Job ID = 10194872 sra ファイルのダウンロード中... Completed: 144318K bytes transferred in 7 seconds (157631K bits/sec), in 1 file. Completed: 144628K bytes transferred in 5 seconds (210888K bits/sec), in 1 file. Completed: 137531K bytes transferred in 8 seconds (136981K bits/sec), in 1 file. Completed: 135719K bytes transferred in 5 seconds (196853K bits/sec), in 1 file. Completed: 155873K bytes transferred in 6 seconds (208569K bits/sec), in 1 file. Completed: 157311K bytes transferred in 5 seconds (244801K 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 3053287 spots for /home/okishinya/chipatlas/results/rn6/SRX2202868/SRR4319755.sra Written 3053287 spots total Written 3086350 spots for /home/okishinya/chipatlas/results/rn6/SRX2202868/SRR4319754.sra Written 3086350 spots total Written 3223305 spots for /home/okishinya/chipatlas/results/rn6/SRX2202868/SRR4319753.sra Written 3223305 spots total Written 3227039 spots for /home/okishinya/chipatlas/results/rn6/SRX2202868/SRR4319752.sra Written 3227039 spots total Written 3408749 spots for /home/okishinya/chipatlas/results/rn6/SRX2202868/SRR4319756.sra Written 3408749 spots total Written 3426526 spots for /home/okishinya/chipatlas/results/rn6/SRX2202868/SRR4319757.sra Written 3426526 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: 00:14:23 19425256 reads; of these: 19425256 (100.00%) were unpaired; of these: 1343660 (6.92%) aligned 0 times 14169993 (72.95%) aligned exactly 1 time 3911603 (20.14%) aligned >1 times 93.08% overall alignment rate Time searching: 00:14:26 Overall time: 00:14:26 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 8 files... [bam_rmdupse_core] 5939620 / 18081596 = 0.3285 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 17:42:50: # Command line: callpeak -t SRX2202868.bam -f BAM -g 2.15e9 -n SRX2202868.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2202868.05 # format = BAM # ChIP-seq file = ['SRX2202868.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 17:42:50: # Command line: callpeak -t SRX2202868.bam -f BAM -g 2.15e9 -n SRX2202868.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2202868.20 # format = BAM # ChIP-seq file = ['SRX2202868.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 17:42:50: # Command line: callpeak -t SRX2202868.bam -f BAM -g 2.15e9 -n SRX2202868.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2202868.10 # format = BAM # ChIP-seq file = ['SRX2202868.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 17:42:50: #1 read tag files... INFO @ Fri, 10 Nov 2017 17:42:50: #1 read tag files... INFO @ Fri, 10 Nov 2017 17:42:50: #1 read tag files... INFO @ Fri, 10 Nov 2017 17:42:50: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 17:42:50: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 17:42:50: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 17:42:57: 1000000 INFO @ Fri, 10 Nov 2017 17:42:58: 1000000 INFO @ Fri, 10 Nov 2017 17:42:58: 1000000 INFO @ Fri, 10 Nov 2017 17:43:04: 2000000 INFO @ Fri, 10 Nov 2017 17:43:06: 2000000 INFO @ Fri, 10 Nov 2017 17:43:06: 2000000 INFO @ Fri, 10 Nov 2017 17:43:11: 3000000 INFO @ Fri, 10 Nov 2017 17:43:14: 3000000 INFO @ Fri, 10 Nov 2017 17:43:14: 3000000 INFO @ Fri, 10 Nov 2017 17:43:18: 4000000 INFO @ Fri, 10 Nov 2017 17:43:22: 4000000 INFO @ Fri, 10 Nov 2017 17:43:22: 4000000 INFO @ Fri, 10 Nov 2017 17:43:25: 5000000 INFO @ Fri, 10 Nov 2017 17:43:30: 5000000 INFO @ Fri, 10 Nov 2017 17:43:30: 5000000 INFO @ Fri, 10 Nov 2017 17:43:32: 6000000 INFO @ Fri, 10 Nov 2017 17:43:38: 6000000 INFO @ Fri, 10 Nov 2017 17:43:38: 6000000 INFO @ Fri, 10 Nov 2017 17:43:39: 7000000 INFO @ Fri, 10 Nov 2017 17:43:46: 7000000 INFO @ Fri, 10 Nov 2017 17:43:46: 7000000 INFO @ Fri, 10 Nov 2017 17:43:46: 8000000 INFO @ Fri, 10 Nov 2017 17:43:53: 9000000 INFO @ Fri, 10 Nov 2017 17:43:54: 8000000 INFO @ Fri, 10 Nov 2017 17:43:54: 8000000 INFO @ Fri, 10 Nov 2017 17:44:01: 10000000 INFO @ Fri, 10 Nov 2017 17:44:02: 9000000 INFO @ Fri, 10 Nov 2017 17:44:02: 9000000 INFO @ Fri, 10 Nov 2017 17:44:08: 11000000 INFO @ Fri, 10 Nov 2017 17:44:10: 10000000 INFO @ Fri, 10 Nov 2017 17:44:10: 10000000 INFO @ Fri, 10 Nov 2017 17:44:15: 12000000 INFO @ Fri, 10 Nov 2017 17:44:16: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 17:44:16: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 17:44:16: #1 total tags in treatment: 12141976 INFO @ Fri, 10 Nov 2017 17:44:16: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 17:44:16: #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 17:44:16: #1 tags after filtering in treatment: 12141801 INFO @ Fri, 10 Nov 2017 17:44:16: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 17:44:16: #1 finished! INFO @ Fri, 10 Nov 2017 17:44:16: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 17:44:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 17:44:18: 11000000 INFO @ Fri, 10 Nov 2017 17:44:18: 11000000 INFO @ Fri, 10 Nov 2017 17:44:19: #2 number of paired peaks: 48244 INFO @ Fri, 10 Nov 2017 17:44:19: start model_add_line... INFO @ Fri, 10 Nov 2017 17:44:19: start X-correlation... INFO @ Fri, 10 Nov 2017 17:44:19: end of X-cor INFO @ Fri, 10 Nov 2017 17:44:19: #2 finished! INFO @ Fri, 10 Nov 2017 17:44:19: #2 predicted fragment length is 157 bps INFO @ Fri, 10 Nov 2017 17:44:19: #2 alternative fragment length(s) may be 157 bps INFO @ Fri, 10 Nov 2017 17:44:19: #2.2 Generate R script for model : SRX2202868.05_model.r INFO @ Fri, 10 Nov 2017 17:44:19: #3 Call peaks... INFO @ Fri, 10 Nov 2017 17:44:19: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 17:44:26: 12000000 INFO @ Fri, 10 Nov 2017 17:44:26: 12000000 INFO @ Fri, 10 Nov 2017 17:44:27: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 17:44:27: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 17:44:27: #1 total tags in treatment: 12141976 INFO @ Fri, 10 Nov 2017 17:44:27: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 17:44:27: #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 17:44:27: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 17:44:27: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 17:44:27: #1 total tags in treatment: 12141976 INFO @ Fri, 10 Nov 2017 17:44:27: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 17:44:27: #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 17:44:28: #1 tags after filtering in treatment: 12141801 INFO @ Fri, 10 Nov 2017 17:44:28: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 17:44:28: #1 finished! INFO @ Fri, 10 Nov 2017 17:44:28: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 17:44:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 17:44:28: #1 tags after filtering in treatment: 12141801 INFO @ Fri, 10 Nov 2017 17:44:28: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 17:44:28: #1 finished! INFO @ Fri, 10 Nov 2017 17:44:28: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 17:44:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 17:44:30: #2 number of paired peaks: 48244 INFO @ Fri, 10 Nov 2017 17:44:30: start model_add_line... INFO @ Fri, 10 Nov 2017 17:44:31: start X-correlation... INFO @ Fri, 10 Nov 2017 17:44:31: end of X-cor INFO @ Fri, 10 Nov 2017 17:44:31: #2 finished! INFO @ Fri, 10 Nov 2017 17:44:31: #2 predicted fragment length is 157 bps INFO @ Fri, 10 Nov 2017 17:44:31: #2 alternative fragment length(s) may be 157 bps INFO @ Fri, 10 Nov 2017 17:44:31: #2.2 Generate R script for model : SRX2202868.10_model.r INFO @ Fri, 10 Nov 2017 17:44:31: #2 number of paired peaks: 48244 INFO @ Fri, 10 Nov 2017 17:44:31: start model_add_line... INFO @ Fri, 10 Nov 2017 17:44:31: #3 Call peaks... INFO @ Fri, 10 Nov 2017 17:44:31: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 17:44:31: start X-correlation... INFO @ Fri, 10 Nov 2017 17:44:31: end of X-cor INFO @ Fri, 10 Nov 2017 17:44:31: #2 finished! INFO @ Fri, 10 Nov 2017 17:44:31: #2 predicted fragment length is 157 bps INFO @ Fri, 10 Nov 2017 17:44:31: #2 alternative fragment length(s) may be 157 bps INFO @ Fri, 10 Nov 2017 17:44:31: #2.2 Generate R script for model : SRX2202868.20_model.r INFO @ Fri, 10 Nov 2017 17:44:31: #3 Call peaks... INFO @ Fri, 10 Nov 2017 17:44:31: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 17:44:50: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 17:45:02: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 17:45:02: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 17:45:08: #4 Write output xls file... SRX2202868.05_peaks.xls INFO @ Fri, 10 Nov 2017 17:45:08: #4 Write peak in narrowPeak format file... SRX2202868.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 17:45:08: #4 Write summits bed file... SRX2202868.05_summits.bed INFO @ Fri, 10 Nov 2017 17:45:08: Done! pass1 - making usageList (54 chroms): 2 millis pass2 - checking and writing primary data (5645 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 17:45:20: #4 Write output xls file... SRX2202868.20_peaks.xls INFO @ Fri, 10 Nov 2017 17:45:20: #4 Write peak in narrowPeak format file... SRX2202868.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 17:45:20: #4 Write summits bed file... SRX2202868.20_summits.bed INFO @ Fri, 10 Nov 2017 17:45:20: Done! pass1 - making usageList (24 chroms): 0 millis pass2 - checking and writing primary data (211 records, 4 fields): 43 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 17:45:21: #4 Write output xls file... SRX2202868.10_peaks.xls INFO @ Fri, 10 Nov 2017 17:45:21: #4 Write peak in narrowPeak format file... SRX2202868.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 17:45:21: #4 Write summits bed file... SRX2202868.10_summits.bed INFO @ Fri, 10 Nov 2017 17:45:21: Done! pass1 - making usageList (38 chroms): 1 millis pass2 - checking and writing primary data (919 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。