Job ID = 10194919 sra ファイルのダウンロード中... Completed: 167422K bytes transferred in 7 seconds (174728K bits/sec), in 1 file. Completed: 163614K bytes transferred in 9 seconds (141747K bits/sec), in 1 file. Completed: 273741K bytes transferred in 13 seconds (169112K bits/sec), in 1 file. Completed: 269175K bytes transferred in 17 seconds (125079K bits/sec), in 1 file. Completed: 267862K bytes transferred in 12 seconds (174497K bits/sec), in 1 file. Completed: 264340K bytes transferred in 11 seconds (186190K bits/sec), in 1 file. 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 3805265 spots for /home/okishinya/chipatlas/results/rn6/SRX2202914/SRR4320029.sra Written 3805265 spots total Written 3909740 spots for /home/okishinya/chipatlas/results/rn6/SRX2202914/SRR4320028.sra Written 3909740 spots total Written 5830068 spots for /home/okishinya/chipatlas/results/rn6/SRX2202914/SRR4320032.sra Written 5830068 spots total Written 5762486 spots for /home/okishinya/chipatlas/results/rn6/SRX2202914/SRR4320033.sra Written 5762486 spots total Written 5815550 spots for /home/okishinya/chipatlas/results/rn6/SRX2202914/SRR4320031.sra Written 5815550 spots total Written 5955083 spots for /home/okishinya/chipatlas/results/rn6/SRX2202914/SRR4320030.sra Written 5955083 spots total rm: cannot remove `[DSE]RX*': 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: 00:00:01 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:49:46 31078192 reads; of these: 31078192 (100.00%) were unpaired; of these: 1110724 (3.57%) aligned 0 times 21623885 (69.58%) aligned exactly 1 time 8343583 (26.85%) aligned >1 times 96.43% overall alignment rate Time searching: 00:49:49 Overall time: 00:49:49 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 11465182 / 29967468 = 0.3826 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 @ Fri, 10 Nov 2017 23:58:56: # Command line: callpeak -t SRX2202914.bam -f BAM -g 2.15e9 -n SRX2202914.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2202914.10 # format = BAM # ChIP-seq file = ['SRX2202914.bam'] # control file = None # effective genome size = 2.15e+09 # 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 # Paired-End mode is off INFO @ Fri, 10 Nov 2017 23:58:56: #1 read tag files... INFO @ Fri, 10 Nov 2017 23:58:56: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 23:58:56: # Command line: callpeak -t SRX2202914.bam -f BAM -g 2.15e9 -n SRX2202914.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2202914.20 # format = BAM # ChIP-seq file = ['SRX2202914.bam'] # control file = None # effective genome size = 2.15e+09 # 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 # Paired-End mode is off INFO @ Fri, 10 Nov 2017 23:58:56: #1 read tag files... INFO @ Fri, 10 Nov 2017 23:58:56: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 23:58:56: # Command line: callpeak -t SRX2202914.bam -f BAM -g 2.15e9 -n SRX2202914.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2202914.05 # format = BAM # ChIP-seq file = ['SRX2202914.bam'] # control file = None # effective genome size = 2.15e+09 # 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 # Paired-End mode is off INFO @ Fri, 10 Nov 2017 23:58:56: #1 read tag files... INFO @ Fri, 10 Nov 2017 23:58:56: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 23:59:04: 1000000 INFO @ Fri, 10 Nov 2017 23:59:07: 1000000 INFO @ Fri, 10 Nov 2017 23:59:08: 1000000 INFO @ Fri, 10 Nov 2017 23:59:13: 2000000 INFO @ Fri, 10 Nov 2017 23:59:18: 2000000 INFO @ Fri, 10 Nov 2017 23:59:20: 2000000 INFO @ Fri, 10 Nov 2017 23:59:21: 3000000 INFO @ Fri, 10 Nov 2017 23:59:29: 4000000 INFO @ Fri, 10 Nov 2017 23:59:29: 3000000 INFO @ Fri, 10 Nov 2017 23:59:32: 3000000 INFO @ Fri, 10 Nov 2017 23:59:37: 5000000 INFO @ Fri, 10 Nov 2017 23:59:41: 4000000 INFO @ Fri, 10 Nov 2017 23:59:45: 4000000 INFO @ Fri, 10 Nov 2017 23:59:45: 6000000 INFO @ Fri, 10 Nov 2017 23:59:52: 5000000 INFO @ Fri, 10 Nov 2017 23:59:54: 7000000 INFO @ Fri, 10 Nov 2017 23:59:57: 5000000 INFO @ Sat, 11 Nov 2017 00:00:02: 8000000 INFO @ Sat, 11 Nov 2017 00:00:03: 6000000 INFO @ Sat, 11 Nov 2017 00:00:09: 6000000 INFO @ Sat, 11 Nov 2017 00:00:10: 9000000 INFO @ Sat, 11 Nov 2017 00:00:14: 7000000 INFO @ Sat, 11 Nov 2017 00:00:25: 7000000 INFO @ Sat, 11 Nov 2017 00:00:26: 10000000 INFO @ Sat, 11 Nov 2017 00:00:26: 8000000 INFO @ Sat, 11 Nov 2017 00:00:37: 9000000 INFO @ Sat, 11 Nov 2017 00:00:40: 8000000 INFO @ Sat, 11 Nov 2017 00:00:41: 11000000 INFO @ Sat, 11 Nov 2017 00:00:48: 10000000 INFO @ Sat, 11 Nov 2017 00:00:55: 9000000 INFO @ Sat, 11 Nov 2017 00:00:57: 12000000 INFO @ Sat, 11 Nov 2017 00:01:00: 11000000 INFO @ Sat, 11 Nov 2017 00:01:11: 10000000 INFO @ Sat, 11 Nov 2017 00:01:11: 12000000 INFO @ Sat, 11 Nov 2017 00:01:12: 13000000 INFO @ Sat, 11 Nov 2017 00:01:22: 13000000 INFO @ Sat, 11 Nov 2017 00:01:26: 11000000 INFO @ Sat, 11 Nov 2017 00:01:28: 14000000 INFO @ Sat, 11 Nov 2017 00:01:34: 14000000 INFO @ Sat, 11 Nov 2017 00:01:41: 12000000 INFO @ Sat, 11 Nov 2017 00:01:43: 15000000 INFO @ Sat, 11 Nov 2017 00:01:45: 15000000 INFO @ Sat, 11 Nov 2017 00:01:55: 13000000 INFO @ Sat, 11 Nov 2017 00:01:55: 16000000 INFO @ Sat, 11 Nov 2017 00:01:57: 16000000 INFO @ Sat, 11 Nov 2017 00:02:06: 17000000 INFO @ Sat, 11 Nov 2017 00:02:09: 14000000 INFO @ Sat, 11 Nov 2017 00:02:11: 17000000 INFO @ Sat, 11 Nov 2017 00:02:18: 18000000 INFO @ Sat, 11 Nov 2017 00:02:22: 15000000 INFO @ Sat, 11 Nov 2017 00:02:24: #1 tag size is determined as 50 bps INFO @ Sat, 11 Nov 2017 00:02:24: #1 tag size = 50 INFO @ Sat, 11 Nov 2017 00:02:24: #1 total tags in treatment: 18502286 INFO @ Sat, 11 Nov 2017 00:02:24: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 00:02:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 00:02:25: #1 tags after filtering in treatment: 18502156 INFO @ Sat, 11 Nov 2017 00:02:25: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 00:02:25: #1 finished! INFO @ Sat, 11 Nov 2017 00:02:25: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 00:02:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 00:02:26: 18000000 INFO @ Sat, 11 Nov 2017 00:02:29: #2 number of paired peaks: 41647 INFO @ Sat, 11 Nov 2017 00:02:29: start model_add_line... INFO @ Sat, 11 Nov 2017 00:02:30: start X-correlation... INFO @ Sat, 11 Nov 2017 00:02:30: end of X-cor INFO @ Sat, 11 Nov 2017 00:02:30: #2 finished! INFO @ Sat, 11 Nov 2017 00:02:30: #2 predicted fragment length is 131 bps INFO @ Sat, 11 Nov 2017 00:02:30: #2 alternative fragment length(s) may be 131 bps INFO @ Sat, 11 Nov 2017 00:02:30: #2.2 Generate R script for model : SRX2202914.20_model.r INFO @ Sat, 11 Nov 2017 00:02:30: #3 Call peaks... INFO @ Sat, 11 Nov 2017 00:02:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 00:02:33: #1 tag size is determined as 50 bps INFO @ Sat, 11 Nov 2017 00:02:33: #1 tag size = 50 INFO @ Sat, 11 Nov 2017 00:02:33: #1 total tags in treatment: 18502286 INFO @ Sat, 11 Nov 2017 00:02:33: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 00:02:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 00:02:34: #1 tags after filtering in treatment: 18502156 INFO @ Sat, 11 Nov 2017 00:02:34: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 00:02:34: #1 finished! INFO @ Sat, 11 Nov 2017 00:02:34: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 00:02:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 00:02:36: 16000000 INFO @ Sat, 11 Nov 2017 00:02:38: #2 number of paired peaks: 41647 INFO @ Sat, 11 Nov 2017 00:02:38: start model_add_line... INFO @ Sat, 11 Nov 2017 00:02:39: start X-correlation... INFO @ Sat, 11 Nov 2017 00:02:39: end of X-cor INFO @ Sat, 11 Nov 2017 00:02:39: #2 finished! INFO @ Sat, 11 Nov 2017 00:02:39: #2 predicted fragment length is 131 bps INFO @ Sat, 11 Nov 2017 00:02:39: #2 alternative fragment length(s) may be 131 bps INFO @ Sat, 11 Nov 2017 00:02:39: #2.2 Generate R script for model : SRX2202914.05_model.r INFO @ Sat, 11 Nov 2017 00:02:39: #3 Call peaks... INFO @ Sat, 11 Nov 2017 00:02:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 00:02:47: 17000000 INFO @ Sat, 11 Nov 2017 00:02:59: 18000000 INFO @ Sat, 11 Nov 2017 00:03:05: #1 tag size is determined as 50 bps INFO @ Sat, 11 Nov 2017 00:03:05: #1 tag size = 50 INFO @ Sat, 11 Nov 2017 00:03:05: #1 total tags in treatment: 18502286 INFO @ Sat, 11 Nov 2017 00:03:05: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 00:03:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 00:03:05: #1 tags after filtering in treatment: 18502156 INFO @ Sat, 11 Nov 2017 00:03:05: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 00:03:05: #1 finished! INFO @ Sat, 11 Nov 2017 00:03:05: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 00:03:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 00:03:09: #2 number of paired peaks: 41647 INFO @ Sat, 11 Nov 2017 00:03:09: start model_add_line... INFO @ Sat, 11 Nov 2017 00:03:10: start X-correlation... INFO @ Sat, 11 Nov 2017 00:03:10: end of X-cor INFO @ Sat, 11 Nov 2017 00:03:10: #2 finished! INFO @ Sat, 11 Nov 2017 00:03:10: #2 predicted fragment length is 131 bps INFO @ Sat, 11 Nov 2017 00:03:10: #2 alternative fragment length(s) may be 131 bps INFO @ Sat, 11 Nov 2017 00:03:10: #2.2 Generate R script for model : SRX2202914.10_model.r INFO @ Sat, 11 Nov 2017 00:03:10: #3 Call peaks... INFO @ Sat, 11 Nov 2017 00:03:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 00:03:25: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 00:03:34: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 00:03:57: #4 Write output xls file... SRX2202914.20_peaks.xls INFO @ Sat, 11 Nov 2017 00:03:57: #4 Write peak in narrowPeak format file... SRX2202914.20_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 00:03:57: #4 Write summits bed file... SRX2202914.20_summits.bed INFO @ Sat, 11 Nov 2017 00:03:58: Done! pass1 - making usageList (58 chroms): 3 millis pass2 - checking and writing primary data (7974 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 00:04:07: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 00:04:07: #4 Write output xls file... SRX2202914.05_peaks.xls INFO @ Sat, 11 Nov 2017 00:04:07: #4 Write peak in narrowPeak format file... SRX2202914.05_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 00:04:08: #4 Write summits bed file... SRX2202914.05_summits.bed INFO @ Sat, 11 Nov 2017 00:04:08: Done! pass1 - making usageList (105 chroms): 6 millis pass2 - checking and writing primary data (22657 records, 4 fields): 42 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 00:04:41: #4 Write output xls file... SRX2202914.10_peaks.xls INFO @ Sat, 11 Nov 2017 00:04:41: #4 Write peak in narrowPeak format file... SRX2202914.10_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 00:04:41: #4 Write summits bed file... SRX2202914.10_summits.bed INFO @ Sat, 11 Nov 2017 00:04:41: Done! pass1 - making usageList (90 chroms): 6 millis pass2 - checking and writing primary data (16058 records, 4 fields): 30 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。