Job ID = 1292516 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 13,475,705 reads read : 13,475,705 reads written : 13,475,705 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:59 13475705 reads; of these: 13475705 (100.00%) were unpaired; of these: 643447 (4.77%) aligned 0 times 7916590 (58.75%) aligned exactly 1 time 4915668 (36.48%) aligned >1 times 95.23% overall alignment rate Time searching: 00:03:59 Overall time: 00:03:59 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] 5623983 / 12832258 = 0.4383 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 @ Sun, 02 Jun 2019 19:20:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466529/SRX466529.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466529/SRX466529.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466529/SRX466529.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466529/SRX466529.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 @ Sun, 02 Jun 2019 19:20:32: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:20:32: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:20:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466529/SRX466529.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466529/SRX466529.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466529/SRX466529.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466529/SRX466529.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 @ Sun, 02 Jun 2019 19:20:32: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:20:32: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:20:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466529/SRX466529.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466529/SRX466529.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466529/SRX466529.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466529/SRX466529.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 @ Sun, 02 Jun 2019 19:20:33: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:20:33: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:20:40: 1000000 INFO @ Sun, 02 Jun 2019 19:20:41: 1000000 INFO @ Sun, 02 Jun 2019 19:20:42: 1000000 INFO @ Sun, 02 Jun 2019 19:20:47: 2000000 INFO @ Sun, 02 Jun 2019 19:20:48: 2000000 INFO @ Sun, 02 Jun 2019 19:20:51: 2000000 INFO @ Sun, 02 Jun 2019 19:20:54: 3000000 INFO @ Sun, 02 Jun 2019 19:20:56: 3000000 INFO @ Sun, 02 Jun 2019 19:21:00: 3000000 INFO @ Sun, 02 Jun 2019 19:21:01: 4000000 INFO @ Sun, 02 Jun 2019 19:21:04: 4000000 INFO @ Sun, 02 Jun 2019 19:21:07: 5000000 INFO @ Sun, 02 Jun 2019 19:21:09: 4000000 INFO @ Sun, 02 Jun 2019 19:21:11: 5000000 INFO @ Sun, 02 Jun 2019 19:21:14: 6000000 INFO @ Sun, 02 Jun 2019 19:21:18: 5000000 INFO @ Sun, 02 Jun 2019 19:21:19: 6000000 INFO @ Sun, 02 Jun 2019 19:21:21: 7000000 INFO @ Sun, 02 Jun 2019 19:21:23: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 19:21:23: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 19:21:23: #1 total tags in treatment: 7208275 INFO @ Sun, 02 Jun 2019 19:21:23: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:21:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 19:21:23: #1 tags after filtering in treatment: 7208275 INFO @ Sun, 02 Jun 2019 19:21:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:21:23: #1 finished! INFO @ Sun, 02 Jun 2019 19:21:23: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:21:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:21:24: #2 number of paired peaks: 4566 INFO @ Sun, 02 Jun 2019 19:21:24: start model_add_line... INFO @ Sun, 02 Jun 2019 19:21:24: start X-correlation... INFO @ Sun, 02 Jun 2019 19:21:24: end of X-cor INFO @ Sun, 02 Jun 2019 19:21:24: #2 finished! INFO @ Sun, 02 Jun 2019 19:21:24: #2 predicted fragment length is 202 bps INFO @ Sun, 02 Jun 2019 19:21:24: #2 alternative fragment length(s) may be 202 bps INFO @ Sun, 02 Jun 2019 19:21:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466529/SRX466529.10_model.r INFO @ Sun, 02 Jun 2019 19:21:24: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:21:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:21:26: 7000000 INFO @ Sun, 02 Jun 2019 19:21:27: 6000000 INFO @ Sun, 02 Jun 2019 19:21:28: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 19:21:28: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 19:21:28: #1 total tags in treatment: 7208275 INFO @ Sun, 02 Jun 2019 19:21:28: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:21:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 19:21:28: #1 tags after filtering in treatment: 7208275 INFO @ Sun, 02 Jun 2019 19:21:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:21:28: #1 finished! INFO @ Sun, 02 Jun 2019 19:21:28: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:21:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:21:29: #2 number of paired peaks: 4566 INFO @ Sun, 02 Jun 2019 19:21:29: start model_add_line... INFO @ Sun, 02 Jun 2019 19:21:29: start X-correlation... INFO @ Sun, 02 Jun 2019 19:21:29: end of X-cor INFO @ Sun, 02 Jun 2019 19:21:29: #2 finished! INFO @ Sun, 02 Jun 2019 19:21:29: #2 predicted fragment length is 202 bps INFO @ Sun, 02 Jun 2019 19:21:29: #2 alternative fragment length(s) may be 202 bps INFO @ Sun, 02 Jun 2019 19:21:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466529/SRX466529.20_model.r INFO @ Sun, 02 Jun 2019 19:21:29: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:21:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:21:36: 7000000 INFO @ Sun, 02 Jun 2019 19:21:37: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 19:21:37: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 19:21:37: #1 total tags in treatment: 7208275 INFO @ Sun, 02 Jun 2019 19:21:37: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:21:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 19:21:37: #1 tags after filtering in treatment: 7208275 INFO @ Sun, 02 Jun 2019 19:21:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:21:37: #1 finished! INFO @ Sun, 02 Jun 2019 19:21:37: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:21:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:21:39: #2 number of paired peaks: 4566 INFO @ Sun, 02 Jun 2019 19:21:39: start model_add_line... INFO @ Sun, 02 Jun 2019 19:21:39: start X-correlation... INFO @ Sun, 02 Jun 2019 19:21:39: end of X-cor INFO @ Sun, 02 Jun 2019 19:21:39: #2 finished! INFO @ Sun, 02 Jun 2019 19:21:39: #2 predicted fragment length is 202 bps INFO @ Sun, 02 Jun 2019 19:21:39: #2 alternative fragment length(s) may be 202 bps INFO @ Sun, 02 Jun 2019 19:21:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466529/SRX466529.05_model.r INFO @ Sun, 02 Jun 2019 19:21:39: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:21:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:21:54: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:21:59: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:22:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466529/SRX466529.10_peaks.xls INFO @ Sun, 02 Jun 2019 19:22:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466529/SRX466529.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:22:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466529/SRX466529.10_summits.bed INFO @ Sun, 02 Jun 2019 19:22:04: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (3953 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:22:09: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:22:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466529/SRX466529.20_peaks.xls INFO @ Sun, 02 Jun 2019 19:22:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466529/SRX466529.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:22:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466529/SRX466529.20_summits.bed INFO @ Sun, 02 Jun 2019 19:22:10: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (2195 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:22:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466529/SRX466529.05_peaks.xls INFO @ Sun, 02 Jun 2019 19:22:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466529/SRX466529.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:22:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466529/SRX466529.05_summits.bed INFO @ Sun, 02 Jun 2019 19:22:19: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (5750 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。