Job ID = 2589749 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 6,363,961 reads read : 6,363,961 reads written : 6,363,961 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR947355.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: 00:00:50 6363961 reads; of these: 6363961 (100.00%) were unpaired; of these: 2580469 (40.55%) aligned 0 times 3233172 (50.80%) aligned exactly 1 time 550320 (8.65%) aligned >1 times 59.45% overall alignment rate Time searching: 00:00:50 Overall time: 00:00:50 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] 685477 / 3783492 = 0.1812 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 18:23:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331124/SRX331124.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331124/SRX331124.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331124/SRX331124.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331124/SRX331124.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 18:23:59: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:23:59: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:24:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331124/SRX331124.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331124/SRX331124.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331124/SRX331124.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331124/SRX331124.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 18:24:00: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:24:00: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:24:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331124/SRX331124.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331124/SRX331124.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331124/SRX331124.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331124/SRX331124.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 18:24:01: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:24:01: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:24:06: 1000000 INFO @ Mon, 12 Aug 2019 18:24:07: 1000000 INFO @ Mon, 12 Aug 2019 18:24:08: 1000000 INFO @ Mon, 12 Aug 2019 18:24:14: 2000000 INFO @ Mon, 12 Aug 2019 18:24:14: 2000000 INFO @ Mon, 12 Aug 2019 18:24:15: 2000000 INFO @ Mon, 12 Aug 2019 18:24:21: 3000000 INFO @ Mon, 12 Aug 2019 18:24:21: 3000000 INFO @ Mon, 12 Aug 2019 18:24:22: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:24:22: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:24:22: #1 total tags in treatment: 3098015 INFO @ Mon, 12 Aug 2019 18:24:22: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:24:22: #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 18:24:22: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:24:22: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:24:22: #1 total tags in treatment: 3098015 INFO @ Mon, 12 Aug 2019 18:24:22: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:24:22: #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 18:24:22: #1 tags after filtering in treatment: 3098015 INFO @ Mon, 12 Aug 2019 18:24:22: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:24:22: #1 finished! INFO @ Mon, 12 Aug 2019 18:24:22: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:24:22: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:24:22: #1 tags after filtering in treatment: 3098015 INFO @ Mon, 12 Aug 2019 18:24:22: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:24:22: #1 finished! INFO @ Mon, 12 Aug 2019 18:24:22: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:24:22: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:24:22: 3000000 INFO @ Mon, 12 Aug 2019 18:24:22: #2 number of paired peaks: 921 WARNING @ Mon, 12 Aug 2019 18:24:22: Fewer paired peaks (921) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 921 pairs to build model! INFO @ Mon, 12 Aug 2019 18:24:22: start model_add_line... INFO @ Mon, 12 Aug 2019 18:24:22: #2 number of paired peaks: 921 WARNING @ Mon, 12 Aug 2019 18:24:22: Fewer paired peaks (921) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 921 pairs to build model! INFO @ Mon, 12 Aug 2019 18:24:22: start model_add_line... INFO @ Mon, 12 Aug 2019 18:24:22: start X-correlation... INFO @ Mon, 12 Aug 2019 18:24:22: end of X-cor INFO @ Mon, 12 Aug 2019 18:24:22: #2 finished! INFO @ Mon, 12 Aug 2019 18:24:22: #2 predicted fragment length is 153 bps INFO @ Mon, 12 Aug 2019 18:24:22: #2 alternative fragment length(s) may be 153 bps INFO @ Mon, 12 Aug 2019 18:24:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331124/SRX331124.05_model.r INFO @ Mon, 12 Aug 2019 18:24:22: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:24:22: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:24:22: start X-correlation... INFO @ Mon, 12 Aug 2019 18:24:22: end of X-cor INFO @ Mon, 12 Aug 2019 18:24:22: #2 finished! INFO @ Mon, 12 Aug 2019 18:24:22: #2 predicted fragment length is 153 bps INFO @ Mon, 12 Aug 2019 18:24:22: #2 alternative fragment length(s) may be 153 bps INFO @ Mon, 12 Aug 2019 18:24:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331124/SRX331124.20_model.r INFO @ Mon, 12 Aug 2019 18:24:22: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:24:22: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:24:23: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:24:23: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:24:23: #1 total tags in treatment: 3098015 INFO @ Mon, 12 Aug 2019 18:24:23: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:24:23: #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 18:24:23: #1 tags after filtering in treatment: 3098015 INFO @ Mon, 12 Aug 2019 18:24:23: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:24:23: #1 finished! INFO @ Mon, 12 Aug 2019 18:24:23: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:24:23: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:24:23: #2 number of paired peaks: 921 WARNING @ Mon, 12 Aug 2019 18:24:23: Fewer paired peaks (921) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 921 pairs to build model! INFO @ Mon, 12 Aug 2019 18:24:23: start model_add_line... INFO @ Mon, 12 Aug 2019 18:24:23: start X-correlation... INFO @ Mon, 12 Aug 2019 18:24:23: end of X-cor INFO @ Mon, 12 Aug 2019 18:24:23: #2 finished! INFO @ Mon, 12 Aug 2019 18:24:23: #2 predicted fragment length is 153 bps INFO @ Mon, 12 Aug 2019 18:24:23: #2 alternative fragment length(s) may be 153 bps INFO @ Mon, 12 Aug 2019 18:24:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331124/SRX331124.10_model.r INFO @ Mon, 12 Aug 2019 18:24:23: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:24:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:24:32: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:24:32: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:24:33: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:24:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331124/SRX331124.05_peaks.xls INFO @ Mon, 12 Aug 2019 18:24:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331124/SRX331124.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:24:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331124/SRX331124.20_peaks.xls INFO @ Mon, 12 Aug 2019 18:24:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331124/SRX331124.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:24:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331124/SRX331124.05_summits.bed INFO @ Mon, 12 Aug 2019 18:24:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331124/SRX331124.20_summits.bed INFO @ Mon, 12 Aug 2019 18:24:37: Done! INFO @ Mon, 12 Aug 2019 18:24:37: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (442 records, 4 fields): 3 millis CompletedMACS2peakCalling pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2226 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:24:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331124/SRX331124.10_peaks.xls INFO @ Mon, 12 Aug 2019 18:24:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331124/SRX331124.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:24:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331124/SRX331124.10_summits.bed INFO @ Mon, 12 Aug 2019 18:24:38: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1132 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。