Job ID = 2589989 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 29,778,468 reads read : 29,778,468 reads written : 29,778,468 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1163641.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: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:22 29778468 reads; of these: 29778468 (100.00%) were unpaired; of these: 2516610 (8.45%) aligned 0 times 22256987 (74.74%) aligned exactly 1 time 5004871 (16.81%) aligned >1 times 91.55% overall alignment rate Time searching: 00:07:22 Overall time: 00:07:22 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 15826698 / 27261858 = 0.5805 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 @ Mon, 12 Aug 2019 19:11:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466575/SRX466575.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466575/SRX466575.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466575/SRX466575.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466575/SRX466575.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Mon, 12 Aug 2019 19:11:30: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:11:30: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:11:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466575/SRX466575.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466575/SRX466575.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466575/SRX466575.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466575/SRX466575.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Mon, 12 Aug 2019 19:11:31: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:11:31: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:11:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466575/SRX466575.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466575/SRX466575.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466575/SRX466575.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466575/SRX466575.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Mon, 12 Aug 2019 19:11:32: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:11:32: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:11:39: 1000000 INFO @ Mon, 12 Aug 2019 19:11:41: 1000000 INFO @ Mon, 12 Aug 2019 19:11:42: 1000000 INFO @ Mon, 12 Aug 2019 19:11:47: 2000000 INFO @ Mon, 12 Aug 2019 19:11:51: 2000000 INFO @ Mon, 12 Aug 2019 19:11:53: 2000000 INFO @ Mon, 12 Aug 2019 19:11:55: 3000000 INFO @ Mon, 12 Aug 2019 19:12:01: 3000000 INFO @ Mon, 12 Aug 2019 19:12:02: 4000000 INFO @ Mon, 12 Aug 2019 19:12:02: 3000000 INFO @ Mon, 12 Aug 2019 19:12:10: 5000000 INFO @ Mon, 12 Aug 2019 19:12:11: 4000000 INFO @ Mon, 12 Aug 2019 19:12:12: 4000000 INFO @ Mon, 12 Aug 2019 19:12:17: 6000000 INFO @ Mon, 12 Aug 2019 19:12:21: 5000000 INFO @ Mon, 12 Aug 2019 19:12:22: 5000000 INFO @ Mon, 12 Aug 2019 19:12:25: 7000000 INFO @ Mon, 12 Aug 2019 19:12:31: 6000000 INFO @ Mon, 12 Aug 2019 19:12:32: 6000000 INFO @ Mon, 12 Aug 2019 19:12:32: 8000000 INFO @ Mon, 12 Aug 2019 19:12:40: 9000000 INFO @ Mon, 12 Aug 2019 19:12:41: 7000000 INFO @ Mon, 12 Aug 2019 19:12:42: 7000000 INFO @ Mon, 12 Aug 2019 19:12:47: 10000000 INFO @ Mon, 12 Aug 2019 19:12:51: 8000000 INFO @ Mon, 12 Aug 2019 19:12:52: 8000000 INFO @ Mon, 12 Aug 2019 19:12:54: 11000000 INFO @ Mon, 12 Aug 2019 19:12:58: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:12:58: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:12:58: #1 total tags in treatment: 11435160 INFO @ Mon, 12 Aug 2019 19:12:58: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:12:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 19:12:58: #1 tags after filtering in treatment: 11435160 INFO @ Mon, 12 Aug 2019 19:12:58: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:12:58: #1 finished! INFO @ Mon, 12 Aug 2019 19:12:58: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:12:58: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:12:59: #2 number of paired peaks: 1606 INFO @ Mon, 12 Aug 2019 19:12:59: start model_add_line... INFO @ Mon, 12 Aug 2019 19:12:59: start X-correlation... INFO @ Mon, 12 Aug 2019 19:12:59: end of X-cor INFO @ Mon, 12 Aug 2019 19:12:59: #2 finished! INFO @ Mon, 12 Aug 2019 19:12:59: #2 predicted fragment length is 101 bps INFO @ Mon, 12 Aug 2019 19:12:59: #2 alternative fragment length(s) may be 2,101 bps INFO @ Mon, 12 Aug 2019 19:12:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466575/SRX466575.10_model.r INFO @ Mon, 12 Aug 2019 19:12:59: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:12:59: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:13:01: 9000000 INFO @ Mon, 12 Aug 2019 19:13:02: 9000000 INFO @ Mon, 12 Aug 2019 19:13:11: 10000000 INFO @ Mon, 12 Aug 2019 19:13:11: 10000000 INFO @ Mon, 12 Aug 2019 19:13:21: 11000000 INFO @ Mon, 12 Aug 2019 19:13:21: 11000000 INFO @ Mon, 12 Aug 2019 19:13:25: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:13:25: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:13:25: #1 total tags in treatment: 11435160 INFO @ Mon, 12 Aug 2019 19:13:25: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:13:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 19:13:25: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:13:25: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:13:25: #1 total tags in treatment: 11435160 INFO @ Mon, 12 Aug 2019 19:13:25: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:13:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 19:13:26: #1 tags after filtering in treatment: 11435160 INFO @ Mon, 12 Aug 2019 19:13:26: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:13:26: #1 finished! INFO @ Mon, 12 Aug 2019 19:13:26: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:13:26: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:13:26: #1 tags after filtering in treatment: 11435160 INFO @ Mon, 12 Aug 2019 19:13:26: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:13:26: #1 finished! INFO @ Mon, 12 Aug 2019 19:13:26: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:13:26: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:13:27: #2 number of paired peaks: 1606 INFO @ Mon, 12 Aug 2019 19:13:27: start model_add_line... INFO @ Mon, 12 Aug 2019 19:13:27: #2 number of paired peaks: 1606 INFO @ Mon, 12 Aug 2019 19:13:27: start model_add_line... INFO @ Mon, 12 Aug 2019 19:13:27: start X-correlation... INFO @ Mon, 12 Aug 2019 19:13:27: end of X-cor INFO @ Mon, 12 Aug 2019 19:13:27: #2 finished! INFO @ Mon, 12 Aug 2019 19:13:27: #2 predicted fragment length is 101 bps INFO @ Mon, 12 Aug 2019 19:13:27: #2 alternative fragment length(s) may be 2,101 bps INFO @ Mon, 12 Aug 2019 19:13:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466575/SRX466575.05_model.r INFO @ Mon, 12 Aug 2019 19:13:27: start X-correlation... INFO @ Mon, 12 Aug 2019 19:13:27: end of X-cor INFO @ Mon, 12 Aug 2019 19:13:27: #2 finished! INFO @ Mon, 12 Aug 2019 19:13:27: #2 predicted fragment length is 101 bps INFO @ Mon, 12 Aug 2019 19:13:27: #2 alternative fragment length(s) may be 2,101 bps INFO @ Mon, 12 Aug 2019 19:13:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466575/SRX466575.20_model.r INFO @ Mon, 12 Aug 2019 19:13:27: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:13:27: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:13:27: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:13:27: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:13:34: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:13:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466575/SRX466575.10_peaks.xls INFO @ Mon, 12 Aug 2019 19:13:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466575/SRX466575.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:13:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466575/SRX466575.10_summits.bed INFO @ Mon, 12 Aug 2019 19:13:48: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (1506 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:14:01: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:14:01: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:14:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466575/SRX466575.05_peaks.xls INFO @ Mon, 12 Aug 2019 19:14:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466575/SRX466575.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:14:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466575/SRX466575.05_summits.bed INFO @ Mon, 12 Aug 2019 19:14:16: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (2221 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:14:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466575/SRX466575.20_peaks.xls INFO @ Mon, 12 Aug 2019 19:14:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466575/SRX466575.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:14:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466575/SRX466575.20_summits.bed INFO @ Mon, 12 Aug 2019 19:14:16: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (929 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。