Job ID = 9028931 sra ファイルのダウンロード中... Completed: 484495K bytes transferred in 6 seconds (590679K 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 --:--:-- 0:00:07 --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:08 --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:09 --:--:-- 0 100 14324 0 14324 0 0 1412 0 --:--:-- 0:00:10 --:--:-- 3822 100 46318 0 46318 0 0 4097 0 --:--:-- 0:00:11 --:--:-- 9435 100 62303 0 62303 0 0 5431 0 --:--:-- 0:00:11 --:--:-- 15300 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 12379255 spots for /home/okishinya/chipatlas/results/dm3/SRX1038030/SRR2039659.sra Written 12379255 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: 00:01:15 12379255 reads; of these: 12379255 (100.00%) were unpaired; of these: 11252646 (90.90%) aligned 0 times 1024216 (8.27%) aligned exactly 1 time 102393 (0.83%) aligned >1 times 9.10% overall alignment rate Time searching: 00:01:15 Overall time: 00:01:15 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] 157229 / 1126609 = 0.1396 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 12:27:09: # Command line: callpeak -t SRX1038030.bam -f BAM -g dm -n SRX1038030.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1038030.20 # format = BAM # ChIP-seq file = ['SRX1038030.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 12:27:09: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:27:09: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:27:09: # Command line: callpeak -t SRX1038030.bam -f BAM -g dm -n SRX1038030.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1038030.05 # format = BAM # ChIP-seq file = ['SRX1038030.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 12:27:09: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:27:09: # Command line: callpeak -t SRX1038030.bam -f BAM -g dm -n SRX1038030.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1038030.10 # format = BAM # ChIP-seq file = ['SRX1038030.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 12:27:09: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:27:09: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:27:09: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:27:15: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 12:27:15: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 12:27:15: #1 total tags in treatment: 969380 INFO @ Sat, 03 Jun 2017 12:27:15: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:27:15: #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 12:27:15: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 12:27:15: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 12:27:15: #1 total tags in treatment: 969380 INFO @ Sat, 03 Jun 2017 12:27:15: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:27:15: #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 12:27:15: #1 tags after filtering in treatment: 969007 INFO @ Sat, 03 Jun 2017 12:27:15: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:27:15: #1 finished! INFO @ Sat, 03 Jun 2017 12:27:15: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:27:15: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 12:27:15: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 12:27:15: #1 total tags in treatment: 969380 INFO @ Sat, 03 Jun 2017 12:27:15: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:27:15: #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 12:27:15: #1 tags after filtering in treatment: 969007 INFO @ Sat, 03 Jun 2017 12:27:15: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:27:15: #1 finished! INFO @ Sat, 03 Jun 2017 12:27:15: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:27:15: #1 tags after filtering in treatment: 969007 INFO @ Sat, 03 Jun 2017 12:27:15: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:27:15: #1 finished! INFO @ Sat, 03 Jun 2017 12:27:15: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:27:16: #2 number of paired peaks: 4646 INFO @ Sat, 03 Jun 2017 12:27:16: start model_add_line... INFO @ Sat, 03 Jun 2017 12:27:16: #2 number of paired peaks: 4646 INFO @ Sat, 03 Jun 2017 12:27:16: start model_add_line... INFO @ Sat, 03 Jun 2017 12:27:16: #2 number of paired peaks: 4646 INFO @ Sat, 03 Jun 2017 12:27:16: start model_add_line... INFO @ Sat, 03 Jun 2017 12:27:21: start X-correlation... INFO @ Sat, 03 Jun 2017 12:27:21: end of X-cor INFO @ Sat, 03 Jun 2017 12:27:21: #2 finished! INFO @ Sat, 03 Jun 2017 12:27:21: #2 predicted fragment length is 157 bps INFO @ Sat, 03 Jun 2017 12:27:21: #2 alternative fragment length(s) may be 157 bps INFO @ Sat, 03 Jun 2017 12:27:21: #2.2 Generate R script for model : SRX1038030.05_model.r INFO @ Sat, 03 Jun 2017 12:27:21: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:27:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:27:21: start X-correlation... INFO @ Sat, 03 Jun 2017 12:27:21: end of X-cor INFO @ Sat, 03 Jun 2017 12:27:21: #2 finished! INFO @ Sat, 03 Jun 2017 12:27:21: #2 predicted fragment length is 157 bps INFO @ Sat, 03 Jun 2017 12:27:21: #2 alternative fragment length(s) may be 157 bps INFO @ Sat, 03 Jun 2017 12:27:21: #2.2 Generate R script for model : SRX1038030.10_model.r INFO @ Sat, 03 Jun 2017 12:27:21: start X-correlation... INFO @ Sat, 03 Jun 2017 12:27:21: end of X-cor INFO @ Sat, 03 Jun 2017 12:27:21: #2 finished! INFO @ Sat, 03 Jun 2017 12:27:21: #2 predicted fragment length is 157 bps INFO @ Sat, 03 Jun 2017 12:27:21: #2 alternative fragment length(s) may be 157 bps INFO @ Sat, 03 Jun 2017 12:27:21: #2.2 Generate R script for model : SRX1038030.20_model.r INFO @ Sat, 03 Jun 2017 12:27:21: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:27:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:27:21: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:27:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:27:28: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:27:28: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:27:28: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Sat, 03 Jun 2017 12:27:33: #4 Write output xls file... SRX1038030.10_peaks.xls INFO @ Sat, 03 Jun 2017 12:27:33: #4 Write peak in narrowPeak format file... SRX1038030.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:27:33: #4 Write summits bed file... SRX1038030.10_summits.bed INFO @ Sat, 03 Jun 2017 12:27:33: Done! INFO @ Sat, 03 Jun 2017 12:27:33: #4 Write output xls file... SRX1038030.20_peaks.xls INFO @ Sat, 03 Jun 2017 12:27:33: #4 Write peak in narrowPeak format file... SRX1038030.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:27:33: #4 Write summits bed file... SRX1038030.20_summits.bed INFO @ Sat, 03 Jun 2017 12:27:33: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (685 records, 4 fields): 4 millis CompletedMACS2peakCalling pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (479 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 12:27:33: #4 Write output xls file... SRX1038030.05_peaks.xls INFO @ Sat, 03 Jun 2017 12:27:33: #4 Write peak in narrowPeak format file... SRX1038030.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:27:33: #4 Write summits bed file... SRX1038030.05_summits.bed INFO @ Sat, 03 Jun 2017 12:27:33: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (1082 records, 4 fields): 5 millis CompletedMACS2peakCalling