Job ID = 9041648 sra ファイルのダウンロード中... Completed: 1518470K bytes transferred in 13 seconds (921362K 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 --:--:-- 0 102 2559 0 2559 0 0 356 0 --:--:-- 0:00:07 --:--:-- 4107 100 33213 0 33213 0 0 3980 0 --:--:-- 0:00:08 --:--:-- 18606 100 96925 0 96925 0 0 10563 0 --:--:-- 0:00:09 --:--:-- 37065 100 128k 0 128k 0 0 13787 0 --:--:-- 0:00:09 --:--:-- 44482 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 47408050 spots for /home/okishinya/chipatlas/results/dm3/SRX1292229/SRR2530406.sra Written 47408050 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: 00:06:02 47408050 reads; of these: 47408050 (100.00%) were unpaired; of these: 19247858 (40.60%) aligned 0 times 19689279 (41.53%) aligned exactly 1 time 8470913 (17.87%) aligned >1 times 59.40% overall alignment rate Time searching: 00:06:02 Overall time: 00:06:02 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] 17033779 / 28160192 = 0.6049 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 01:09:13: # Command line: callpeak -t SRX1292229.bam -f BAM -g dm -n SRX1292229.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1292229.20 # format = BAM # ChIP-seq file = ['SRX1292229.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 01:09:13: #1 read tag files... INFO @ Mon, 05 Jun 2017 01:09:13: #1 read treatment tags... INFO @ Mon, 05 Jun 2017 01:09:13: # Command line: callpeak -t SRX1292229.bam -f BAM -g dm -n SRX1292229.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1292229.05 # format = BAM # ChIP-seq file = ['SRX1292229.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 01:09:13: #1 read tag files... INFO @ Mon, 05 Jun 2017 01:09:13: #1 read treatment tags... INFO @ Mon, 05 Jun 2017 01:09:13: # Command line: callpeak -t SRX1292229.bam -f BAM -g dm -n SRX1292229.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1292229.10 # format = BAM # ChIP-seq file = ['SRX1292229.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 01:09:13: #1 read tag files... INFO @ Mon, 05 Jun 2017 01:09:13: #1 read treatment tags... INFO @ Mon, 05 Jun 2017 01:09:19: 1000000 INFO @ Mon, 05 Jun 2017 01:09:19: 1000000 INFO @ Mon, 05 Jun 2017 01:09:19: 1000000 INFO @ Mon, 05 Jun 2017 01:09:26: 2000000 INFO @ Mon, 05 Jun 2017 01:09:26: 2000000 INFO @ Mon, 05 Jun 2017 01:09:26: 2000000 INFO @ Mon, 05 Jun 2017 01:09:32: 3000000 INFO @ Mon, 05 Jun 2017 01:09:32: 3000000 INFO @ Mon, 05 Jun 2017 01:09:32: 3000000 INFO @ Mon, 05 Jun 2017 01:09:38: 4000000 INFO @ Mon, 05 Jun 2017 01:09:38: 4000000 INFO @ Mon, 05 Jun 2017 01:09:38: 4000000 INFO @ Mon, 05 Jun 2017 01:09:45: 5000000 INFO @ Mon, 05 Jun 2017 01:09:45: 5000000 INFO @ Mon, 05 Jun 2017 01:09:45: 5000000 INFO @ Mon, 05 Jun 2017 01:09:51: 6000000 INFO @ Mon, 05 Jun 2017 01:09:51: 6000000 INFO @ Mon, 05 Jun 2017 01:09:51: 6000000 INFO @ Mon, 05 Jun 2017 01:09:57: 7000000 INFO @ Mon, 05 Jun 2017 01:09:57: 7000000 INFO @ Mon, 05 Jun 2017 01:09:57: 7000000 INFO @ Mon, 05 Jun 2017 01:10:03: 8000000 INFO @ Mon, 05 Jun 2017 01:10:03: 8000000 INFO @ Mon, 05 Jun 2017 01:10:03: 8000000 INFO @ Mon, 05 Jun 2017 01:10:09: 9000000 INFO @ Mon, 05 Jun 2017 01:10:09: 9000000 INFO @ Mon, 05 Jun 2017 01:10:09: 9000000 INFO @ Mon, 05 Jun 2017 01:10:15: 10000000 INFO @ Mon, 05 Jun 2017 01:10:15: 10000000 INFO @ Mon, 05 Jun 2017 01:10:15: 10000000 INFO @ Mon, 05 Jun 2017 01:10:21: 11000000 INFO @ Mon, 05 Jun 2017 01:10:21: 11000000 INFO @ Mon, 05 Jun 2017 01:10:21: 11000000 INFO @ Mon, 05 Jun 2017 01:10:21: #1 tag size is determined as 40 bps INFO @ Mon, 05 Jun 2017 01:10:21: #1 tag size = 40 INFO @ Mon, 05 Jun 2017 01:10:21: #1 total tags in treatment: 11126413 INFO @ Mon, 05 Jun 2017 01:10:21: #1 user defined the maximum tags... INFO @ Mon, 05 Jun 2017 01:10:21: #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 01:10:22: #1 tag size is determined as 40 bps INFO @ Mon, 05 Jun 2017 01:10:22: #1 tag size = 40 INFO @ Mon, 05 Jun 2017 01:10:22: #1 total tags in treatment: 11126413 INFO @ Mon, 05 Jun 2017 01:10:22: #1 user defined the maximum tags... INFO @ Mon, 05 Jun 2017 01:10:22: #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 01:10:22: #1 tag size is determined as 40 bps INFO @ Mon, 05 Jun 2017 01:10:22: #1 tag size = 40 INFO @ Mon, 05 Jun 2017 01:10:22: #1 total tags in treatment: 11126413 INFO @ Mon, 05 Jun 2017 01:10:22: #1 user defined the maximum tags... INFO @ Mon, 05 Jun 2017 01:10:22: #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 01:10:24: #1 tags after filtering in treatment: 11121466 INFO @ Mon, 05 Jun 2017 01:10:24: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Jun 2017 01:10:24: #1 finished! INFO @ Mon, 05 Jun 2017 01:10:24: #2 Build Peak Model... INFO @ Mon, 05 Jun 2017 01:10:24: #1 tags after filtering in treatment: 11121466 INFO @ Mon, 05 Jun 2017 01:10:24: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Jun 2017 01:10:24: #1 finished! INFO @ Mon, 05 Jun 2017 01:10:24: #2 Build Peak Model... INFO @ Mon, 05 Jun 2017 01:10:24: #1 tags after filtering in treatment: 11121466 INFO @ Mon, 05 Jun 2017 01:10:24: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Jun 2017 01:10:24: #1 finished! INFO @ Mon, 05 Jun 2017 01:10:24: #2 Build Peak Model... INFO @ Mon, 05 Jun 2017 01:10:26: #2 number of paired peaks: 476 WARNING @ Mon, 05 Jun 2017 01:10:26: Fewer paired peaks (476) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 476 pairs to build model! INFO @ Mon, 05 Jun 2017 01:10:26: start model_add_line... INFO @ Mon, 05 Jun 2017 01:10:26: #2 number of paired peaks: 476 WARNING @ Mon, 05 Jun 2017 01:10:26: Fewer paired peaks (476) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 476 pairs to build model! INFO @ Mon, 05 Jun 2017 01:10:26: start model_add_line... INFO @ Mon, 05 Jun 2017 01:10:26: #2 number of paired peaks: 476 WARNING @ Mon, 05 Jun 2017 01:10:26: Fewer paired peaks (476) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 476 pairs to build model! INFO @ Mon, 05 Jun 2017 01:10:26: start model_add_line... INFO @ Mon, 05 Jun 2017 01:10:30: start X-correlation... INFO @ Mon, 05 Jun 2017 01:10:30: end of X-cor INFO @ Mon, 05 Jun 2017 01:10:30: #2 finished! INFO @ Mon, 05 Jun 2017 01:10:30: #2 predicted fragment length is 41 bps INFO @ Mon, 05 Jun 2017 01:10:30: #2 alternative fragment length(s) may be 41 bps INFO @ Mon, 05 Jun 2017 01:10:30: #2.2 Generate R script for model : SRX1292229.10_model.r WARNING @ Mon, 05 Jun 2017 01:10:30: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 05 Jun 2017 01:10:30: #2 You may need to consider one of the other alternative d(s): 41 WARNING @ Mon, 05 Jun 2017 01:10:30: #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 01:10:30: #3 Call peaks... INFO @ Mon, 05 Jun 2017 01:10:30: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 05 Jun 2017 01:10:30: start X-correlation... INFO @ Mon, 05 Jun 2017 01:10:30: end of X-cor INFO @ Mon, 05 Jun 2017 01:10:30: #2 finished! INFO @ Mon, 05 Jun 2017 01:10:30: #2 predicted fragment length is 41 bps INFO @ Mon, 05 Jun 2017 01:10:30: #2 alternative fragment length(s) may be 41 bps INFO @ Mon, 05 Jun 2017 01:10:30: #2.2 Generate R script for model : SRX1292229.05_model.r WARNING @ Mon, 05 Jun 2017 01:10:30: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 05 Jun 2017 01:10:30: #2 You may need to consider one of the other alternative d(s): 41 WARNING @ Mon, 05 Jun 2017 01:10:30: #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 01:10:30: #3 Call peaks... INFO @ Mon, 05 Jun 2017 01:10:30: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 05 Jun 2017 01:10:30: start X-correlation... INFO @ Mon, 05 Jun 2017 01:10:30: end of X-cor INFO @ Mon, 05 Jun 2017 01:10:30: #2 finished! INFO @ Mon, 05 Jun 2017 01:10:30: #2 predicted fragment length is 41 bps INFO @ Mon, 05 Jun 2017 01:10:30: #2 alternative fragment length(s) may be 41 bps INFO @ Mon, 05 Jun 2017 01:10:30: #2.2 Generate R script for model : SRX1292229.20_model.r WARNING @ Mon, 05 Jun 2017 01:10:30: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 05 Jun 2017 01:10:30: #2 You may need to consider one of the other alternative d(s): 41 WARNING @ Mon, 05 Jun 2017 01:10:30: #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 01:10:30: #3 Call peaks... INFO @ Mon, 05 Jun 2017 01:10:30: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 05 Jun 2017 01:11:28: #3 Call peaks for each chromosome... INFO @ Mon, 05 Jun 2017 01:11:30: #3 Call peaks for each chromosome... INFO @ Mon, 05 Jun 2017 01:11:31: #3 Call peaks for each chromosome... INFO @ Mon, 05 Jun 2017 01:12:10: #4 Write output xls file... SRX1292229.20_peaks.xls INFO @ Mon, 05 Jun 2017 01:12:10: #4 Write peak in narrowPeak format file... SRX1292229.20_peaks.narrowPeak INFO @ Mon, 05 Jun 2017 01:12:10: #4 Write summits bed file... SRX1292229.20_summits.bed INFO @ Mon, 05 Jun 2017 01:12:10: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (901 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 05 Jun 2017 01:12:13: #4 Write output xls file... SRX1292229.10_peaks.xls INFO @ Mon, 05 Jun 2017 01:12:13: #4 Write peak in narrowPeak format file... SRX1292229.10_peaks.narrowPeak INFO @ Mon, 05 Jun 2017 01:12:13: #4 Write summits bed file... SRX1292229.10_summits.bed INFO @ Mon, 05 Jun 2017 01:12:13: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1639 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 05 Jun 2017 01:12:16: #4 Write output xls file... SRX1292229.05_peaks.xls INFO @ Mon, 05 Jun 2017 01:12:16: #4 Write peak in narrowPeak format file... SRX1292229.05_peaks.narrowPeak INFO @ Mon, 05 Jun 2017 01:12:16: #4 Write summits bed file... SRX1292229.05_summits.bed INFO @ Mon, 05 Jun 2017 01:12:16: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4460 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。