Job ID = 9029578 sra ファイルのダウンロード中... Completed: 719146K bytes transferred in 10 seconds (549907K 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 7663 0 7663 0 0 1031 0 --:--:-- 0:00:07 --:--:-- 9133 100 38317 0 38317 0 0 4461 0 --:--:-- 0:00:08 --:--:-- 19158 100 92921 0 92921 0 0 9863 0 --:--:-- 0:00:09 --:--:-- 32799 100 94792 0 94792 0 0 10061 0 --:--:-- 0:00:09 --:--:-- 33448 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 21591462 spots for /home/okishinya/chipatlas/results/dm3/SRX1848131/SRR3671294.sra Written 21591462 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:16 21591462 reads; of these: 21591462 (100.00%) were unpaired; of these: 4619871 (21.40%) aligned 0 times 14061497 (65.13%) aligned exactly 1 time 2910094 (13.48%) aligned >1 times 78.60% overall alignment rate Time searching: 00:07:17 Overall time: 00:07:17 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] 11499922 / 16971591 = 0.6776 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 14:24:36: # Command line: callpeak -t SRX1848131.bam -f BAM -g dm -n SRX1848131.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1848131.05 # format = BAM # ChIP-seq file = ['SRX1848131.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 14:24:36: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:24:36: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:24:36: # Command line: callpeak -t SRX1848131.bam -f BAM -g dm -n SRX1848131.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1848131.20 # format = BAM # ChIP-seq file = ['SRX1848131.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 14:24:36: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:24:36: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:24:36: # Command line: callpeak -t SRX1848131.bam -f BAM -g dm -n SRX1848131.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1848131.10 # format = BAM # ChIP-seq file = ['SRX1848131.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 14:24:36: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:24:36: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:24:42: 1000000 INFO @ Sat, 03 Jun 2017 14:24:43: 1000000 INFO @ Sat, 03 Jun 2017 14:24:43: 1000000 INFO @ Sat, 03 Jun 2017 14:24:49: 2000000 INFO @ Sat, 03 Jun 2017 14:24:50: 2000000 INFO @ Sat, 03 Jun 2017 14:24:50: 2000000 INFO @ Sat, 03 Jun 2017 14:24:55: 3000000 INFO @ Sat, 03 Jun 2017 14:24:57: 3000000 INFO @ Sat, 03 Jun 2017 14:24:57: 3000000 INFO @ Sat, 03 Jun 2017 14:25:01: 4000000 INFO @ Sat, 03 Jun 2017 14:25:04: 4000000 INFO @ Sat, 03 Jun 2017 14:25:04: 4000000 INFO @ Sat, 03 Jun 2017 14:25:07: 5000000 INFO @ Sat, 03 Jun 2017 14:25:10: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 14:25:10: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 14:25:10: #1 total tags in treatment: 5471669 INFO @ Sat, 03 Jun 2017 14:25:10: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:25:10: #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 14:25:11: 5000000 INFO @ Sat, 03 Jun 2017 14:25:11: 5000000 INFO @ Sat, 03 Jun 2017 14:25:11: #1 tags after filtering in treatment: 5468443 INFO @ Sat, 03 Jun 2017 14:25:11: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:25:11: #1 finished! INFO @ Sat, 03 Jun 2017 14:25:11: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:25:13: #2 number of paired peaks: 2232 INFO @ Sat, 03 Jun 2017 14:25:13: start model_add_line... INFO @ Sat, 03 Jun 2017 14:25:14: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 14:25:14: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 14:25:14: #1 total tags in treatment: 5471669 INFO @ Sat, 03 Jun 2017 14:25:14: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:25:14: #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 14:25:14: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 14:25:14: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 14:25:14: #1 total tags in treatment: 5471669 INFO @ Sat, 03 Jun 2017 14:25:14: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:25:14: #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 14:25:15: #1 tags after filtering in treatment: 5468443 INFO @ Sat, 03 Jun 2017 14:25:15: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:25:15: #1 finished! INFO @ Sat, 03 Jun 2017 14:25:15: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:25:15: #1 tags after filtering in treatment: 5468443 INFO @ Sat, 03 Jun 2017 14:25:15: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:25:15: #1 finished! INFO @ Sat, 03 Jun 2017 14:25:15: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:25:16: #2 number of paired peaks: 2232 INFO @ Sat, 03 Jun 2017 14:25:16: start model_add_line... INFO @ Sat, 03 Jun 2017 14:25:16: #2 number of paired peaks: 2232 INFO @ Sat, 03 Jun 2017 14:25:16: start model_add_line... INFO @ Sat, 03 Jun 2017 14:25:20: start X-correlation... INFO @ Sat, 03 Jun 2017 14:25:20: end of X-cor INFO @ Sat, 03 Jun 2017 14:25:20: #2 finished! INFO @ Sat, 03 Jun 2017 14:25:20: #2 predicted fragment length is 171 bps INFO @ Sat, 03 Jun 2017 14:25:20: #2 alternative fragment length(s) may be 171,580 bps INFO @ Sat, 03 Jun 2017 14:25:20: #2.2 Generate R script for model : SRX1848131.10_model.r INFO @ Sat, 03 Jun 2017 14:25:20: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:25:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:25:24: start X-correlation... INFO @ Sat, 03 Jun 2017 14:25:24: end of X-cor INFO @ Sat, 03 Jun 2017 14:25:24: #2 finished! INFO @ Sat, 03 Jun 2017 14:25:24: #2 predicted fragment length is 171 bps INFO @ Sat, 03 Jun 2017 14:25:24: #2 alternative fragment length(s) may be 171,580 bps INFO @ Sat, 03 Jun 2017 14:25:24: #2.2 Generate R script for model : SRX1848131.20_model.r INFO @ Sat, 03 Jun 2017 14:25:24: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:25:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:25:24: start X-correlation... INFO @ Sat, 03 Jun 2017 14:25:24: end of X-cor INFO @ Sat, 03 Jun 2017 14:25:24: #2 finished! INFO @ Sat, 03 Jun 2017 14:25:24: #2 predicted fragment length is 171 bps INFO @ Sat, 03 Jun 2017 14:25:24: #2 alternative fragment length(s) may be 171,580 bps INFO @ Sat, 03 Jun 2017 14:25:24: #2.2 Generate R script for model : SRX1848131.05_model.r INFO @ Sat, 03 Jun 2017 14:25:24: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:25:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:25:56: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:25:56: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:25:56: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:26:21: #4 Write output xls file... SRX1848131.20_peaks.xls INFO @ Sat, 03 Jun 2017 14:26:21: #4 Write peak in narrowPeak format file... SRX1848131.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:26:21: #4 Write summits bed file... SRX1848131.20_summits.bed INFO @ Sat, 03 Jun 2017 14:26:21: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1806 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 14:26:24: #4 Write output xls file... SRX1848131.10_peaks.xls INFO @ Sat, 03 Jun 2017 14:26:24: #4 Write peak in narrowPeak format file... SRX1848131.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:26:24: #4 Write summits bed file... SRX1848131.10_summits.bed INFO @ Sat, 03 Jun 2017 14:26:24: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4644 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 14:26:27: #4 Write output xls file... SRX1848131.05_peaks.xls INFO @ Sat, 03 Jun 2017 14:26:27: #4 Write peak in narrowPeak format file... SRX1848131.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:26:27: #4 Write summits bed file... SRX1848131.05_summits.bed INFO @ Sat, 03 Jun 2017 14:26:27: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8151 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。