Job ID = 1290614 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 9,419,509 reads read : 9,419,509 reads written : 9,419,509 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:08 9419509 reads; of these: 9419509 (100.00%) were unpaired; of these: 152056 (1.61%) aligned 0 times 8163367 (86.66%) aligned exactly 1 time 1104086 (11.72%) aligned >1 times 98.39% overall alignment rate Time searching: 00:03:10 Overall time: 00:03:10 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] 1089508 / 9267453 = 0.1176 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 @ Sat, 01 Jun 2019 21:51:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3043403/SRX3043403.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3043403/SRX3043403.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3043403/SRX3043403.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3043403/SRX3043403.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 @ Sat, 01 Jun 2019 21:51:05: #1 read tag files... INFO @ Sat, 01 Jun 2019 21:51:05: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 21:51:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3043403/SRX3043403.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3043403/SRX3043403.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3043403/SRX3043403.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3043403/SRX3043403.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 @ Sat, 01 Jun 2019 21:51:05: #1 read tag files... INFO @ Sat, 01 Jun 2019 21:51:05: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 21:51:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3043403/SRX3043403.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3043403/SRX3043403.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3043403/SRX3043403.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3043403/SRX3043403.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 @ Sat, 01 Jun 2019 21:51:05: #1 read tag files... INFO @ Sat, 01 Jun 2019 21:51:05: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 21:51:15: 1000000 INFO @ Sat, 01 Jun 2019 21:51:15: 1000000 INFO @ Sat, 01 Jun 2019 21:51:16: 1000000 INFO @ Sat, 01 Jun 2019 21:51:26: 2000000 INFO @ Sat, 01 Jun 2019 21:51:27: 2000000 INFO @ Sat, 01 Jun 2019 21:51:28: 2000000 INFO @ Sat, 01 Jun 2019 21:51:37: 3000000 INFO @ Sat, 01 Jun 2019 21:51:39: 3000000 INFO @ Sat, 01 Jun 2019 21:51:39: 3000000 INFO @ Sat, 01 Jun 2019 21:51:49: 4000000 INFO @ Sat, 01 Jun 2019 21:51:50: 4000000 INFO @ Sat, 01 Jun 2019 21:51:50: 4000000 INFO @ Sat, 01 Jun 2019 21:51:59: 5000000 INFO @ Sat, 01 Jun 2019 21:52:01: 5000000 INFO @ Sat, 01 Jun 2019 21:52:02: 5000000 INFO @ Sat, 01 Jun 2019 21:52:09: 6000000 INFO @ Sat, 01 Jun 2019 21:52:13: 6000000 INFO @ Sat, 01 Jun 2019 21:52:14: 6000000 INFO @ Sat, 01 Jun 2019 21:52:20: 7000000 INFO @ Sat, 01 Jun 2019 21:52:25: 7000000 INFO @ Sat, 01 Jun 2019 21:52:27: 7000000 INFO @ Sat, 01 Jun 2019 21:52:30: 8000000 INFO @ Sat, 01 Jun 2019 21:52:32: #1 tag size is determined as 50 bps INFO @ Sat, 01 Jun 2019 21:52:32: #1 tag size = 50 INFO @ Sat, 01 Jun 2019 21:52:32: #1 total tags in treatment: 8177945 INFO @ Sat, 01 Jun 2019 21:52:32: #1 user defined the maximum tags... INFO @ Sat, 01 Jun 2019 21:52:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 01 Jun 2019 21:52:32: #1 tags after filtering in treatment: 8177945 INFO @ Sat, 01 Jun 2019 21:52:32: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 01 Jun 2019 21:52:32: #1 finished! INFO @ Sat, 01 Jun 2019 21:52:32: #2 Build Peak Model... INFO @ Sat, 01 Jun 2019 21:52:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 01 Jun 2019 21:52:33: #2 number of paired peaks: 1251 INFO @ Sat, 01 Jun 2019 21:52:33: start model_add_line... INFO @ Sat, 01 Jun 2019 21:52:33: start X-correlation... INFO @ Sat, 01 Jun 2019 21:52:33: end of X-cor INFO @ Sat, 01 Jun 2019 21:52:33: #2 finished! INFO @ Sat, 01 Jun 2019 21:52:33: #2 predicted fragment length is 170 bps INFO @ Sat, 01 Jun 2019 21:52:33: #2 alternative fragment length(s) may be 170 bps INFO @ Sat, 01 Jun 2019 21:52:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3043403/SRX3043403.10_model.r INFO @ Sat, 01 Jun 2019 21:52:33: #3 Call peaks... INFO @ Sat, 01 Jun 2019 21:52:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 01 Jun 2019 21:52:37: 8000000 INFO @ Sat, 01 Jun 2019 21:52:38: #1 tag size is determined as 50 bps INFO @ Sat, 01 Jun 2019 21:52:38: #1 tag size = 50 INFO @ Sat, 01 Jun 2019 21:52:38: #1 total tags in treatment: 8177945 INFO @ Sat, 01 Jun 2019 21:52:38: #1 user defined the maximum tags... INFO @ Sat, 01 Jun 2019 21:52:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 01 Jun 2019 21:52:38: 8000000 INFO @ Sat, 01 Jun 2019 21:52:39: #1 tags after filtering in treatment: 8177945 INFO @ Sat, 01 Jun 2019 21:52:39: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 01 Jun 2019 21:52:39: #1 finished! INFO @ Sat, 01 Jun 2019 21:52:39: #2 Build Peak Model... INFO @ Sat, 01 Jun 2019 21:52:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 01 Jun 2019 21:52:39: #2 number of paired peaks: 1251 INFO @ Sat, 01 Jun 2019 21:52:39: start model_add_line... INFO @ Sat, 01 Jun 2019 21:52:40: start X-correlation... INFO @ Sat, 01 Jun 2019 21:52:40: end of X-cor INFO @ Sat, 01 Jun 2019 21:52:40: #2 finished! INFO @ Sat, 01 Jun 2019 21:52:40: #2 predicted fragment length is 170 bps INFO @ Sat, 01 Jun 2019 21:52:40: #2 alternative fragment length(s) may be 170 bps INFO @ Sat, 01 Jun 2019 21:52:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3043403/SRX3043403.20_model.r INFO @ Sat, 01 Jun 2019 21:52:40: #3 Call peaks... INFO @ Sat, 01 Jun 2019 21:52:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 01 Jun 2019 21:52:40: #1 tag size is determined as 50 bps INFO @ Sat, 01 Jun 2019 21:52:40: #1 tag size = 50 INFO @ Sat, 01 Jun 2019 21:52:40: #1 total tags in treatment: 8177945 INFO @ Sat, 01 Jun 2019 21:52:40: #1 user defined the maximum tags... INFO @ Sat, 01 Jun 2019 21:52:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 01 Jun 2019 21:52:40: #1 tags after filtering in treatment: 8177945 INFO @ Sat, 01 Jun 2019 21:52:40: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 01 Jun 2019 21:52:40: #1 finished! INFO @ Sat, 01 Jun 2019 21:52:40: #2 Build Peak Model... INFO @ Sat, 01 Jun 2019 21:52:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 01 Jun 2019 21:52:41: #2 number of paired peaks: 1251 INFO @ Sat, 01 Jun 2019 21:52:41: start model_add_line... INFO @ Sat, 01 Jun 2019 21:52:41: start X-correlation... INFO @ Sat, 01 Jun 2019 21:52:41: end of X-cor INFO @ Sat, 01 Jun 2019 21:52:41: #2 finished! INFO @ Sat, 01 Jun 2019 21:52:41: #2 predicted fragment length is 170 bps INFO @ Sat, 01 Jun 2019 21:52:41: #2 alternative fragment length(s) may be 170 bps INFO @ Sat, 01 Jun 2019 21:52:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3043403/SRX3043403.05_model.r INFO @ Sat, 01 Jun 2019 21:52:41: #3 Call peaks... INFO @ Sat, 01 Jun 2019 21:52:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 01 Jun 2019 21:52:59: #3 Call peaks for each chromosome... INFO @ Sat, 01 Jun 2019 21:53:05: #3 Call peaks for each chromosome... INFO @ Sat, 01 Jun 2019 21:53:07: #3 Call peaks for each chromosome... INFO @ Sat, 01 Jun 2019 21:53:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3043403/SRX3043403.10_peaks.xls INFO @ Sat, 01 Jun 2019 21:53:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3043403/SRX3043403.10_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 21:53:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3043403/SRX3043403.10_summits.bed INFO @ Sat, 01 Jun 2019 21:53:12: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3663 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 01 Jun 2019 21:53:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3043403/SRX3043403.20_peaks.xls INFO @ Sat, 01 Jun 2019 21:53:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3043403/SRX3043403.20_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 21:53:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3043403/SRX3043403.20_summits.bed INFO @ Sat, 01 Jun 2019 21:53:18: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (2306 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 01 Jun 2019 21:53:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3043403/SRX3043403.05_peaks.xls INFO @ Sat, 01 Jun 2019 21:53:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3043403/SRX3043403.05_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 21:53:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3043403/SRX3043403.05_summits.bed INFO @ Sat, 01 Jun 2019 21:53:20: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (5113 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。