Job ID = 2589919 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 6,899,874 reads read : 6,899,874 reads written : 6,899,874 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR947563.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: 00:01:05 6899874 reads; of these: 6899874 (100.00%) were unpaired; of these: 761235 (11.03%) aligned 0 times 5150891 (74.65%) aligned exactly 1 time 987748 (14.32%) aligned >1 times 88.97% overall alignment rate Time searching: 00:01:05 Overall time: 00:01:05 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_rmdupse_core] 996956 / 6138639 = 0.1624 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 18:47:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331326/SRX331326.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331326/SRX331326.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331326/SRX331326.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331326/SRX331326.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 18:47:56: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:47:56: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:47:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331326/SRX331326.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331326/SRX331326.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331326/SRX331326.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331326/SRX331326.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 18:47:57: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:47:57: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:47:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331326/SRX331326.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331326/SRX331326.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331326/SRX331326.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331326/SRX331326.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 18:47:58: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:47:58: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:48:03: 1000000 INFO @ Mon, 12 Aug 2019 18:48:05: 1000000 INFO @ Mon, 12 Aug 2019 18:48:06: 1000000 INFO @ Mon, 12 Aug 2019 18:48:10: 2000000 INFO @ Mon, 12 Aug 2019 18:48:12: 2000000 INFO @ Mon, 12 Aug 2019 18:48:13: 2000000 INFO @ Mon, 12 Aug 2019 18:48:17: 3000000 INFO @ Mon, 12 Aug 2019 18:48:20: 3000000 INFO @ Mon, 12 Aug 2019 18:48:21: 3000000 INFO @ Mon, 12 Aug 2019 18:48:24: 4000000 INFO @ Mon, 12 Aug 2019 18:48:28: 4000000 INFO @ Mon, 12 Aug 2019 18:48:29: 4000000 INFO @ Mon, 12 Aug 2019 18:48:30: 5000000 INFO @ Mon, 12 Aug 2019 18:48:31: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:48:31: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:48:31: #1 total tags in treatment: 5141683 INFO @ Mon, 12 Aug 2019 18:48:31: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:48:31: #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 18:48:31: #1 tags after filtering in treatment: 5141683 INFO @ Mon, 12 Aug 2019 18:48:31: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:48:31: #1 finished! INFO @ Mon, 12 Aug 2019 18:48:31: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:48:31: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:48:32: #2 number of paired peaks: 812 WARNING @ Mon, 12 Aug 2019 18:48:32: Fewer paired peaks (812) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 812 pairs to build model! INFO @ Mon, 12 Aug 2019 18:48:32: start model_add_line... INFO @ Mon, 12 Aug 2019 18:48:32: start X-correlation... INFO @ Mon, 12 Aug 2019 18:48:32: end of X-cor INFO @ Mon, 12 Aug 2019 18:48:32: #2 finished! INFO @ Mon, 12 Aug 2019 18:48:32: #2 predicted fragment length is 161 bps INFO @ Mon, 12 Aug 2019 18:48:32: #2 alternative fragment length(s) may be 161 bps INFO @ Mon, 12 Aug 2019 18:48:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331326/SRX331326.05_model.r INFO @ Mon, 12 Aug 2019 18:48:32: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:48:32: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:48:35: 5000000 INFO @ Mon, 12 Aug 2019 18:48:36: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:48:36: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:48:36: #1 total tags in treatment: 5141683 INFO @ Mon, 12 Aug 2019 18:48:36: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:48:36: #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 18:48:36: 5000000 INFO @ Mon, 12 Aug 2019 18:48:36: #1 tags after filtering in treatment: 5141683 INFO @ Mon, 12 Aug 2019 18:48:36: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:48:36: #1 finished! INFO @ Mon, 12 Aug 2019 18:48:36: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:48:36: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:48:37: #2 number of paired peaks: 812 WARNING @ Mon, 12 Aug 2019 18:48:37: Fewer paired peaks (812) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 812 pairs to build model! INFO @ Mon, 12 Aug 2019 18:48:37: start model_add_line... INFO @ Mon, 12 Aug 2019 18:48:37: start X-correlation... INFO @ Mon, 12 Aug 2019 18:48:37: end of X-cor INFO @ Mon, 12 Aug 2019 18:48:37: #2 finished! INFO @ Mon, 12 Aug 2019 18:48:37: #2 predicted fragment length is 161 bps INFO @ Mon, 12 Aug 2019 18:48:37: #2 alternative fragment length(s) may be 161 bps INFO @ Mon, 12 Aug 2019 18:48:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331326/SRX331326.10_model.r INFO @ Mon, 12 Aug 2019 18:48:37: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:48:37: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:48:37: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:48:37: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:48:37: #1 total tags in treatment: 5141683 INFO @ Mon, 12 Aug 2019 18:48:37: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:48:37: #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 18:48:37: #1 tags after filtering in treatment: 5141683 INFO @ Mon, 12 Aug 2019 18:48:37: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:48:37: #1 finished! INFO @ Mon, 12 Aug 2019 18:48:37: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:48:37: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:48:38: #2 number of paired peaks: 812 WARNING @ Mon, 12 Aug 2019 18:48:38: Fewer paired peaks (812) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 812 pairs to build model! INFO @ Mon, 12 Aug 2019 18:48:38: start model_add_line... INFO @ Mon, 12 Aug 2019 18:48:38: start X-correlation... INFO @ Mon, 12 Aug 2019 18:48:38: end of X-cor INFO @ Mon, 12 Aug 2019 18:48:38: #2 finished! INFO @ Mon, 12 Aug 2019 18:48:38: #2 predicted fragment length is 161 bps INFO @ Mon, 12 Aug 2019 18:48:38: #2 alternative fragment length(s) may be 161 bps INFO @ Mon, 12 Aug 2019 18:48:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331326/SRX331326.20_model.r INFO @ Mon, 12 Aug 2019 18:48:38: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:48:38: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:48:48: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:48:53: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:48:54: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:48:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331326/SRX331326.05_peaks.xls INFO @ Mon, 12 Aug 2019 18:48:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331326/SRX331326.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:48:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331326/SRX331326.05_summits.bed INFO @ Mon, 12 Aug 2019 18:48:55: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (3662 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:49:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331326/SRX331326.10_peaks.xls INFO @ Mon, 12 Aug 2019 18:49:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331326/SRX331326.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:49:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331326/SRX331326.10_summits.bed INFO @ Mon, 12 Aug 2019 18:49:00: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (2263 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:49:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331326/SRX331326.20_peaks.xls INFO @ Mon, 12 Aug 2019 18:49:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331326/SRX331326.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:49:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331326/SRX331326.20_summits.bed INFO @ Mon, 12 Aug 2019 18:49:01: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1153 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。