Job ID = 2003717 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 11,316,544 reads read : 11,316,544 reads written : 11,316,544 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1267405.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: 00:00:02 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:42 11316544 reads; of these: 11316544 (100.00%) were unpaired; of these: 873671 (7.72%) aligned 0 times 7465519 (65.97%) aligned exactly 1 time 2977354 (26.31%) aligned >1 times 92.28% overall alignment rate Time searching: 00:08:45 Overall time: 00:08:45 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] 9138197 / 10442873 = 0.8751 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 13:56:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX530451/SRX530451.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX530451/SRX530451.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX530451/SRX530451.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX530451/SRX530451.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 13:56:40: #1 read tag files... INFO @ Fri, 05 Jul 2019 13:56:40: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 13:56:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX530451/SRX530451.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX530451/SRX530451.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX530451/SRX530451.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX530451/SRX530451.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 13:56:41: #1 read tag files... INFO @ Fri, 05 Jul 2019 13:56:41: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 13:56:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX530451/SRX530451.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX530451/SRX530451.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX530451/SRX530451.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX530451/SRX530451.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 13:56:42: #1 read tag files... INFO @ Fri, 05 Jul 2019 13:56:42: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 13:56:48: 1000000 INFO @ Fri, 05 Jul 2019 13:56:49: 1000000 INFO @ Fri, 05 Jul 2019 13:56:50: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 13:56:50: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 13:56:50: #1 total tags in treatment: 1304676 INFO @ Fri, 05 Jul 2019 13:56:50: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 13:56:50: #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 13:56:51: #1 tags after filtering in treatment: 1304336 INFO @ Fri, 05 Jul 2019 13:56:51: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 13:56:51: #1 finished! INFO @ Fri, 05 Jul 2019 13:56:51: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 13:56:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 13:56:51: 1000000 INFO @ Fri, 05 Jul 2019 13:56:52: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 13:56:52: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 13:56:52: #1 total tags in treatment: 1304676 INFO @ Fri, 05 Jul 2019 13:56:52: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 13:56:52: #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 13:56:52: #1 tags after filtering in treatment: 1304336 INFO @ Fri, 05 Jul 2019 13:56:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 13:56:52: #1 finished! INFO @ Fri, 05 Jul 2019 13:56:52: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 13:56:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 13:56:53: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 13:56:53: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 13:56:53: #1 total tags in treatment: 1304676 INFO @ Fri, 05 Jul 2019 13:56:53: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 13:56:53: #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 13:56:54: #1 tags after filtering in treatment: 1304336 INFO @ Fri, 05 Jul 2019 13:56:54: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 13:56:54: #1 finished! INFO @ Fri, 05 Jul 2019 13:56:54: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 13:56:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 13:56:55: #2 number of paired peaks: 58215 INFO @ Fri, 05 Jul 2019 13:56:55: start model_add_line... INFO @ Fri, 05 Jul 2019 13:56:55: start X-correlation... INFO @ Fri, 05 Jul 2019 13:56:55: end of X-cor INFO @ Fri, 05 Jul 2019 13:56:55: #2 finished! INFO @ Fri, 05 Jul 2019 13:56:55: #2 predicted fragment length is 295 bps INFO @ Fri, 05 Jul 2019 13:56:55: #2 alternative fragment length(s) may be 295 bps INFO @ Fri, 05 Jul 2019 13:56:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX530451/SRX530451.05_model.r INFO @ Fri, 05 Jul 2019 13:56:55: #3 Call peaks... INFO @ Fri, 05 Jul 2019 13:56:55: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 13:56:56: #2 number of paired peaks: 58215 INFO @ Fri, 05 Jul 2019 13:56:56: start model_add_line... INFO @ Fri, 05 Jul 2019 13:56:56: start X-correlation... INFO @ Fri, 05 Jul 2019 13:56:56: end of X-cor INFO @ Fri, 05 Jul 2019 13:56:56: #2 finished! INFO @ Fri, 05 Jul 2019 13:56:56: #2 predicted fragment length is 295 bps INFO @ Fri, 05 Jul 2019 13:56:56: #2 alternative fragment length(s) may be 295 bps INFO @ Fri, 05 Jul 2019 13:56:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX530451/SRX530451.10_model.r INFO @ Fri, 05 Jul 2019 13:56:56: #3 Call peaks... INFO @ Fri, 05 Jul 2019 13:56:56: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 13:56:58: #2 number of paired peaks: 58215 INFO @ Fri, 05 Jul 2019 13:56:58: start model_add_line... INFO @ Fri, 05 Jul 2019 13:56:58: start X-correlation... INFO @ Fri, 05 Jul 2019 13:56:58: end of X-cor INFO @ Fri, 05 Jul 2019 13:56:58: #2 finished! INFO @ Fri, 05 Jul 2019 13:56:58: #2 predicted fragment length is 295 bps INFO @ Fri, 05 Jul 2019 13:56:58: #2 alternative fragment length(s) may be 295 bps INFO @ Fri, 05 Jul 2019 13:56:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX530451/SRX530451.20_model.r INFO @ Fri, 05 Jul 2019 13:56:58: #3 Call peaks... INFO @ Fri, 05 Jul 2019 13:56:58: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 13:57:00: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 13:57:01: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 13:57:02: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX530451/SRX530451.05_peaks.xls INFO @ Fri, 05 Jul 2019 13:57:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX530451/SRX530451.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 13:57:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX530451/SRX530451.05_summits.bed INFO @ Fri, 05 Jul 2019 13:57:02: Done! pass1 - making usageList (25 chroms): 2 millis pass2 - checking and writing primary data (229 records, 4 fields): 3 millis INFO @ Fri, 05 Jul 2019 13:57:03: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 13:57:03: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX530451/SRX530451.10_peaks.xls INFO @ Fri, 05 Jul 2019 13:57:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX530451/SRX530451.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 13:57:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX530451/SRX530451.10_summits.bed INFO @ Fri, 05 Jul 2019 13:57:03: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (113 records, 4 fields): 3 millis INFO @ Fri, 05 Jul 2019 13:57:05: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX530451/SRX530451.20_peaks.xls INFO @ Fri, 05 Jul 2019 13:57:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX530451/SRX530451.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 13:57:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX530451/SRX530451.20_summits.bed INFO @ Fri, 05 Jul 2019 13:57:05: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (37 records, 4 fields): 2 millis CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。