Job ID = 9029425 sra ファイルのダウンロード中... Completed: 76675K bytes transferred in 3 seconds (157809K 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 --:--:-- 0 100 20110 0 20110 0 0 2546 0 --:--:-- 0:00:07 --:--:-- 15747 100 59820 0 59820 0 0 6853 0 --:--:-- 0:00:08 --:--:-- 28418 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 1635857 spots for /home/okishinya/chipatlas/results/dm3/SRX1743171/SRR3476582.sra Written 1635857 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: 00:00:31 1635857 reads; of these: 1635857 (100.00%) were unpaired; of these: 841529 (51.44%) aligned 0 times 722490 (44.17%) aligned exactly 1 time 71838 (4.39%) aligned >1 times 48.56% overall alignment rate Time searching: 00:00:31 Overall time: 00:00:31 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] 267606 / 794328 = 0.3369 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 13:36:58: # Command line: callpeak -t SRX1743171.bam -f BAM -g dm -n SRX1743171.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1743171.10 # format = BAM # ChIP-seq file = ['SRX1743171.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 13:36:58: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:36:58: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:36:58: # Command line: callpeak -t SRX1743171.bam -f BAM -g dm -n SRX1743171.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1743171.05 # format = BAM # ChIP-seq file = ['SRX1743171.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 13:36:58: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:36:58: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:36:59: # Command line: callpeak -t SRX1743171.bam -f BAM -g dm -n SRX1743171.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1743171.20 # format = BAM # ChIP-seq file = ['SRX1743171.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 13:36:59: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:36:59: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:37:02: #1 tag size is determined as 75 bps INFO @ Sat, 03 Jun 2017 13:37:02: #1 tag size = 75 INFO @ Sat, 03 Jun 2017 13:37:02: #1 total tags in treatment: 526722 INFO @ Sat, 03 Jun 2017 13:37:02: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:37:02: #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 13:37:02: #1 tags after filtering in treatment: 526496 INFO @ Sat, 03 Jun 2017 13:37:02: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:37:02: #1 finished! INFO @ Sat, 03 Jun 2017 13:37:02: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:37:02: #1 tag size is determined as 75 bps INFO @ Sat, 03 Jun 2017 13:37:02: #1 tag size = 75 INFO @ Sat, 03 Jun 2017 13:37:02: #1 total tags in treatment: 526722 INFO @ Sat, 03 Jun 2017 13:37:02: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:37:02: #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 13:37:02: #1 tag size is determined as 75 bps INFO @ Sat, 03 Jun 2017 13:37:02: #1 tag size = 75 INFO @ Sat, 03 Jun 2017 13:37:02: #1 total tags in treatment: 526722 INFO @ Sat, 03 Jun 2017 13:37:02: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:37:02: #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 13:37:02: #1 tags after filtering in treatment: 526496 INFO @ Sat, 03 Jun 2017 13:37:02: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:37:02: #1 finished! INFO @ Sat, 03 Jun 2017 13:37:02: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:37:03: #1 tags after filtering in treatment: 526496 INFO @ Sat, 03 Jun 2017 13:37:03: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:37:03: #1 finished! INFO @ Sat, 03 Jun 2017 13:37:03: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:37:03: #2 number of paired peaks: 4333 INFO @ Sat, 03 Jun 2017 13:37:03: start model_add_line... INFO @ Sat, 03 Jun 2017 13:37:03: #2 number of paired peaks: 4333 INFO @ Sat, 03 Jun 2017 13:37:03: start model_add_line... INFO @ Sat, 03 Jun 2017 13:37:03: #2 number of paired peaks: 4333 INFO @ Sat, 03 Jun 2017 13:37:03: start model_add_line... INFO @ Sat, 03 Jun 2017 13:37:05: start X-correlation... INFO @ Sat, 03 Jun 2017 13:37:05: end of X-cor INFO @ Sat, 03 Jun 2017 13:37:05: #2 finished! INFO @ Sat, 03 Jun 2017 13:37:05: #2 predicted fragment length is 189 bps INFO @ Sat, 03 Jun 2017 13:37:05: #2 alternative fragment length(s) may be 189 bps INFO @ Sat, 03 Jun 2017 13:37:05: #2.2 Generate R script for model : SRX1743171.10_model.r INFO @ Sat, 03 Jun 2017 13:37:05: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:37:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:37:05: start X-correlation... INFO @ Sat, 03 Jun 2017 13:37:05: end of X-cor INFO @ Sat, 03 Jun 2017 13:37:05: #2 finished! INFO @ Sat, 03 Jun 2017 13:37:05: #2 predicted fragment length is 189 bps INFO @ Sat, 03 Jun 2017 13:37:05: #2 alternative fragment length(s) may be 189 bps INFO @ Sat, 03 Jun 2017 13:37:05: #2.2 Generate R script for model : SRX1743171.20_model.r INFO @ Sat, 03 Jun 2017 13:37:05: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:37:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:37:05: start X-correlation... INFO @ Sat, 03 Jun 2017 13:37:05: end of X-cor INFO @ Sat, 03 Jun 2017 13:37:05: #2 finished! INFO @ Sat, 03 Jun 2017 13:37:05: #2 predicted fragment length is 189 bps INFO @ Sat, 03 Jun 2017 13:37:05: #2 alternative fragment length(s) may be 189 bps INFO @ Sat, 03 Jun 2017 13:37:05: #2.2 Generate R script for model : SRX1743171.05_model.r INFO @ Sat, 03 Jun 2017 13:37:05: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:37:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:37:09: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:37:09: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:37:09: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:37:11: #4 Write output xls file... SRX1743171.10_peaks.xls INFO @ Sat, 03 Jun 2017 13:37:11: #4 Write peak in narrowPeak format file... SRX1743171.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:37:11: #4 Write summits bed file... SRX1743171.10_summits.bed INFO @ Sat, 03 Jun 2017 13:37:11: Done! pass1 - making usageList (9 chroms): 8 millis pass2 - checking and writing primary data (510 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:37:11: #4 Write output xls file... SRX1743171.20_peaks.xls INFO @ Sat, 03 Jun 2017 13:37:11: #4 Write peak in narrowPeak format file... SRX1743171.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:37:11: #4 Write summits bed file... SRX1743171.20_summits.bed INFO @ Sat, 03 Jun 2017 13:37:11: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (166 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Jun 2017 13:37:12: #4 Write output xls file... SRX1743171.05_peaks.xls INFO @ Sat, 03 Jun 2017 13:37:12: #4 Write peak in narrowPeak format file... SRX1743171.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:37:12: #4 Write summits bed file... SRX1743171.05_summits.bed INFO @ Sat, 03 Jun 2017 13:37:12: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1041 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。