Job ID = 2589900 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 7,603,807 reads read : 7,603,807 reads written : 7,603,807 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR947541.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: 00:01:36 7603807 reads; of these: 7603807 (100.00%) were unpaired; of these: 827657 (10.88%) aligned 0 times 5492694 (72.24%) aligned exactly 1 time 1283456 (16.88%) aligned >1 times 89.12% overall alignment rate Time searching: 00:01:36 Overall time: 00:01:36 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] 1068793 / 6776150 = 0.1577 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 18:45:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331304/SRX331304.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331304/SRX331304.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331304/SRX331304.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331304/SRX331304.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 18:45:53: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:45:53: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:45:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331304/SRX331304.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331304/SRX331304.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331304/SRX331304.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331304/SRX331304.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 18:45:54: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:45:54: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:45:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331304/SRX331304.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331304/SRX331304.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331304/SRX331304.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331304/SRX331304.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 18:45:55: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:45:55: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:46:00: 1000000 INFO @ Mon, 12 Aug 2019 18:46:01: 1000000 INFO @ Mon, 12 Aug 2019 18:46:02: 1000000 INFO @ Mon, 12 Aug 2019 18:46:07: 2000000 INFO @ Mon, 12 Aug 2019 18:46:08: 2000000 INFO @ Mon, 12 Aug 2019 18:46:09: 2000000 INFO @ Mon, 12 Aug 2019 18:46:13: 3000000 INFO @ Mon, 12 Aug 2019 18:46:15: 3000000 INFO @ Mon, 12 Aug 2019 18:46:15: 3000000 INFO @ Mon, 12 Aug 2019 18:46:20: 4000000 INFO @ Mon, 12 Aug 2019 18:46:21: 4000000 INFO @ Mon, 12 Aug 2019 18:46:22: 4000000 INFO @ Mon, 12 Aug 2019 18:46:27: 5000000 INFO @ Mon, 12 Aug 2019 18:46:28: 5000000 INFO @ Mon, 12 Aug 2019 18:46:29: 5000000 INFO @ Mon, 12 Aug 2019 18:46:32: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:46:32: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:46:32: #1 total tags in treatment: 5707357 INFO @ Mon, 12 Aug 2019 18:46:32: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:46:32: #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 18:46:32: #1 tags after filtering in treatment: 5707357 INFO @ Mon, 12 Aug 2019 18:46:32: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:46:32: #1 finished! INFO @ Mon, 12 Aug 2019 18:46:32: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:46:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:46:32: #2 number of paired peaks: 608 WARNING @ Mon, 12 Aug 2019 18:46:32: Fewer paired peaks (608) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 608 pairs to build model! INFO @ Mon, 12 Aug 2019 18:46:32: start model_add_line... INFO @ Mon, 12 Aug 2019 18:46:33: start X-correlation... INFO @ Mon, 12 Aug 2019 18:46:33: end of X-cor INFO @ Mon, 12 Aug 2019 18:46:33: #2 finished! INFO @ Mon, 12 Aug 2019 18:46:33: #2 predicted fragment length is 100 bps INFO @ Mon, 12 Aug 2019 18:46:33: #2 alternative fragment length(s) may be 100 bps INFO @ Mon, 12 Aug 2019 18:46:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331304/SRX331304.05_model.r INFO @ Mon, 12 Aug 2019 18:46:33: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:46:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:46:33: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:46:33: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:46:33: #1 total tags in treatment: 5707357 INFO @ Mon, 12 Aug 2019 18:46:33: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:46:33: #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 18:46:33: #1 tags after filtering in treatment: 5707357 INFO @ Mon, 12 Aug 2019 18:46:33: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:46:33: #1 finished! INFO @ Mon, 12 Aug 2019 18:46:33: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:46:33: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:46:34: #2 number of paired peaks: 608 WARNING @ Mon, 12 Aug 2019 18:46:34: Fewer paired peaks (608) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 608 pairs to build model! INFO @ Mon, 12 Aug 2019 18:46:34: start model_add_line... INFO @ Mon, 12 Aug 2019 18:46:34: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:46:34: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:46:34: #1 total tags in treatment: 5707357 INFO @ Mon, 12 Aug 2019 18:46:34: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:46:34: #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 18:46:34: start X-correlation... INFO @ Mon, 12 Aug 2019 18:46:34: end of X-cor INFO @ Mon, 12 Aug 2019 18:46:34: #2 finished! INFO @ Mon, 12 Aug 2019 18:46:34: #2 predicted fragment length is 100 bps INFO @ Mon, 12 Aug 2019 18:46:34: #2 alternative fragment length(s) may be 100 bps INFO @ Mon, 12 Aug 2019 18:46:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331304/SRX331304.10_model.r INFO @ Mon, 12 Aug 2019 18:46:34: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:46:34: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:46:34: #1 tags after filtering in treatment: 5707357 INFO @ Mon, 12 Aug 2019 18:46:34: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:46:34: #1 finished! INFO @ Mon, 12 Aug 2019 18:46:34: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:46:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:46:34: #2 number of paired peaks: 608 WARNING @ Mon, 12 Aug 2019 18:46:34: Fewer paired peaks (608) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 608 pairs to build model! INFO @ Mon, 12 Aug 2019 18:46:34: start model_add_line... INFO @ Mon, 12 Aug 2019 18:46:34: start X-correlation... INFO @ Mon, 12 Aug 2019 18:46:34: end of X-cor INFO @ Mon, 12 Aug 2019 18:46:34: #2 finished! INFO @ Mon, 12 Aug 2019 18:46:34: #2 predicted fragment length is 100 bps INFO @ Mon, 12 Aug 2019 18:46:34: #2 alternative fragment length(s) may be 100 bps INFO @ Mon, 12 Aug 2019 18:46:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331304/SRX331304.20_model.r INFO @ Mon, 12 Aug 2019 18:46:34: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:46:34: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:46:49: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:46:51: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:46:51: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:46:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331304/SRX331304.05_peaks.xls INFO @ Mon, 12 Aug 2019 18:46:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331304/SRX331304.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:46:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331304/SRX331304.05_summits.bed INFO @ Mon, 12 Aug 2019 18:46:58: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (2463 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:46:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331304/SRX331304.10_peaks.xls INFO @ Mon, 12 Aug 2019 18:46:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331304/SRX331304.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:46:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331304/SRX331304.10_summits.bed INFO @ Mon, 12 Aug 2019 18:46:59: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1247 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:47:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331304/SRX331304.20_peaks.xls INFO @ Mon, 12 Aug 2019 18:47:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331304/SRX331304.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:47:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331304/SRX331304.20_summits.bed INFO @ Mon, 12 Aug 2019 18:47:00: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (463 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。