Job ID = 4303047 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 9,596,946 reads read : 9,596,946 reads written : 9,596,946 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1198444.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: 00:01:23 9596946 reads; of these: 9596946 (100.00%) were unpaired; of these: 1727578 (18.00%) aligned 0 times 6661893 (69.42%) aligned exactly 1 time 1207475 (12.58%) aligned >1 times 82.00% overall alignment rate Time searching: 00:01:23 Overall time: 00:01:23 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] 2530553 / 7869368 = 0.3216 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 12 Dec 2019 00:37:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494912/SRX494912.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494912/SRX494912.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494912/SRX494912.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494912/SRX494912.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 @ Thu, 12 Dec 2019 00:37:38: #1 read tag files... INFO @ Thu, 12 Dec 2019 00:37:38: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 00:37:42: 1000000 INFO @ Thu, 12 Dec 2019 00:37:46: 2000000 INFO @ Thu, 12 Dec 2019 00:37:50: 3000000 INFO @ Thu, 12 Dec 2019 00:37:54: 4000000 INFO @ Thu, 12 Dec 2019 00:37:58: 5000000 INFO @ Thu, 12 Dec 2019 00:37:59: #1 tag size is determined as 42 bps INFO @ Thu, 12 Dec 2019 00:37:59: #1 tag size = 42 INFO @ Thu, 12 Dec 2019 00:37:59: #1 total tags in treatment: 5338815 INFO @ Thu, 12 Dec 2019 00:37:59: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 00:37:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 00:37:59: #1 tags after filtering in treatment: 5338815 INFO @ Thu, 12 Dec 2019 00:37:59: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 00:37:59: #1 finished! INFO @ Thu, 12 Dec 2019 00:37:59: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 00:37:59: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 00:37:59: #2 number of paired peaks: 639 WARNING @ Thu, 12 Dec 2019 00:37:59: Fewer paired peaks (639) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 639 pairs to build model! INFO @ Thu, 12 Dec 2019 00:37:59: start model_add_line... INFO @ Thu, 12 Dec 2019 00:37:59: start X-correlation... INFO @ Thu, 12 Dec 2019 00:37:59: end of X-cor INFO @ Thu, 12 Dec 2019 00:37:59: #2 finished! INFO @ Thu, 12 Dec 2019 00:37:59: #2 predicted fragment length is 124 bps INFO @ Thu, 12 Dec 2019 00:37:59: #2 alternative fragment length(s) may be 124 bps INFO @ Thu, 12 Dec 2019 00:37:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494912/SRX494912.05_model.r INFO @ Thu, 12 Dec 2019 00:38:00: #3 Call peaks... INFO @ Thu, 12 Dec 2019 00:38:00: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 00:38:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494912/SRX494912.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494912/SRX494912.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494912/SRX494912.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494912/SRX494912.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 @ Thu, 12 Dec 2019 00:38:07: #1 read tag files... INFO @ Thu, 12 Dec 2019 00:38:07: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 00:38:08: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 00:38:11: 1000000 INFO @ Thu, 12 Dec 2019 00:38:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494912/SRX494912.05_peaks.xls INFO @ Thu, 12 Dec 2019 00:38:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494912/SRX494912.05_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 00:38:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494912/SRX494912.05_summits.bed INFO @ Thu, 12 Dec 2019 00:38:13: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1099 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 12 Dec 2019 00:38:15: 2000000 INFO @ Thu, 12 Dec 2019 00:38:19: 3000000 INFO @ Thu, 12 Dec 2019 00:38:23: 4000000 INFO @ Thu, 12 Dec 2019 00:38:27: 5000000 INFO @ Thu, 12 Dec 2019 00:38:28: #1 tag size is determined as 42 bps INFO @ Thu, 12 Dec 2019 00:38:28: #1 tag size = 42 INFO @ Thu, 12 Dec 2019 00:38:28: #1 total tags in treatment: 5338815 INFO @ Thu, 12 Dec 2019 00:38:28: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 00:38:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 00:38:28: #1 tags after filtering in treatment: 5338815 INFO @ Thu, 12 Dec 2019 00:38:28: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 00:38:28: #1 finished! INFO @ Thu, 12 Dec 2019 00:38:28: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 00:38:28: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 00:38:29: #2 number of paired peaks: 639 WARNING @ Thu, 12 Dec 2019 00:38:29: Fewer paired peaks (639) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 639 pairs to build model! INFO @ Thu, 12 Dec 2019 00:38:29: start model_add_line... INFO @ Thu, 12 Dec 2019 00:38:29: start X-correlation... INFO @ Thu, 12 Dec 2019 00:38:29: end of X-cor INFO @ Thu, 12 Dec 2019 00:38:29: #2 finished! INFO @ Thu, 12 Dec 2019 00:38:29: #2 predicted fragment length is 124 bps INFO @ Thu, 12 Dec 2019 00:38:29: #2 alternative fragment length(s) may be 124 bps INFO @ Thu, 12 Dec 2019 00:38:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494912/SRX494912.10_model.r INFO @ Thu, 12 Dec 2019 00:38:29: #3 Call peaks... INFO @ Thu, 12 Dec 2019 00:38:29: #3 Pre-compute pvalue-qvalue table... BedGraph に変換中... INFO @ Thu, 12 Dec 2019 00:38:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494912/SRX494912.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494912/SRX494912.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494912/SRX494912.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494912/SRX494912.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 @ Thu, 12 Dec 2019 00:38:37: #1 read tag files... INFO @ Thu, 12 Dec 2019 00:38:37: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 00:38:38: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 00:38:41: 1000000 INFO @ Thu, 12 Dec 2019 00:38:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494912/SRX494912.10_peaks.xls INFO @ Thu, 12 Dec 2019 00:38:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494912/SRX494912.10_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 00:38:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494912/SRX494912.10_summits.bed INFO @ Thu, 12 Dec 2019 00:38:43: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (556 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Thu, 12 Dec 2019 00:38:45: 2000000 INFO @ Thu, 12 Dec 2019 00:38:49: 3000000 INFO @ Thu, 12 Dec 2019 00:38:53: 4000000 INFO @ Thu, 12 Dec 2019 00:38:57: 5000000 INFO @ Thu, 12 Dec 2019 00:38:58: #1 tag size is determined as 42 bps INFO @ Thu, 12 Dec 2019 00:38:58: #1 tag size = 42 INFO @ Thu, 12 Dec 2019 00:38:58: #1 total tags in treatment: 5338815 INFO @ Thu, 12 Dec 2019 00:38:58: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 00:38:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 00:38:58: #1 tags after filtering in treatment: 5338815 INFO @ Thu, 12 Dec 2019 00:38:58: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 00:38:58: #1 finished! INFO @ Thu, 12 Dec 2019 00:38:58: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 00:38:58: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 00:38:59: #2 number of paired peaks: 639 WARNING @ Thu, 12 Dec 2019 00:38:59: Fewer paired peaks (639) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 639 pairs to build model! INFO @ Thu, 12 Dec 2019 00:38:59: start model_add_line... INFO @ Thu, 12 Dec 2019 00:38:59: start X-correlation... INFO @ Thu, 12 Dec 2019 00:38:59: end of X-cor INFO @ Thu, 12 Dec 2019 00:38:59: #2 finished! INFO @ Thu, 12 Dec 2019 00:38:59: #2 predicted fragment length is 124 bps INFO @ Thu, 12 Dec 2019 00:38:59: #2 alternative fragment length(s) may be 124 bps INFO @ Thu, 12 Dec 2019 00:38:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494912/SRX494912.20_model.r INFO @ Thu, 12 Dec 2019 00:38:59: #3 Call peaks... INFO @ Thu, 12 Dec 2019 00:38:59: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 00:39:08: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 00:39:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494912/SRX494912.20_peaks.xls INFO @ Thu, 12 Dec 2019 00:39:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494912/SRX494912.20_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 00:39:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494912/SRX494912.20_summits.bed INFO @ Thu, 12 Dec 2019 00:39:13: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (242 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。