Job ID = 2589994 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 19,796,325 reads read : 19,796,325 reads written : 19,796,325 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1163650.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: 00:05:11 19796325 reads; of these: 19796325 (100.00%) were unpaired; of these: 4872389 (24.61%) aligned 0 times 11636276 (58.78%) aligned exactly 1 time 3287660 (16.61%) aligned >1 times 75.39% overall alignment rate Time searching: 00:05:11 Overall time: 00:05:11 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 8 files... [bam_rmdupse_core] 9745157 / 14923936 = 0.6530 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 19:06:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466584/SRX466584.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466584/SRX466584.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466584/SRX466584.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466584/SRX466584.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 19:06:00: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:06:00: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:06:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466584/SRX466584.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466584/SRX466584.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466584/SRX466584.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466584/SRX466584.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 19:06:01: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:06:01: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:06:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466584/SRX466584.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466584/SRX466584.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466584/SRX466584.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466584/SRX466584.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 19:06:02: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:06:02: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:06:10: 1000000 INFO @ Mon, 12 Aug 2019 19:06:12: 1000000 INFO @ Mon, 12 Aug 2019 19:06:15: 1000000 INFO @ Mon, 12 Aug 2019 19:06:18: 2000000 INFO @ Mon, 12 Aug 2019 19:06:23: 2000000 INFO @ Mon, 12 Aug 2019 19:06:26: 2000000 INFO @ Mon, 12 Aug 2019 19:06:26: 3000000 INFO @ Mon, 12 Aug 2019 19:06:34: 4000000 INFO @ Mon, 12 Aug 2019 19:06:34: 3000000 INFO @ Mon, 12 Aug 2019 19:06:37: 3000000 INFO @ Mon, 12 Aug 2019 19:06:42: 5000000 INFO @ Mon, 12 Aug 2019 19:06:43: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:06:43: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:06:43: #1 total tags in treatment: 5178779 INFO @ Mon, 12 Aug 2019 19:06:43: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:06:43: #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 19:06:43: #1 tags after filtering in treatment: 5178779 INFO @ Mon, 12 Aug 2019 19:06:43: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:06:43: #1 finished! INFO @ Mon, 12 Aug 2019 19:06:43: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:06:43: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:06:44: #2 number of paired peaks: 2738 INFO @ Mon, 12 Aug 2019 19:06:44: start model_add_line... INFO @ Mon, 12 Aug 2019 19:06:44: start X-correlation... INFO @ Mon, 12 Aug 2019 19:06:44: end of X-cor INFO @ Mon, 12 Aug 2019 19:06:44: #2 finished! INFO @ Mon, 12 Aug 2019 19:06:44: #2 predicted fragment length is 158 bps INFO @ Mon, 12 Aug 2019 19:06:44: #2 alternative fragment length(s) may be 158 bps INFO @ Mon, 12 Aug 2019 19:06:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466584/SRX466584.05_model.r INFO @ Mon, 12 Aug 2019 19:06:44: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:06:44: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:06:45: 4000000 INFO @ Mon, 12 Aug 2019 19:06:48: 4000000 INFO @ Mon, 12 Aug 2019 19:06:56: 5000000 INFO @ Mon, 12 Aug 2019 19:06:58: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:06:58: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:06:58: #1 total tags in treatment: 5178779 INFO @ Mon, 12 Aug 2019 19:06:58: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:06:58: #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 19:06:58: #1 tags after filtering in treatment: 5178779 INFO @ Mon, 12 Aug 2019 19:06:58: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:06:58: #1 finished! INFO @ Mon, 12 Aug 2019 19:06:58: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:06:58: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:06:59: 5000000 INFO @ Mon, 12 Aug 2019 19:06:59: #2 number of paired peaks: 2738 INFO @ Mon, 12 Aug 2019 19:06:59: start model_add_line... INFO @ Mon, 12 Aug 2019 19:06:59: start X-correlation... INFO @ Mon, 12 Aug 2019 19:06:59: end of X-cor INFO @ Mon, 12 Aug 2019 19:06:59: #2 finished! INFO @ Mon, 12 Aug 2019 19:06:59: #2 predicted fragment length is 158 bps INFO @ Mon, 12 Aug 2019 19:06:59: #2 alternative fragment length(s) may be 158 bps INFO @ Mon, 12 Aug 2019 19:06:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466584/SRX466584.10_model.r INFO @ Mon, 12 Aug 2019 19:06:59: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:06:59: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:07:00: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:07:00: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:07:00: #1 total tags in treatment: 5178779 INFO @ Mon, 12 Aug 2019 19:07:00: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:07:00: #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 19:07:00: #1 tags after filtering in treatment: 5178779 INFO @ Mon, 12 Aug 2019 19:07:00: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:07:00: #1 finished! INFO @ Mon, 12 Aug 2019 19:07:00: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:07:00: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:07:01: #2 number of paired peaks: 2738 INFO @ Mon, 12 Aug 2019 19:07:01: start model_add_line... INFO @ Mon, 12 Aug 2019 19:07:01: start X-correlation... INFO @ Mon, 12 Aug 2019 19:07:01: end of X-cor INFO @ Mon, 12 Aug 2019 19:07:01: #2 finished! INFO @ Mon, 12 Aug 2019 19:07:01: #2 predicted fragment length is 158 bps INFO @ Mon, 12 Aug 2019 19:07:01: #2 alternative fragment length(s) may be 158 bps INFO @ Mon, 12 Aug 2019 19:07:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466584/SRX466584.20_model.r INFO @ Mon, 12 Aug 2019 19:07:01: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:07:01: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:07:02: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:07:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466584/SRX466584.05_peaks.xls INFO @ Mon, 12 Aug 2019 19:07:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466584/SRX466584.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:07:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466584/SRX466584.05_summits.bed INFO @ Mon, 12 Aug 2019 19:07:10: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (5241 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:07:18: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:07:20: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:07:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466584/SRX466584.10_peaks.xls INFO @ Mon, 12 Aug 2019 19:07:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466584/SRX466584.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:07:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466584/SRX466584.10_summits.bed INFO @ Mon, 12 Aug 2019 19:07:27: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (3952 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:07:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466584/SRX466584.20_peaks.xls INFO @ Mon, 12 Aug 2019 19:07:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466584/SRX466584.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:07:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466584/SRX466584.20_summits.bed INFO @ Mon, 12 Aug 2019 19:07:27: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (2668 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。