Job ID = 9029490 sra ファイルのダウンロード中... Completed: 323016K bytes transferred in 5 seconds (489083K 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 14324 0 14324 0 0 1871 0 --:--:-- 0:00:07 --:--:-- 14395 100 38318 0 38318 0 0 4515 0 --:--:-- 0:00:08 --:--:-- 21007 100 54864 0 54864 0 0 6193 0 --:--:-- 0:00:08 --:--:-- 24983 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 12657966 spots for /home/okishinya/chipatlas/results/dm3/SRX1794244/SRR3575288.sra Written 12657966 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: 00:04:13 12657966 reads; of these: 12657966 (100.00%) were unpaired; of these: 314422 (2.48%) aligned 0 times 10078960 (79.63%) aligned exactly 1 time 2264584 (17.89%) aligned >1 times 97.52% overall alignment rate Time searching: 00:04:13 Overall time: 00:04:13 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] 1688071 / 12343544 = 0.1368 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 14:02:18: # Command line: callpeak -t SRX1794244.bam -f BAM -g dm -n SRX1794244.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1794244.05 # format = BAM # ChIP-seq file = ['SRX1794244.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 14:02:18: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:02:18: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:02:18: # Command line: callpeak -t SRX1794244.bam -f BAM -g dm -n SRX1794244.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1794244.10 # format = BAM # ChIP-seq file = ['SRX1794244.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 14:02:18: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:02:18: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:02:18: # Command line: callpeak -t SRX1794244.bam -f BAM -g dm -n SRX1794244.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1794244.20 # format = BAM # ChIP-seq file = ['SRX1794244.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 14:02:18: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:02:18: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:02:24: 1000000 INFO @ Sat, 03 Jun 2017 14:02:24: 1000000 INFO @ Sat, 03 Jun 2017 14:02:24: 1000000 INFO @ Sat, 03 Jun 2017 14:02:30: 2000000 INFO @ Sat, 03 Jun 2017 14:02:30: 2000000 INFO @ Sat, 03 Jun 2017 14:02:30: 2000000 INFO @ Sat, 03 Jun 2017 14:02:36: 3000000 INFO @ Sat, 03 Jun 2017 14:02:36: 3000000 INFO @ Sat, 03 Jun 2017 14:02:38: 3000000 INFO @ Sat, 03 Jun 2017 14:02:42: 4000000 INFO @ Sat, 03 Jun 2017 14:02:43: 4000000 INFO @ Sat, 03 Jun 2017 14:02:45: 4000000 INFO @ Sat, 03 Jun 2017 14:02:49: 5000000 INFO @ Sat, 03 Jun 2017 14:02:50: 5000000 INFO @ Sat, 03 Jun 2017 14:02:52: 5000000 INFO @ Sat, 03 Jun 2017 14:02:55: 6000000 INFO @ Sat, 03 Jun 2017 14:02:57: 6000000 INFO @ Sat, 03 Jun 2017 14:03:00: 6000000 INFO @ Sat, 03 Jun 2017 14:03:01: 7000000 INFO @ Sat, 03 Jun 2017 14:03:04: 7000000 INFO @ Sat, 03 Jun 2017 14:03:07: 8000000 INFO @ Sat, 03 Jun 2017 14:03:07: 7000000 INFO @ Sat, 03 Jun 2017 14:03:10: 8000000 INFO @ Sat, 03 Jun 2017 14:03:13: 9000000 INFO @ Sat, 03 Jun 2017 14:03:14: 8000000 INFO @ Sat, 03 Jun 2017 14:03:17: 9000000 INFO @ Sat, 03 Jun 2017 14:03:19: 10000000 INFO @ Sat, 03 Jun 2017 14:03:22: 9000000 INFO @ Sat, 03 Jun 2017 14:03:23: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 14:03:23: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 14:03:23: #1 total tags in treatment: 10655473 INFO @ Sat, 03 Jun 2017 14:03:23: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:03:23: #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 14:03:24: 10000000 INFO @ Sat, 03 Jun 2017 14:03:25: #1 tags after filtering in treatment: 10653216 INFO @ Sat, 03 Jun 2017 14:03:25: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:03:25: #1 finished! INFO @ Sat, 03 Jun 2017 14:03:25: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:03:28: #2 number of paired peaks: 8138 INFO @ Sat, 03 Jun 2017 14:03:28: start model_add_line... INFO @ Sat, 03 Jun 2017 14:03:29: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 14:03:29: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 14:03:29: #1 total tags in treatment: 10655473 INFO @ Sat, 03 Jun 2017 14:03:29: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:03:29: #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 14:03:29: 10000000 INFO @ Sat, 03 Jun 2017 14:03:31: #1 tags after filtering in treatment: 10653216 INFO @ Sat, 03 Jun 2017 14:03:31: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:03:31: #1 finished! INFO @ Sat, 03 Jun 2017 14:03:31: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:03:33: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 14:03:33: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 14:03:33: #1 total tags in treatment: 10655473 INFO @ Sat, 03 Jun 2017 14:03:33: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:03:33: #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 14:03:33: #2 number of paired peaks: 8138 INFO @ Sat, 03 Jun 2017 14:03:33: start model_add_line... INFO @ Sat, 03 Jun 2017 14:03:35: #1 tags after filtering in treatment: 10653216 INFO @ Sat, 03 Jun 2017 14:03:35: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:03:35: #1 finished! INFO @ Sat, 03 Jun 2017 14:03:35: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:03:38: #2 number of paired peaks: 8138 INFO @ Sat, 03 Jun 2017 14:03:38: start model_add_line... INFO @ Sat, 03 Jun 2017 14:04:24: start X-correlation... INFO @ Sat, 03 Jun 2017 14:04:24: end of X-cor INFO @ Sat, 03 Jun 2017 14:04:24: #2 finished! INFO @ Sat, 03 Jun 2017 14:04:24: #2 predicted fragment length is 139 bps INFO @ Sat, 03 Jun 2017 14:04:24: #2 alternative fragment length(s) may be 139 bps INFO @ Sat, 03 Jun 2017 14:04:24: #2.2 Generate R script for model : SRX1794244.05_model.r INFO @ Sat, 03 Jun 2017 14:04:24: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:04:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:04:29: start X-correlation... INFO @ Sat, 03 Jun 2017 14:04:29: end of X-cor INFO @ Sat, 03 Jun 2017 14:04:29: #2 finished! INFO @ Sat, 03 Jun 2017 14:04:29: #2 predicted fragment length is 139 bps INFO @ Sat, 03 Jun 2017 14:04:29: #2 alternative fragment length(s) may be 139 bps INFO @ Sat, 03 Jun 2017 14:04:29: #2.2 Generate R script for model : SRX1794244.10_model.r INFO @ Sat, 03 Jun 2017 14:04:29: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:04:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:04:33: start X-correlation... INFO @ Sat, 03 Jun 2017 14:04:33: end of X-cor INFO @ Sat, 03 Jun 2017 14:04:33: #2 finished! INFO @ Sat, 03 Jun 2017 14:04:33: #2 predicted fragment length is 139 bps INFO @ Sat, 03 Jun 2017 14:04:33: #2 alternative fragment length(s) may be 139 bps INFO @ Sat, 03 Jun 2017 14:04:33: #2.2 Generate R script for model : SRX1794244.20_model.r INFO @ Sat, 03 Jun 2017 14:04:33: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:04:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:05:26: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:05:31: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:05:37: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Jun 2017 14:06:25: #4 Write output xls file... SRX1794244.10_peaks.xls INFO @ Sat, 03 Jun 2017 14:06:26: #4 Write peak in narrowPeak format file... SRX1794244.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:06:26: #4 Write summits bed file... SRX1794244.10_summits.bed INFO @ Sat, 03 Jun 2017 14:06:26: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8643 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 14:06:26: #4 Write output xls file... SRX1794244.20_peaks.xls INFO @ Sat, 03 Jun 2017 14:06:26: #4 Write peak in narrowPeak format file... SRX1794244.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:06:26: #4 Write summits bed file... SRX1794244.20_summits.bed INFO @ Sat, 03 Jun 2017 14:06:26: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (5755 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 14:06:27: #4 Write output xls file... SRX1794244.05_peaks.xls INFO @ Sat, 03 Jun 2017 14:06:27: #4 Write peak in narrowPeak format file... SRX1794244.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:06:27: #4 Write summits bed file... SRX1794244.05_summits.bed INFO @ Sat, 03 Jun 2017 14:06:27: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (10889 records, 4 fields): 15 millis CompletedMACS2peakCalling BigWig に変換しました。