Job ID = 10194897 sra ファイルのダウンロード中... Completed: 179500K bytes transferred in 8 seconds (178630K bits/sec), in 1 file. Completed: 179720K bytes transferred in 11 seconds (124494K bits/sec), in 1 file. Completed: 171130K bytes transferred in 5 seconds (240752K bits/sec), in 1 file. Completed: 168808K bytes transferred in 7 seconds (173520K bits/sec), in 1 file. Completed: 201971K bytes transferred in 10 seconds (152969K bits/sec), in 1 file. Completed: 203807K bytes transferred in 9 seconds (168784K 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 3837456 spots for /home/okishinya/chipatlas/results/rn6/SRX2202892/SRR4319898.sra Written 3837456 spots total Written 3794434 spots for /home/okishinya/chipatlas/results/rn6/SRX2202892/SRR4319899.sra Written 3794434 spots total Written 4002101 spots for /home/okishinya/chipatlas/results/rn6/SRX2202892/SRR4319897.sra Written 4002101 spots total Written 4011016 spots for /home/okishinya/chipatlas/results/rn6/SRX2202892/SRR4319896.sra Written 4011016 spots total Written 4435125 spots for /home/okishinya/chipatlas/results/rn6/SRX2202892/SRR4319901.sra Written 4435125 spots total Written 4411632 spots for /home/okishinya/chipatlas/results/rn6/SRX2202892/SRR4319900.sra Written 4411632 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: 00:17:57 24491764 reads; of these: 24491764 (100.00%) were unpaired; of these: 1172770 (4.79%) aligned 0 times 17827172 (72.79%) aligned exactly 1 time 5491822 (22.42%) aligned >1 times 95.21% overall alignment rate Time searching: 00:18:01 Overall time: 00:18:01 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] 3939282 / 23318994 = 0.1689 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 18:43:07: # Command line: callpeak -t SRX2202892.bam -f BAM -g 2.15e9 -n SRX2202892.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2202892.05 # format = BAM # ChIP-seq file = ['SRX2202892.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 18:43:07: #1 read tag files... INFO @ Fri, 10 Nov 2017 18:43:07: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 18:43:07: # Command line: callpeak -t SRX2202892.bam -f BAM -g 2.15e9 -n SRX2202892.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2202892.10 # format = BAM # ChIP-seq file = ['SRX2202892.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 18:43:07: #1 read tag files... INFO @ Fri, 10 Nov 2017 18:43:07: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 18:43:07: # Command line: callpeak -t SRX2202892.bam -f BAM -g 2.15e9 -n SRX2202892.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2202892.20 # format = BAM # ChIP-seq file = ['SRX2202892.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 18:43:07: #1 read tag files... INFO @ Fri, 10 Nov 2017 18:43:07: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 18:43:13: 1000000 INFO @ Fri, 10 Nov 2017 18:43:13: 1000000 INFO @ Fri, 10 Nov 2017 18:43:14: 1000000 INFO @ Fri, 10 Nov 2017 18:43:20: 2000000 INFO @ Fri, 10 Nov 2017 18:43:20: 2000000 INFO @ Fri, 10 Nov 2017 18:43:21: 2000000 INFO @ Fri, 10 Nov 2017 18:43:26: 3000000 INFO @ Fri, 10 Nov 2017 18:43:26: 3000000 INFO @ Fri, 10 Nov 2017 18:43:28: 3000000 INFO @ Fri, 10 Nov 2017 18:43:32: 4000000 INFO @ Fri, 10 Nov 2017 18:43:33: 4000000 INFO @ Fri, 10 Nov 2017 18:43:36: 4000000 INFO @ Fri, 10 Nov 2017 18:43:38: 5000000 INFO @ Fri, 10 Nov 2017 18:43:40: 5000000 INFO @ Fri, 10 Nov 2017 18:43:43: 5000000 INFO @ Fri, 10 Nov 2017 18:43:43: 6000000 INFO @ Fri, 10 Nov 2017 18:43:47: 6000000 INFO @ Fri, 10 Nov 2017 18:43:49: 7000000 INFO @ Fri, 10 Nov 2017 18:43:51: 6000000 INFO @ Fri, 10 Nov 2017 18:43:54: 7000000 INFO @ Fri, 10 Nov 2017 18:43:55: 8000000 INFO @ Fri, 10 Nov 2017 18:43:58: 7000000 INFO @ Fri, 10 Nov 2017 18:44:01: 8000000 INFO @ Fri, 10 Nov 2017 18:44:01: 9000000 INFO @ Fri, 10 Nov 2017 18:44:05: 8000000 INFO @ Fri, 10 Nov 2017 18:44:07: 10000000 INFO @ Fri, 10 Nov 2017 18:44:08: 9000000 INFO @ Fri, 10 Nov 2017 18:44:13: 9000000 INFO @ Fri, 10 Nov 2017 18:44:13: 11000000 INFO @ Fri, 10 Nov 2017 18:44:15: 10000000 INFO @ Fri, 10 Nov 2017 18:44:19: 12000000 INFO @ Fri, 10 Nov 2017 18:44:20: 10000000 INFO @ Fri, 10 Nov 2017 18:44:22: 11000000 INFO @ Fri, 10 Nov 2017 18:44:25: 13000000 INFO @ Fri, 10 Nov 2017 18:44:27: 11000000 INFO @ Fri, 10 Nov 2017 18:44:29: 12000000 INFO @ Fri, 10 Nov 2017 18:44:31: 14000000 INFO @ Fri, 10 Nov 2017 18:44:34: 12000000 INFO @ Fri, 10 Nov 2017 18:44:36: 13000000 INFO @ Fri, 10 Nov 2017 18:44:37: 15000000 INFO @ Fri, 10 Nov 2017 18:44:41: 13000000 INFO @ Fri, 10 Nov 2017 18:44:43: 16000000 INFO @ Fri, 10 Nov 2017 18:44:43: 14000000 INFO @ Fri, 10 Nov 2017 18:44:48: 17000000 INFO @ Fri, 10 Nov 2017 18:44:49: 14000000 INFO @ Fri, 10 Nov 2017 18:44:50: 15000000 INFO @ Fri, 10 Nov 2017 18:44:54: 18000000 INFO @ Fri, 10 Nov 2017 18:44:56: 15000000 INFO @ Fri, 10 Nov 2017 18:44:57: 16000000 INFO @ Fri, 10 Nov 2017 18:45:01: 19000000 INFO @ Fri, 10 Nov 2017 18:45:03: 16000000 INFO @ Fri, 10 Nov 2017 18:45:03: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 18:45:03: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 18:45:03: #1 total tags in treatment: 19379712 INFO @ Fri, 10 Nov 2017 18:45:03: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 18:45:03: #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 18:45:04: #1 tags after filtering in treatment: 19379577 INFO @ Fri, 10 Nov 2017 18:45:04: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 18:45:04: #1 finished! INFO @ Fri, 10 Nov 2017 18:45:04: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 18:45:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 18:45:04: 17000000 INFO @ Fri, 10 Nov 2017 18:45:07: #2 number of paired peaks: 35937 INFO @ Fri, 10 Nov 2017 18:45:07: start model_add_line... INFO @ Fri, 10 Nov 2017 18:45:07: start X-correlation... INFO @ Fri, 10 Nov 2017 18:45:07: end of X-cor INFO @ Fri, 10 Nov 2017 18:45:07: #2 finished! INFO @ Fri, 10 Nov 2017 18:45:07: #2 predicted fragment length is 142 bps INFO @ Fri, 10 Nov 2017 18:45:07: #2 alternative fragment length(s) may be 142 bps INFO @ Fri, 10 Nov 2017 18:45:07: #2.2 Generate R script for model : SRX2202892.10_model.r INFO @ Fri, 10 Nov 2017 18:45:07: #3 Call peaks... INFO @ Fri, 10 Nov 2017 18:45:07: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 18:45:11: 17000000 INFO @ Fri, 10 Nov 2017 18:45:11: 18000000 INFO @ Fri, 10 Nov 2017 18:45:18: 18000000 INFO @ Fri, 10 Nov 2017 18:45:19: 19000000 INFO @ Fri, 10 Nov 2017 18:45:22: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 18:45:22: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 18:45:22: #1 total tags in treatment: 19379712 INFO @ Fri, 10 Nov 2017 18:45:22: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 18:45:22: #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 18:45:22: #1 tags after filtering in treatment: 19379577 INFO @ Fri, 10 Nov 2017 18:45:22: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 18:45:22: #1 finished! INFO @ Fri, 10 Nov 2017 18:45:22: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 18:45:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 18:45:25: #2 number of paired peaks: 35937 INFO @ Fri, 10 Nov 2017 18:45:25: start model_add_line... INFO @ Fri, 10 Nov 2017 18:45:26: 19000000 INFO @ Fri, 10 Nov 2017 18:45:26: start X-correlation... INFO @ Fri, 10 Nov 2017 18:45:26: end of X-cor INFO @ Fri, 10 Nov 2017 18:45:26: #2 finished! INFO @ Fri, 10 Nov 2017 18:45:26: #2 predicted fragment length is 142 bps INFO @ Fri, 10 Nov 2017 18:45:26: #2 alternative fragment length(s) may be 142 bps INFO @ Fri, 10 Nov 2017 18:45:26: #2.2 Generate R script for model : SRX2202892.20_model.r INFO @ Fri, 10 Nov 2017 18:45:26: #3 Call peaks... INFO @ Fri, 10 Nov 2017 18:45:26: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 18:45:28: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 18:45:28: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 18:45:28: #1 total tags in treatment: 19379712 INFO @ Fri, 10 Nov 2017 18:45:28: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 18:45:28: #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 18:45:29: #1 tags after filtering in treatment: 19379577 INFO @ Fri, 10 Nov 2017 18:45:29: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 18:45:29: #1 finished! INFO @ Fri, 10 Nov 2017 18:45:29: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 18:45:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 18:45:32: #2 number of paired peaks: 35937 INFO @ Fri, 10 Nov 2017 18:45:32: start model_add_line... INFO @ Fri, 10 Nov 2017 18:45:32: start X-correlation... INFO @ Fri, 10 Nov 2017 18:45:32: end of X-cor INFO @ Fri, 10 Nov 2017 18:45:32: #2 finished! INFO @ Fri, 10 Nov 2017 18:45:32: #2 predicted fragment length is 142 bps INFO @ Fri, 10 Nov 2017 18:45:32: #2 alternative fragment length(s) may be 142 bps INFO @ Fri, 10 Nov 2017 18:45:32: #2.2 Generate R script for model : SRX2202892.05_model.r INFO @ Fri, 10 Nov 2017 18:45:32: #3 Call peaks... INFO @ Fri, 10 Nov 2017 18:45:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 18:45:54: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 18:46:12: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 18:46:23: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 18:46:24: #4 Write output xls file... SRX2202892.10_peaks.xls INFO @ Fri, 10 Nov 2017 18:46:24: #4 Write peak in narrowPeak format file... SRX2202892.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 18:46:24: #4 Write summits bed file... SRX2202892.10_summits.bed INFO @ Fri, 10 Nov 2017 18:46:24: Done! pass1 - making usageList (46 chroms): 2 millis pass2 - checking and writing primary data (4648 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 18:46:37: #4 Write output xls file... SRX2202892.20_peaks.xls INFO @ Fri, 10 Nov 2017 18:46:37: #4 Write peak in narrowPeak format file... SRX2202892.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 18:46:37: #4 Write summits bed file... SRX2202892.20_summits.bed INFO @ Fri, 10 Nov 2017 18:46:37: Done! pass1 - making usageList (33 chroms): 1 millis pass2 - checking and writing primary data (578 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 18:46:53: #4 Write output xls file... SRX2202892.05_peaks.xls INFO @ Fri, 10 Nov 2017 18:46:53: #4 Write peak in narrowPeak format file... SRX2202892.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 18:46:53: #4 Write summits bed file... SRX2202892.05_summits.bed INFO @ Fri, 10 Nov 2017 18:46:53: Done! pass1 - making usageList (79 chroms): 3 millis pass2 - checking and writing primary data (12856 records, 4 fields): 18 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。