Job ID = 2640724 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 16,823,762 reads read : 16,823,762 reads written : 16,823,762 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1302418.sra.cache’: No such file or directory 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: 00:00:00 Multiseed full-index search: 00:07:28 16823762 reads; of these: 16823762 (100.00%) were unpaired; of these: 975289 (5.80%) aligned 0 times 12333509 (73.31%) aligned exactly 1 time 3514964 (20.89%) aligned >1 times 94.20% overall alignment rate Time searching: 00:07:30 Overall time: 00:07:30 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] 748047 / 15848473 = 0.0472 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 18:43:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX555168/SRX555168.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX555168/SRX555168.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX555168/SRX555168.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX555168/SRX555168.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 @ Sat, 24 Aug 2019 18:43:25: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:43:25: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:43:33: 1000000 INFO @ Sat, 24 Aug 2019 18:43:40: 2000000 INFO @ Sat, 24 Aug 2019 18:43:48: 3000000 INFO @ Sat, 24 Aug 2019 18:43:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX555168/SRX555168.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX555168/SRX555168.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX555168/SRX555168.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX555168/SRX555168.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 @ Sat, 24 Aug 2019 18:43:55: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:43:55: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:43:55: 4000000 INFO @ Sat, 24 Aug 2019 18:44:03: 5000000 INFO @ Sat, 24 Aug 2019 18:44:05: 1000000 INFO @ Sat, 24 Aug 2019 18:44:10: 6000000 INFO @ Sat, 24 Aug 2019 18:44:14: 2000000 INFO @ Sat, 24 Aug 2019 18:44:18: 7000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 18:44:24: 3000000 INFO @ Sat, 24 Aug 2019 18:44:25: 8000000 INFO @ Sat, 24 Aug 2019 18:44:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX555168/SRX555168.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX555168/SRX555168.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX555168/SRX555168.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX555168/SRX555168.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 @ Sat, 24 Aug 2019 18:44:25: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:44:25: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:44:32: 9000000 INFO @ Sat, 24 Aug 2019 18:44:34: 4000000 INFO @ Sat, 24 Aug 2019 18:44:36: 1000000 INFO @ Sat, 24 Aug 2019 18:44:39: 10000000 INFO @ Sat, 24 Aug 2019 18:44:44: 5000000 INFO @ Sat, 24 Aug 2019 18:44:47: 11000000 INFO @ Sat, 24 Aug 2019 18:44:47: 2000000 INFO @ Sat, 24 Aug 2019 18:44:54: 12000000 INFO @ Sat, 24 Aug 2019 18:44:55: 6000000 INFO @ Sat, 24 Aug 2019 18:44:58: 3000000 INFO @ Sat, 24 Aug 2019 18:45:01: 13000000 INFO @ Sat, 24 Aug 2019 18:45:06: 7000000 INFO @ Sat, 24 Aug 2019 18:45:09: 4000000 INFO @ Sat, 24 Aug 2019 18:45:09: 14000000 INFO @ Sat, 24 Aug 2019 18:45:16: 15000000 INFO @ Sat, 24 Aug 2019 18:45:16: 8000000 INFO @ Sat, 24 Aug 2019 18:45:17: #1 tag size is determined as 42 bps INFO @ Sat, 24 Aug 2019 18:45:17: #1 tag size = 42 INFO @ Sat, 24 Aug 2019 18:45:17: #1 total tags in treatment: 15100426 INFO @ Sat, 24 Aug 2019 18:45:17: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:45:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 18:45:17: #1 tags after filtering in treatment: 15100227 INFO @ Sat, 24 Aug 2019 18:45:17: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:45:17: #1 finished! INFO @ Sat, 24 Aug 2019 18:45:17: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:45:17: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:45:18: 5000000 INFO @ Sat, 24 Aug 2019 18:45:20: #2 number of paired peaks: 33959 INFO @ Sat, 24 Aug 2019 18:45:20: start model_add_line... INFO @ Sat, 24 Aug 2019 18:45:21: start X-correlation... INFO @ Sat, 24 Aug 2019 18:45:21: end of X-cor INFO @ Sat, 24 Aug 2019 18:45:21: #2 finished! INFO @ Sat, 24 Aug 2019 18:45:21: #2 predicted fragment length is 125 bps INFO @ Sat, 24 Aug 2019 18:45:21: #2 alternative fragment length(s) may be 125 bps INFO @ Sat, 24 Aug 2019 18:45:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX555168/SRX555168.05_model.r INFO @ Sat, 24 Aug 2019 18:45:21: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:45:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:45:27: 9000000 INFO @ Sat, 24 Aug 2019 18:45:28: 6000000 INFO @ Sat, 24 Aug 2019 18:45:37: 10000000 INFO @ Sat, 24 Aug 2019 18:45:39: 7000000 INFO @ Sat, 24 Aug 2019 18:45:48: 11000000 INFO @ Sat, 24 Aug 2019 18:45:49: 8000000 INFO @ Sat, 24 Aug 2019 18:45:58: 12000000 INFO @ Sat, 24 Aug 2019 18:45:59: 9000000 INFO @ Sat, 24 Aug 2019 18:46:08: 13000000 INFO @ Sat, 24 Aug 2019 18:46:09: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:46:10: 10000000 INFO @ Sat, 24 Aug 2019 18:46:18: 14000000 INFO @ Sat, 24 Aug 2019 18:46:20: 11000000 INFO @ Sat, 24 Aug 2019 18:46:29: 15000000 INFO @ Sat, 24 Aug 2019 18:46:30: #1 tag size is determined as 42 bps INFO @ Sat, 24 Aug 2019 18:46:30: #1 tag size = 42 INFO @ Sat, 24 Aug 2019 18:46:30: #1 total tags in treatment: 15100426 INFO @ Sat, 24 Aug 2019 18:46:30: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:46:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 18:46:30: #1 tags after filtering in treatment: 15100227 INFO @ Sat, 24 Aug 2019 18:46:30: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:46:30: #1 finished! INFO @ Sat, 24 Aug 2019 18:46:30: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:46:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:46:30: 12000000 INFO @ Sat, 24 Aug 2019 18:46:33: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX555168/SRX555168.05_peaks.xls INFO @ Sat, 24 Aug 2019 18:46:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX555168/SRX555168.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:46:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX555168/SRX555168.05_summits.bed INFO @ Sat, 24 Aug 2019 18:46:33: Done! INFO @ Sat, 24 Aug 2019 18:46:33: #2 number of paired peaks: 33959 INFO @ Sat, 24 Aug 2019 18:46:33: start model_add_line... pass1 - making usageList (57 chroms): 3 millis pass2 - checking and writing primary data (6677 records, 4 fields): 14 millis INFO @ Sat, 24 Aug 2019 18:46:33: start X-correlation... CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:46:33: end of X-cor INFO @ Sat, 24 Aug 2019 18:46:33: #2 finished! INFO @ Sat, 24 Aug 2019 18:46:33: #2 predicted fragment length is 125 bps INFO @ Sat, 24 Aug 2019 18:46:33: #2 alternative fragment length(s) may be 125 bps INFO @ Sat, 24 Aug 2019 18:46:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX555168/SRX555168.10_model.r INFO @ Sat, 24 Aug 2019 18:46:33: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:46:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:46:39: 13000000 INFO @ Sat, 24 Aug 2019 18:46:48: 14000000 INFO @ Sat, 24 Aug 2019 18:46:57: 15000000 INFO @ Sat, 24 Aug 2019 18:46:58: #1 tag size is determined as 42 bps INFO @ Sat, 24 Aug 2019 18:46:58: #1 tag size = 42 INFO @ Sat, 24 Aug 2019 18:46:58: #1 total tags in treatment: 15100426 INFO @ Sat, 24 Aug 2019 18:46:58: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:46:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 18:46:59: #1 tags after filtering in treatment: 15100227 INFO @ Sat, 24 Aug 2019 18:46:59: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:46:59: #1 finished! INFO @ Sat, 24 Aug 2019 18:46:59: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:46:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:47:02: #2 number of paired peaks: 33959 INFO @ Sat, 24 Aug 2019 18:47:02: start model_add_line... INFO @ Sat, 24 Aug 2019 18:47:02: start X-correlation... INFO @ Sat, 24 Aug 2019 18:47:02: end of X-cor INFO @ Sat, 24 Aug 2019 18:47:02: #2 finished! INFO @ Sat, 24 Aug 2019 18:47:02: #2 predicted fragment length is 125 bps INFO @ Sat, 24 Aug 2019 18:47:02: #2 alternative fragment length(s) may be 125 bps INFO @ Sat, 24 Aug 2019 18:47:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX555168/SRX555168.20_model.r INFO @ Sat, 24 Aug 2019 18:47:02: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:47:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:47:22: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:47:46: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX555168/SRX555168.10_peaks.xls INFO @ Sat, 24 Aug 2019 18:47:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX555168/SRX555168.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:47:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX555168/SRX555168.10_summits.bed INFO @ Sat, 24 Aug 2019 18:47:46: Done! pass1 - making usageList (42 chroms): 1 millis pass2 - checking and writing primary data (2038 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:47:50: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:48:15: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX555168/SRX555168.20_peaks.xls INFO @ Sat, 24 Aug 2019 18:48:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX555168/SRX555168.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:48:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX555168/SRX555168.20_summits.bed INFO @ Sat, 24 Aug 2019 18:48:15: Done! pass1 - making usageList (29 chroms): 2 millis pass2 - checking and writing primary data (558 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。