Job ID = 2002179 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/ERR235755.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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:02 17937658 reads; of these: 17937658 (100.00%) were unpaired; of these: 4323537 (24.10%) aligned 0 times 10713218 (59.72%) aligned exactly 1 time 2900903 (16.17%) aligned >1 times 75.90% overall alignment rate Time searching: 00:08:03 Overall time: 00:08:03 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] 2399155 / 13614121 = 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 11:06:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX210260/ERX210260.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX210260/ERX210260.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX210260/ERX210260.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX210260/ERX210260.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 11:06:18: #1 read tag files... INFO @ Fri, 05 Jul 2019 11:06:18: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 11:06:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX210260/ERX210260.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX210260/ERX210260.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX210260/ERX210260.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX210260/ERX210260.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 11:06:19: #1 read tag files... INFO @ Fri, 05 Jul 2019 11:06:19: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 11:06:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX210260/ERX210260.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX210260/ERX210260.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX210260/ERX210260.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX210260/ERX210260.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 11:06:20: #1 read tag files... INFO @ Fri, 05 Jul 2019 11:06:20: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 11:06:26: 1000000 INFO @ Fri, 05 Jul 2019 11:06:28: 1000000 INFO @ Fri, 05 Jul 2019 11:06:28: 1000000 INFO @ Fri, 05 Jul 2019 11:06:33: 2000000 INFO @ Fri, 05 Jul 2019 11:06:35: 2000000 INFO @ Fri, 05 Jul 2019 11:06:36: 2000000 INFO @ Fri, 05 Jul 2019 11:06:40: 3000000 INFO @ Fri, 05 Jul 2019 11:06:42: 3000000 INFO @ Fri, 05 Jul 2019 11:06:44: 3000000 INFO @ Fri, 05 Jul 2019 11:06:47: 4000000 INFO @ Fri, 05 Jul 2019 11:06:48: 4000000 INFO @ Fri, 05 Jul 2019 11:06:52: 4000000 INFO @ Fri, 05 Jul 2019 11:06:54: 5000000 INFO @ Fri, 05 Jul 2019 11:06:55: 5000000 INFO @ Fri, 05 Jul 2019 11:07:00: 5000000 INFO @ Fri, 05 Jul 2019 11:07:01: 6000000 INFO @ Fri, 05 Jul 2019 11:07:01: 6000000 INFO @ Fri, 05 Jul 2019 11:07:08: 7000000 INFO @ Fri, 05 Jul 2019 11:07:08: 7000000 INFO @ Fri, 05 Jul 2019 11:07:08: 6000000 INFO @ Fri, 05 Jul 2019 11:07:14: 8000000 INFO @ Fri, 05 Jul 2019 11:07:15: 8000000 INFO @ Fri, 05 Jul 2019 11:07:16: 7000000 INFO @ Fri, 05 Jul 2019 11:07:21: 9000000 INFO @ Fri, 05 Jul 2019 11:07:22: 9000000 INFO @ Fri, 05 Jul 2019 11:07:24: 8000000 INFO @ Fri, 05 Jul 2019 11:07:27: 10000000 INFO @ Fri, 05 Jul 2019 11:07:28: 10000000 INFO @ Fri, 05 Jul 2019 11:07:32: 9000000 INFO @ Fri, 05 Jul 2019 11:07:34: 11000000 INFO @ Fri, 05 Jul 2019 11:07:36: 11000000 INFO @ Fri, 05 Jul 2019 11:07:36: #1 tag size is determined as 42 bps INFO @ Fri, 05 Jul 2019 11:07:36: #1 tag size = 42 INFO @ Fri, 05 Jul 2019 11:07:36: #1 total tags in treatment: 11214966 INFO @ Fri, 05 Jul 2019 11:07:36: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 11:07:36: #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 11:07:36: #1 tags after filtering in treatment: 11214743 INFO @ Fri, 05 Jul 2019 11:07:36: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 11:07:36: #1 finished! INFO @ Fri, 05 Jul 2019 11:07:36: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 11:07:36: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 11:07:37: #1 tag size is determined as 42 bps INFO @ Fri, 05 Jul 2019 11:07:37: #1 tag size = 42 INFO @ Fri, 05 Jul 2019 11:07:37: #1 total tags in treatment: 11214966 INFO @ Fri, 05 Jul 2019 11:07:37: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 11:07:37: #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 11:07:38: #1 tags after filtering in treatment: 11214743 INFO @ Fri, 05 Jul 2019 11:07:38: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 11:07:38: #1 finished! INFO @ Fri, 05 Jul 2019 11:07:38: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 11:07:38: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 11:07:39: #2 number of paired peaks: 59405 INFO @ Fri, 05 Jul 2019 11:07:39: start model_add_line... INFO @ Fri, 05 Jul 2019 11:07:39: start X-correlation... INFO @ Fri, 05 Jul 2019 11:07:39: end of X-cor INFO @ Fri, 05 Jul 2019 11:07:39: #2 finished! INFO @ Fri, 05 Jul 2019 11:07:39: #2 predicted fragment length is 132 bps INFO @ Fri, 05 Jul 2019 11:07:39: #2 alternative fragment length(s) may be 132 bps INFO @ Fri, 05 Jul 2019 11:07:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX210260/ERX210260.20_model.r INFO @ Fri, 05 Jul 2019 11:07:39: #3 Call peaks... INFO @ Fri, 05 Jul 2019 11:07:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 11:07:40: 10000000 INFO @ Fri, 05 Jul 2019 11:07:41: #2 number of paired peaks: 59405 INFO @ Fri, 05 Jul 2019 11:07:43: start model_add_line... INFO @ Fri, 05 Jul 2019 11:07:44: start X-correlation... INFO @ Fri, 05 Jul 2019 11:07:44: end of X-cor INFO @ Fri, 05 Jul 2019 11:07:44: #2 finished! INFO @ Fri, 05 Jul 2019 11:07:44: #2 predicted fragment length is 132 bps INFO @ Fri, 05 Jul 2019 11:07:44: #2 alternative fragment length(s) may be 132 bps INFO @ Fri, 05 Jul 2019 11:07:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX210260/ERX210260.05_model.r INFO @ Fri, 05 Jul 2019 11:07:44: #3 Call peaks... INFO @ Fri, 05 Jul 2019 11:07:44: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 11:07:52: 11000000 INFO @ Fri, 05 Jul 2019 11:07:53: #1 tag size is determined as 42 bps INFO @ Fri, 05 Jul 2019 11:07:53: #1 tag size = 42 INFO @ Fri, 05 Jul 2019 11:07:53: #1 total tags in treatment: 11214966 INFO @ Fri, 05 Jul 2019 11:07:53: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 11:07:53: #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 11:07:54: #1 tags after filtering in treatment: 11214743 INFO @ Fri, 05 Jul 2019 11:07:54: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 11:07:54: #1 finished! INFO @ Fri, 05 Jul 2019 11:07:54: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 11:07:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 11:07:57: #2 number of paired peaks: 59405 INFO @ Fri, 05 Jul 2019 11:07:57: start model_add_line... INFO @ Fri, 05 Jul 2019 11:07:57: start X-correlation... INFO @ Fri, 05 Jul 2019 11:07:57: end of X-cor INFO @ Fri, 05 Jul 2019 11:07:57: #2 finished! INFO @ Fri, 05 Jul 2019 11:07:57: #2 predicted fragment length is 132 bps INFO @ Fri, 05 Jul 2019 11:07:57: #2 alternative fragment length(s) may be 132 bps INFO @ Fri, 05 Jul 2019 11:07:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX210260/ERX210260.10_model.r INFO @ Fri, 05 Jul 2019 11:07:57: #3 Call peaks... INFO @ Fri, 05 Jul 2019 11:07:57: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 11:08:16: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 11:08:20: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 11:08:34: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX210260/ERX210260.20_peaks.xls INFO @ Fri, 05 Jul 2019 11:08:35: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 11:08:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX210260/ERX210260.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 11:08:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX210260/ERX210260.20_summits.bed INFO @ Fri, 05 Jul 2019 11:08:35: Done! pass1 - making usageList (80 chroms): 8 millis pass2 - checking and writing primary data (16128 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 11:08:39: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX210260/ERX210260.05_peaks.xls INFO @ Fri, 05 Jul 2019 11:08:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX210260/ERX210260.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 11:08:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX210260/ERX210260.05_summits.bed INFO @ Fri, 05 Jul 2019 11:08:40: Done! pass1 - making usageList (141 chroms): 10 millis pass2 - checking and writing primary data (41679 records, 4 fields): 57 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 11:08:54: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX210260/ERX210260.10_peaks.xls INFO @ Fri, 05 Jul 2019 11:08:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX210260/ERX210260.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 11:08:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX210260/ERX210260.10_summits.bed INFO @ Fri, 05 Jul 2019 11:08:55: Done! pass1 - making usageList (117 chroms): 10 millis pass2 - checking and writing primary data (27856 records, 4 fields): 39 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。