ Sat, 03 Jun 2017 14:30:31: 5000000 INFO @ Sat, 03 Jun 2017 14:30:31: 5000000 INFO @ Sat, 03 Jun 2017 14:30:36: 6000000 INFO @ Sat, 03 Jun 2017 14:30:43: 6000000 INFO @ Sat, 03 Jun 2017 14:30:43: 6000000 INFO @ Sat, 03 Jun 2017 14:30:46: 7000000 INFO @ Sat, 03 Jun 2017 14:30:55: 7000000 INFO @ Sat, 03 Jun 2017 14:30:55: 7000000 INFO @ Sat, 03 Jun 2017 14:30:55: 8000000 INFO @ Sat, 03 Jun 2017 14:31:04: 9000000 INFO @ Sat, 03 Jun 2017 14:31:05: 8000000 INFO @ Sat, 03 Jun 2017 14:31:05: 8000000 INFO @ Sat, 03 Jun 2017 14:31:12: 10000000 INFO @ Sat, 03 Jun 2017 14:31:15: 9000000 INFO @ Sat, 03 Jun 2017 14:31:15: 9000000 INFO @ Sat, 03 Jun 2017 14:31:21: 11000000 INFO @ Sat, 03 Jun 2017 14:31:24: 10000000 INFO @ Sat, 03 Jun 2017 14:31:24: 10000000 INFO @ Sat, 03 Jun 2017 14:31:30: 12000000 INFO @ Sat, 03 Jun 2017 14:31:31: #1 tag size is determined as 101 bps INFO @ Sat, 03 Jun 2017 14:31:31: #1 tag size = 101 INFO @ Sat, 03 Jun 2017 14:31:31: #1 total tags in treatment: 12104818 INFO @ Sat, 03 Jun 2017 14:31:31: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:31:31: #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 14:31:33: 11000000 INFO @ Sat, 03 Jun 2017 14:31:33: 11000000 INFO @ Sat, 03 Jun 2017 14:31:34: #1 tags after filtering in treatment: 12094810 INFO @ Sat, 03 Jun 2017 14:31:34: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:31:34: #1 finished! INFO @ Sat, 03 Jun 2017 14:31:34: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:31:36: #2 number of paired peaks: 133 WARNING @ Sat, 03 Jun 2017 14:31:36: Fewer paired peaks (133) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 133 pairs to build model! INFO @ Sat, 03 Jun 2017 14:31:36: start model_add_line... INFO @ Sat, 03 Jun 2017 14:31:37: start X-correlation... INFO @ Sat, 03 Jun 2017 14:31:37: end of X-cor INFO @ Sat, 03 Jun 2017 14:31:37: #2 finished! INFO @ Sat, 03 Jun 2017 14:31:37: #2 predicted fragment length is 102 bps INFO @ Sat, 03 Jun 2017 14:31:37: #2 alternative fragment length(s) may be 102 bps INFO @ Sat, 03 Jun 2017 14:31:37: #2.2 Generate R script for model : SRX1840075.10_model.r WARNING @ Sat, 03 Jun 2017 14:31:37: #2 Since the d (102) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 14:31:37: #2 You may need to consider one of the other alternative d(s): 102 WARNING @ Sat, 03 Jun 2017 14:31:37: #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 14:31:37: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:31:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:31:43: 12000000 INFO @ Sat, 03 Jun 2017 14:31:43: 12000000 INFO @ Sat, 03 Jun 2017 14:31:44: #1 tag size is determined as 101 bps INFO @ Sat, 03 Jun 2017 14:31:44: #1 tag size = 101 INFO @ Sat, 03 Jun 2017 14:31:44: #1 total tags in treatment: 12104818 INFO @ Sat, 03 Jun 2017 14:31:44: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:31:44: #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 14:31:44: #1 tag size is determined as 101 bps INFO @ Sat, 03 Jun 2017 14:31:44: #1 tag size = 101 INFO @ Sat, 03 Jun 2017 14:31:44: #1 total tags in treatment: 12104818 INFO @ Sat, 03 Jun 2017 14:31:44: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:31:44: #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 14:31:47: #1 tags after filtering in treatment: 12094810 INFO @ Sat, 03 Jun 2017 14:31:47: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:31:47: #1 finished! INFO @ Sat, 03 Jun 2017 14:31:47: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:31:47: #1 tags after filtering in treatment: 12094810 INFO @ Sat, 03 Jun 2017 14:31:47: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:31:47: #1 finished! INFO @ Sat, 03 Jun 2017 14:31:47: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:31:49: #2 number of paired peaks: 133 WARNING @ Sat, 03 Jun 2017 14:31:49: Fewer paired peaks (133) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 133 pairs to build model! INFO @ Sat, 03 Jun 2017 14:31:49: start model_add_line... INFO @ Sat, 03 Jun 2017 14:31:49: #2 number of paired peaks: 133 WARNING @ Sat, 03 Jun 2017 14:31:49: Fewer paired peaks (133) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 133 pairs to build model! INFO @ Sat, 03 Jun 2017 14:31:49: start model_add_line... INFO @ Sat, 03 Jun 2017 14:31:50: start X-correlation... INFO @ Sat, 03 Jun 2017 14:31:50: end of X-cor INFO @ Sat, 03 Jun 2017 14:31:50: #2 finished! INFO @ Sat, 03 Jun 2017 14:31:50: #2 predicted fragment length is 102 bps INFO @ Sat, 03 Jun 2017 14:31:50: #2 alternative fragment length(s) may be 102 bps INFO @ Sat, 03 Jun 2017 14:31:50: #2.2 Generate R script for model : SRX1840075.20_model.r INFO @ Sat, 03 Jun 2017 14:31:50: start X-correlation... WARNING @ Sat, 03 Jun 2017 14:31:50: #2 Since the d (102) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 14:31:50: #2 You may need to consider one of the other alternative d(s): 102 WARNING @ Sat, 03 Jun 2017 14:31:50: #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 14:31:50: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:31:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:31:50: end of X-cor INFO @ Sat, 03 Jun 2017 14:31:50: #2 finished! INFO @ Sat, 03 Jun 2017 14:31:50: #2 predicted fragment length is 102 bps INFO @ Sat, 03 Jun 2017 14:31:50: #2 alternative fragment length(s) may be 102 bps INFO @ Sat, 03 Jun 2017 14:31:50: #2.2 Generate R script for model : SRX1840075.05_model.r WARNING @ Sat, 03 Jun 2017 14:31:50: #2 Since the d (102) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 14:31:50: #2 You may need to consider one of the other alternative d(s): 102 WARNING @ Sat, 03 Jun 2017 14:31:50: #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 14:31:50: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:31:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:32:46: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:32:53: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:32:55: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:33:34: #4 Write output xls file... SRX1840075.10_peaks.xls INFO @ Sat, 03 Jun 2017 14:33:34: #4 Write peak in narrowPeak format file... SRX1840075.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:33:34: #4 Write summits bed file... SRX1840075.10_summits.bed INFO @ Sat, 03 Jun 2017 14:33:34: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (787 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 14:33:39: #4 Write output xls file... SRX1840075.20_peaks.xls INFO @ Sat, 03 Jun 2017 14:33:39: #4 Write peak in narrowPeak format file... SRX1840075.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:33:39: #4 Write summits bed file... SRX1840075.20_summits.bed INFO @ Sat, 03 Jun 2017 14:33:39: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (488 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 14:33:42: #4 Write output xls file... SRX1840075.05_peaks.xls INFO @ Sat, 03 Jun 2017 14:33:42: #4 Write peak in narrowPeak format file... SRX1840075.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:33:42: #4 Write summits bed file... SRX1840075.05_summits.bed INFO @ Sat, 03 Jun 2017 14:33:42: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (1357 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。