Job ID = 10194883 sra ファイルのダウンロード中... Completed: 165865K bytes transferred in 8 seconds (166080K bits/sec), in 1 file. Completed: 166191K bytes transferred in 6 seconds (225844K bits/sec), in 1 file. Completed: 158363K bytes transferred in 6 seconds (211647K bits/sec), in 1 file. Completed: 156228K bytes transferred in 6 seconds (192657K bits/sec), in 1 file. Completed: 178915K bytes transferred in 5 seconds (250509K bits/sec), in 1 file. Completed: 180830K bytes transferred in 6 seconds (244345K 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 3537229 spots for /home/okishinya/chipatlas/results/rn6/SRX2202878/SRR4319815.sra Written 3537229 spots total Written 3576696 spots for /home/okishinya/chipatlas/results/rn6/SRX2202878/SRR4319814.sra Written 3576696 spots total Written 3732908 spots for /home/okishinya/chipatlas/results/rn6/SRX2202878/SRR4319812.sra Written 3732908 spots total Written 3728351 spots for /home/okishinya/chipatlas/results/rn6/SRX2202878/SRR4319813.sra Written 3728351 spots total Written 3935327 spots for /home/okishinya/chipatlas/results/rn6/SRX2202878/SRR4319816.sra Written 3935327 spots total Written 3962121 spots for /home/okishinya/chipatlas/results/rn6/SRX2202878/SRR4319817.sra Written 3962121 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: 00:00:00 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:17:43 22472632 reads; of these: 22472632 (100.00%) were unpaired; of these: 778675 (3.46%) aligned 0 times 16268532 (72.39%) aligned exactly 1 time 5425425 (24.14%) aligned >1 times 96.54% overall alignment rate Time searching: 00:17:46 Overall time: 00:17:46 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 12 files... [bam_rmdupse_core] 2099018 / 21693957 = 0.0968 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 18:01:30: # Command line: callpeak -t SRX2202878.bam -f BAM -g 2.15e9 -n SRX2202878.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2202878.05 # format = BAM # ChIP-seq file = ['SRX2202878.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 18:01:30: # Command line: callpeak -t SRX2202878.bam -f BAM -g 2.15e9 -n SRX2202878.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2202878.10 # format = BAM # ChIP-seq file = ['SRX2202878.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 18:01:30: #1 read tag files... INFO @ Fri, 10 Nov 2017 18:01:30: #1 read tag files... INFO @ Fri, 10 Nov 2017 18:01:30: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 18:01:30: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 18:01:30: # Command line: callpeak -t SRX2202878.bam -f BAM -g 2.15e9 -n SRX2202878.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2202878.20 # format = BAM # ChIP-seq file = ['SRX2202878.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 18:01:30: #1 read tag files... INFO @ Fri, 10 Nov 2017 18:01:30: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 18:01:37: 1000000 INFO @ Fri, 10 Nov 2017 18:01:37: 1000000 INFO @ Fri, 10 Nov 2017 18:01:37: 1000000 INFO @ Fri, 10 Nov 2017 18:01:43: 2000000 INFO @ Fri, 10 Nov 2017 18:01:45: 2000000 INFO @ Fri, 10 Nov 2017 18:01:45: 2000000 INFO @ Fri, 10 Nov 2017 18:01:50: 3000000 INFO @ Fri, 10 Nov 2017 18:01:53: 3000000 INFO @ Fri, 10 Nov 2017 18:01:53: 3000000 INFO @ Fri, 10 Nov 2017 18:01:57: 4000000 INFO @ Fri, 10 Nov 2017 18:02:00: 4000000 INFO @ Fri, 10 Nov 2017 18:02:00: 4000000 INFO @ Fri, 10 Nov 2017 18:02:03: 5000000 INFO @ Fri, 10 Nov 2017 18:02:08: 5000000 INFO @ Fri, 10 Nov 2017 18:02:08: 5000000 INFO @ Fri, 10 Nov 2017 18:02:10: 6000000 INFO @ Fri, 10 Nov 2017 18:02:15: 6000000 INFO @ Fri, 10 Nov 2017 18:02:15: 6000000 INFO @ Fri, 10 Nov 2017 18:02:17: 7000000 INFO @ Fri, 10 Nov 2017 18:02:23: 7000000 INFO @ Fri, 10 Nov 2017 18:02:23: 7000000 INFO @ Fri, 10 Nov 2017 18:02:23: 8000000 INFO @ Fri, 10 Nov 2017 18:02:30: 9000000 INFO @ Fri, 10 Nov 2017 18:02:30: 8000000 INFO @ Fri, 10 Nov 2017 18:02:30: 8000000 INFO @ Fri, 10 Nov 2017 18:02:37: 10000000 INFO @ Fri, 10 Nov 2017 18:02:38: 9000000 INFO @ Fri, 10 Nov 2017 18:02:38: 9000000 INFO @ Fri, 10 Nov 2017 18:02:44: 11000000 INFO @ Fri, 10 Nov 2017 18:02:45: 10000000 INFO @ Fri, 10 Nov 2017 18:02:45: 10000000 INFO @ Fri, 10 Nov 2017 18:02:52: 12000000 INFO @ Fri, 10 Nov 2017 18:02:52: 11000000 INFO @ Fri, 10 Nov 2017 18:02:52: 11000000 INFO @ Fri, 10 Nov 2017 18:02:59: 13000000 INFO @ Fri, 10 Nov 2017 18:03:00: 12000000 INFO @ Fri, 10 Nov 2017 18:03:00: 12000000 INFO @ Fri, 10 Nov 2017 18:03:06: 14000000 INFO @ Fri, 10 Nov 2017 18:03:07: 13000000 INFO @ Fri, 10 Nov 2017 18:03:07: 13000000 INFO @ Fri, 10 Nov 2017 18:03:13: 15000000 INFO @ Fri, 10 Nov 2017 18:03:14: 14000000 INFO @ Fri, 10 Nov 2017 18:03:15: 14000000 INFO @ Fri, 10 Nov 2017 18:03:20: 16000000 INFO @ Fri, 10 Nov 2017 18:03:22: 15000000 INFO @ Fri, 10 Nov 2017 18:03:22: 15000000 INFO @ Fri, 10 Nov 2017 18:03:27: 17000000 INFO @ Fri, 10 Nov 2017 18:03:29: 16000000 INFO @ Fri, 10 Nov 2017 18:03:30: 16000000 INFO @ Fri, 10 Nov 2017 18:03:34: 18000000 INFO @ Fri, 10 Nov 2017 18:03:37: 17000000 INFO @ Fri, 10 Nov 2017 18:03:37: 17000000 INFO @ Fri, 10 Nov 2017 18:03:41: 19000000 INFO @ Fri, 10 Nov 2017 18:03:44: 18000000 INFO @ Fri, 10 Nov 2017 18:03:44: 18000000 INFO @ Fri, 10 Nov 2017 18:03:45: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 18:03:45: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 18:03:45: #1 total tags in treatment: 19594939 INFO @ Fri, 10 Nov 2017 18:03:45: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 18:03:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 18:03:46: #1 tags after filtering in treatment: 19594774 INFO @ Fri, 10 Nov 2017 18:03:46: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 18:03:46: #1 finished! INFO @ Fri, 10 Nov 2017 18:03:46: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 18:03:46: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 18:03:48: #2 number of paired peaks: 18213 INFO @ Fri, 10 Nov 2017 18:03:48: start model_add_line... INFO @ Fri, 10 Nov 2017 18:03:49: start X-correlation... INFO @ Fri, 10 Nov 2017 18:03:49: end of X-cor INFO @ Fri, 10 Nov 2017 18:03:49: #2 finished! INFO @ Fri, 10 Nov 2017 18:03:49: #2 predicted fragment length is 122 bps INFO @ Fri, 10 Nov 2017 18:03:49: #2 alternative fragment length(s) may be 57,122 bps INFO @ Fri, 10 Nov 2017 18:03:49: #2.2 Generate R script for model : SRX2202878.10_model.r INFO @ Fri, 10 Nov 2017 18:03:49: #3 Call peaks... INFO @ Fri, 10 Nov 2017 18:03:49: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 18:03:51: 19000000 INFO @ Fri, 10 Nov 2017 18:03:52: 19000000 INFO @ Fri, 10 Nov 2017 18:03:56: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 18:03:56: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 18:03:56: #1 total tags in treatment: 19594939 INFO @ Fri, 10 Nov 2017 18:03:56: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 18:03:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 18:03:56: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 18:03:56: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 18:03:56: #1 total tags in treatment: 19594939 INFO @ Fri, 10 Nov 2017 18:03:56: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 18:03:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 18:03:57: #1 tags after filtering in treatment: 19594774 INFO @ Fri, 10 Nov 2017 18:03:57: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 18:03:57: #1 finished! INFO @ Fri, 10 Nov 2017 18:03:57: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 18:03:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 18:03:57: #1 tags after filtering in treatment: 19594774 INFO @ Fri, 10 Nov 2017 18:03:57: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 18:03:57: #1 finished! INFO @ Fri, 10 Nov 2017 18:03:57: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 18:03:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 18:03:59: #2 number of paired peaks: 18213 INFO @ Fri, 10 Nov 2017 18:03:59: start model_add_line... INFO @ Fri, 10 Nov 2017 18:03:59: start X-correlation... INFO @ Fri, 10 Nov 2017 18:03:59: end of X-cor INFO @ Fri, 10 Nov 2017 18:03:59: #2 finished! INFO @ Fri, 10 Nov 2017 18:03:59: #2 predicted fragment length is 122 bps INFO @ Fri, 10 Nov 2017 18:03:59: #2 alternative fragment length(s) may be 57,122 bps INFO @ Fri, 10 Nov 2017 18:03:59: #2.2 Generate R script for model : SRX2202878.20_model.r INFO @ Fri, 10 Nov 2017 18:03:59: #3 Call peaks... INFO @ Fri, 10 Nov 2017 18:03:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 18:03:59: #2 number of paired peaks: 18213 INFO @ Fri, 10 Nov 2017 18:03:59: start model_add_line... INFO @ Fri, 10 Nov 2017 18:04:00: start X-correlation... INFO @ Fri, 10 Nov 2017 18:04:00: end of X-cor INFO @ Fri, 10 Nov 2017 18:04:00: #2 finished! INFO @ Fri, 10 Nov 2017 18:04:00: #2 predicted fragment length is 122 bps INFO @ Fri, 10 Nov 2017 18:04:00: #2 alternative fragment length(s) may be 57,122 bps INFO @ Fri, 10 Nov 2017 18:04:00: #2.2 Generate R script for model : SRX2202878.05_model.r INFO @ Fri, 10 Nov 2017 18:04:00: #3 Call peaks... INFO @ Fri, 10 Nov 2017 18:04:00: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 18:04:38: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 18:04:47: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 18:04:48: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 18:05:04: #4 Write output xls file... SRX2202878.10_peaks.xls INFO @ Fri, 10 Nov 2017 18:05:04: #4 Write peak in narrowPeak format file... SRX2202878.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 18:05:04: #4 Write summits bed file... SRX2202878.10_summits.bed INFO @ Fri, 10 Nov 2017 18:05:04: Done! pass1 - making usageList (42 chroms): 1 millis pass2 - checking and writing primary data (602 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 18:05:14: #4 Write output xls file... SRX2202878.05_peaks.xls INFO @ Fri, 10 Nov 2017 18:05:14: #4 Write peak in narrowPeak format file... SRX2202878.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 18:05:14: #4 Write summits bed file... SRX2202878.05_summits.bed INFO @ Fri, 10 Nov 2017 18:05:14: Done! pass1 - making usageList (46 chroms): 1 millis pass2 - checking and writing primary data (1426 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 18:05:17: #4 Write output xls file... SRX2202878.20_peaks.xls INFO @ Fri, 10 Nov 2017 18:05:17: #4 Write peak in narrowPeak format file... SRX2202878.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 18:05:17: #4 Write summits bed file... SRX2202878.20_summits.bed INFO @ Fri, 10 Nov 2017 18:05:17: Done! pass1 - making usageList (33 chroms): 1 millis pass2 - checking and writing primary data (341 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。