Job ID = 2002165 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 17,937,658 reads read : 17,937,658 reads written : 17,937,658 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR458090.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: 00:00:01 Multiseed full-index search: 00:07:28 17937658 reads; of these: 17937658 (100.00%) were unpaired; of these: 4323563 (24.10%) aligned 0 times 10713365 (59.73%) aligned exactly 1 time 2900730 (16.17%) aligned >1 times 75.90% overall alignment rate Time searching: 00:07:31 Overall time: 00:07:31 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_rmdupse_core] 2398762 / 13614095 = 0.1762 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, 05 Jul 2019 10:56:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX190368/ERX190368.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX190368/ERX190368.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX190368/ERX190368.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX190368/ERX190368.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, 05 Jul 2019 10:56:18: #1 read tag files... INFO @ Fri, 05 Jul 2019 10:56:18: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 10:56:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX190368/ERX190368.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX190368/ERX190368.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX190368/ERX190368.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX190368/ERX190368.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, 05 Jul 2019 10:56:18: #1 read tag files... INFO @ Fri, 05 Jul 2019 10:56:18: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 10:56:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX190368/ERX190368.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX190368/ERX190368.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX190368/ERX190368.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX190368/ERX190368.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, 05 Jul 2019 10:56:19: #1 read tag files... INFO @ Fri, 05 Jul 2019 10:56:19: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 10:56:25: 1000000 INFO @ Fri, 05 Jul 2019 10:56:26: 1000000 INFO @ Fri, 05 Jul 2019 10:56:26: 1000000 INFO @ Fri, 05 Jul 2019 10:56:32: 2000000 INFO @ Fri, 05 Jul 2019 10:56:33: 2000000 INFO @ Fri, 05 Jul 2019 10:56:34: 2000000 INFO @ Fri, 05 Jul 2019 10:56:39: 3000000 INFO @ Fri, 05 Jul 2019 10:56:40: 3000000 INFO @ Fri, 05 Jul 2019 10:56:42: 3000000 INFO @ Fri, 05 Jul 2019 10:56:46: 4000000 INFO @ Fri, 05 Jul 2019 10:56:47: 4000000 INFO @ Fri, 05 Jul 2019 10:56:50: 4000000 INFO @ Fri, 05 Jul 2019 10:56:52: 5000000 INFO @ Fri, 05 Jul 2019 10:56:54: 5000000 INFO @ Fri, 05 Jul 2019 10:56:57: 5000000 INFO @ Fri, 05 Jul 2019 10:56:59: 6000000 INFO @ Fri, 05 Jul 2019 10:57:01: 6000000 INFO @ Fri, 05 Jul 2019 10:57:05: 6000000 INFO @ Fri, 05 Jul 2019 10:57:06: 7000000 INFO @ Fri, 05 Jul 2019 10:57:08: 7000000 INFO @ Fri, 05 Jul 2019 10:57:12: 7000000 INFO @ Fri, 05 Jul 2019 10:57:13: 8000000 INFO @ Fri, 05 Jul 2019 10:57:15: 8000000 INFO @ Fri, 05 Jul 2019 10:57:19: 9000000 INFO @ Fri, 05 Jul 2019 10:57:20: 8000000 INFO @ Fri, 05 Jul 2019 10:57:21: 9000000 INFO @ Fri, 05 Jul 2019 10:57:26: 10000000 INFO @ Fri, 05 Jul 2019 10:57:28: 9000000 INFO @ Fri, 05 Jul 2019 10:57:28: 10000000 INFO @ Fri, 05 Jul 2019 10:57:33: 11000000 INFO @ Fri, 05 Jul 2019 10:57:35: #1 tag size is determined as 42 bps INFO @ Fri, 05 Jul 2019 10:57:35: #1 tag size = 42 INFO @ Fri, 05 Jul 2019 10:57:35: #1 total tags in treatment: 11215333 INFO @ Fri, 05 Jul 2019 10:57:35: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 10:57:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 10:57:35: #1 tags after filtering in treatment: 11215093 INFO @ Fri, 05 Jul 2019 10:57:35: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 10:57:35: #1 finished! INFO @ Fri, 05 Jul 2019 10:57:35: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 10:57:35: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 10:57:35: 11000000 INFO @ Fri, 05 Jul 2019 10:57:35: 10000000 INFO @ Fri, 05 Jul 2019 10:57:37: #1 tag size is determined as 42 bps INFO @ Fri, 05 Jul 2019 10:57:37: #1 tag size = 42 INFO @ Fri, 05 Jul 2019 10:57:37: #1 total tags in treatment: 11215333 INFO @ Fri, 05 Jul 2019 10:57:37: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 10:57:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 10:57:37: #1 tags after filtering in treatment: 11215093 INFO @ Fri, 05 Jul 2019 10:57:37: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 10:57:37: #1 finished! INFO @ Fri, 05 Jul 2019 10:57:37: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 10:57:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 10:57:38: #2 number of paired peaks: 59427 INFO @ Fri, 05 Jul 2019 10:57:38: start model_add_line... INFO @ Fri, 05 Jul 2019 10:57:38: start X-correlation... INFO @ Fri, 05 Jul 2019 10:57:39: end of X-cor INFO @ Fri, 05 Jul 2019 10:57:39: #2 finished! INFO @ Fri, 05 Jul 2019 10:57:39: #2 predicted fragment length is 131 bps INFO @ Fri, 05 Jul 2019 10:57:39: #2 alternative fragment length(s) may be 131 bps INFO @ Fri, 05 Jul 2019 10:57:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX190368/ERX190368.05_model.r INFO @ Fri, 05 Jul 2019 10:57:39: #3 Call peaks... INFO @ Fri, 05 Jul 2019 10:57:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 10:57:40: #2 number of paired peaks: 59427 INFO @ Fri, 05 Jul 2019 10:57:40: start model_add_line... INFO @ Fri, 05 Jul 2019 10:57:41: start X-correlation... INFO @ Fri, 05 Jul 2019 10:57:41: end of X-cor INFO @ Fri, 05 Jul 2019 10:57:41: #2 finished! INFO @ Fri, 05 Jul 2019 10:57:41: #2 predicted fragment length is 131 bps INFO @ Fri, 05 Jul 2019 10:57:41: #2 alternative fragment length(s) may be 131 bps INFO @ Fri, 05 Jul 2019 10:57:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX190368/ERX190368.20_model.r INFO @ Fri, 05 Jul 2019 10:57:41: #3 Call peaks... INFO @ Fri, 05 Jul 2019 10:57:41: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 10:57:43: 11000000 INFO @ Fri, 05 Jul 2019 10:57:45: #1 tag size is determined as 42 bps INFO @ Fri, 05 Jul 2019 10:57:45: #1 tag size = 42 INFO @ Fri, 05 Jul 2019 10:57:45: #1 total tags in treatment: 11215333 INFO @ Fri, 05 Jul 2019 10:57:45: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 10:57:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 10:57:45: #1 tags after filtering in treatment: 11215093 INFO @ Fri, 05 Jul 2019 10:57:45: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 10:57:45: #1 finished! INFO @ Fri, 05 Jul 2019 10:57:45: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 10:57:45: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 10:57:49: #2 number of paired peaks: 59427 INFO @ Fri, 05 Jul 2019 10:57:49: start model_add_line... INFO @ Fri, 05 Jul 2019 10:57:49: start X-correlation... INFO @ Fri, 05 Jul 2019 10:57:49: end of X-cor INFO @ Fri, 05 Jul 2019 10:57:49: #2 finished! INFO @ Fri, 05 Jul 2019 10:57:49: #2 predicted fragment length is 131 bps INFO @ Fri, 05 Jul 2019 10:57:49: #2 alternative fragment length(s) may be 131 bps INFO @ Fri, 05 Jul 2019 10:57:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX190368/ERX190368.10_model.r INFO @ Fri, 05 Jul 2019 10:57:49: #3 Call peaks... INFO @ Fri, 05 Jul 2019 10:57:49: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 10:58:16: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 10:58:17: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 10:58:26: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 10:58:35: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX190368/ERX190368.05_peaks.xls INFO @ Fri, 05 Jul 2019 10:58:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX190368/ERX190368.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 10:58:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX190368/ERX190368.05_summits.bed INFO @ Fri, 05 Jul 2019 10:58:36: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX190368/ERX190368.20_peaks.xls INFO @ Fri, 05 Jul 2019 10:58:36: Done! INFO @ Fri, 05 Jul 2019 10:58:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX190368/ERX190368.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 10:58:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX190368/ERX190368.20_summits.bed INFO @ Fri, 05 Jul 2019 10:58:36: Done! pass1 - making usageList (79 chroms): 7 millis pass1 - making usageList (137 chroms): 13 millis pass2 - checking and writing primary data (16162 records, 4 fields): 32 millis pass2 - checking and writing primary data (41653 records, 4 fields): 62 millis CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 10:58:46: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX190368/ERX190368.10_peaks.xls INFO @ Fri, 05 Jul 2019 10:58:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX190368/ERX190368.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 10:58:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX190368/ERX190368.10_summits.bed INFO @ Fri, 05 Jul 2019 10:58:46: Done! pass1 - making usageList (112 chroms): 7 millis pass2 - checking and writing primary data (27885 records, 4 fields): 321 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。