Job ID = 1290654 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 13,268,521 reads read : 26,537,042 reads written : 13,268,521 reads 0-length : 13,268,521 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: 00:03:09 13268521 reads; of these: 13268521 (100.00%) were unpaired; of these: 1756454 (13.24%) aligned 0 times 10451040 (78.77%) aligned exactly 1 time 1061027 (8.00%) aligned >1 times 86.76% overall alignment rate Time searching: 00:03:09 Overall time: 00:03:09 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_sort_core] merging from 8 files... [bam_rmdupse_core] 2404759 / 11512067 = 0.2089 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 22:00:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4082360/SRX4082360.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4082360/SRX4082360.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4082360/SRX4082360.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4082360/SRX4082360.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 22:00:45: #1 read tag files... INFO @ Sat, 01 Jun 2019 22:00:45: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 22:00:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4082360/SRX4082360.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4082360/SRX4082360.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4082360/SRX4082360.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4082360/SRX4082360.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 22:00:45: #1 read tag files... INFO @ Sat, 01 Jun 2019 22:00:45: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 22:00:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4082360/SRX4082360.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4082360/SRX4082360.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4082360/SRX4082360.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4082360/SRX4082360.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 22:00:45: #1 read tag files... INFO @ Sat, 01 Jun 2019 22:00:45: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 22:00:53: 1000000 INFO @ Sat, 01 Jun 2019 22:00:53: 1000000 INFO @ Sat, 01 Jun 2019 22:00:54: 1000000 INFO @ Sat, 01 Jun 2019 22:00:59: 2000000 INFO @ Sat, 01 Jun 2019 22:01:02: 2000000 INFO @ Sat, 01 Jun 2019 22:01:02: 2000000 INFO @ Sat, 01 Jun 2019 22:01:07: 3000000 INFO @ Sat, 01 Jun 2019 22:01:10: 3000000 INFO @ Sat, 01 Jun 2019 22:01:10: 3000000 INFO @ Sat, 01 Jun 2019 22:01:13: 4000000 INFO @ Sat, 01 Jun 2019 22:01:18: 4000000 INFO @ Sat, 01 Jun 2019 22:01:18: 4000000 INFO @ Sat, 01 Jun 2019 22:01:20: 5000000 INFO @ Sat, 01 Jun 2019 22:01:25: 5000000 INFO @ Sat, 01 Jun 2019 22:01:26: 5000000 INFO @ Sat, 01 Jun 2019 22:01:27: 6000000 INFO @ Sat, 01 Jun 2019 22:01:33: 6000000 INFO @ Sat, 01 Jun 2019 22:01:34: 7000000 INFO @ Sat, 01 Jun 2019 22:01:34: 6000000 INFO @ Sat, 01 Jun 2019 22:01:41: 8000000 INFO @ Sat, 01 Jun 2019 22:01:41: 7000000 INFO @ Sat, 01 Jun 2019 22:01:42: 7000000 INFO @ Sat, 01 Jun 2019 22:01:47: 9000000 INFO @ Sat, 01 Jun 2019 22:01:48: #1 tag size is determined as 50 bps INFO @ Sat, 01 Jun 2019 22:01:48: #1 tag size = 50 INFO @ Sat, 01 Jun 2019 22:01:48: #1 total tags in treatment: 9107308 INFO @ Sat, 01 Jun 2019 22:01:48: #1 user defined the maximum tags... INFO @ Sat, 01 Jun 2019 22:01:48: #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 22:01:48: #1 tags after filtering in treatment: 9107308 INFO @ Sat, 01 Jun 2019 22:01:48: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 01 Jun 2019 22:01:48: #1 finished! INFO @ Sat, 01 Jun 2019 22:01:48: #2 Build Peak Model... INFO @ Sat, 01 Jun 2019 22:01:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 01 Jun 2019 22:01:49: 8000000 INFO @ Sat, 01 Jun 2019 22:01:50: #2 number of paired peaks: 4776 INFO @ Sat, 01 Jun 2019 22:01:50: start model_add_line... INFO @ Sat, 01 Jun 2019 22:01:50: 8000000 INFO @ Sat, 01 Jun 2019 22:01:50: start X-correlation... INFO @ Sat, 01 Jun 2019 22:01:50: end of X-cor INFO @ Sat, 01 Jun 2019 22:01:50: #2 finished! INFO @ Sat, 01 Jun 2019 22:01:50: #2 predicted fragment length is 175 bps INFO @ Sat, 01 Jun 2019 22:01:50: #2 alternative fragment length(s) may be 4,175 bps INFO @ Sat, 01 Jun 2019 22:01:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4082360/SRX4082360.20_model.r INFO @ Sat, 01 Jun 2019 22:01:50: #3 Call peaks... INFO @ Sat, 01 Jun 2019 22:01:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 01 Jun 2019 22:01:57: 9000000 INFO @ Sat, 01 Jun 2019 22:01:58: 9000000 INFO @ Sat, 01 Jun 2019 22:01:58: #1 tag size is determined as 50 bps INFO @ Sat, 01 Jun 2019 22:01:58: #1 tag size = 50 INFO @ Sat, 01 Jun 2019 22:01:58: #1 total tags in treatment: 9107308 INFO @ Sat, 01 Jun 2019 22:01:58: #1 user defined the maximum tags... INFO @ Sat, 01 Jun 2019 22:01:58: #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 22:01:58: #1 tags after filtering in treatment: 9107308 INFO @ Sat, 01 Jun 2019 22:01:58: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 01 Jun 2019 22:01:58: #1 finished! INFO @ Sat, 01 Jun 2019 22:01:58: #2 Build Peak Model... INFO @ Sat, 01 Jun 2019 22:01:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 01 Jun 2019 22:01:58: #1 tag size is determined as 50 bps INFO @ Sat, 01 Jun 2019 22:01:58: #1 tag size = 50 INFO @ Sat, 01 Jun 2019 22:01:58: #1 total tags in treatment: 9107308 INFO @ Sat, 01 Jun 2019 22:01:58: #1 user defined the maximum tags... INFO @ Sat, 01 Jun 2019 22:01:58: #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 22:01:59: #1 tags after filtering in treatment: 9107308 INFO @ Sat, 01 Jun 2019 22:01:59: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 01 Jun 2019 22:01:59: #1 finished! INFO @ Sat, 01 Jun 2019 22:01:59: #2 Build Peak Model... INFO @ Sat, 01 Jun 2019 22:01:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 01 Jun 2019 22:01:59: #2 number of paired peaks: 4776 INFO @ Sat, 01 Jun 2019 22:01:59: start model_add_line... INFO @ Sat, 01 Jun 2019 22:01:59: start X-correlation... INFO @ Sat, 01 Jun 2019 22:01:59: end of X-cor INFO @ Sat, 01 Jun 2019 22:01:59: #2 finished! INFO @ Sat, 01 Jun 2019 22:01:59: #2 predicted fragment length is 175 bps INFO @ Sat, 01 Jun 2019 22:01:59: #2 alternative fragment length(s) may be 4,175 bps INFO @ Sat, 01 Jun 2019 22:01:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4082360/SRX4082360.05_model.r INFO @ Sat, 01 Jun 2019 22:01:59: #3 Call peaks... INFO @ Sat, 01 Jun 2019 22:01:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 01 Jun 2019 22:02:00: #2 number of paired peaks: 4776 INFO @ Sat, 01 Jun 2019 22:02:00: start model_add_line... INFO @ Sat, 01 Jun 2019 22:02:00: start X-correlation... INFO @ Sat, 01 Jun 2019 22:02:00: end of X-cor INFO @ Sat, 01 Jun 2019 22:02:00: #2 finished! INFO @ Sat, 01 Jun 2019 22:02:00: #2 predicted fragment length is 175 bps INFO @ Sat, 01 Jun 2019 22:02:00: #2 alternative fragment length(s) may be 4,175 bps INFO @ Sat, 01 Jun 2019 22:02:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4082360/SRX4082360.10_model.r INFO @ Sat, 01 Jun 2019 22:02:00: #3 Call peaks... INFO @ Sat, 01 Jun 2019 22:02:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 01 Jun 2019 22:02:19: #3 Call peaks for each chromosome... INFO @ Sat, 01 Jun 2019 22:02:29: #3 Call peaks for each chromosome... INFO @ Sat, 01 Jun 2019 22:02:29: #3 Call peaks for each chromosome... INFO @ Sat, 01 Jun 2019 22:02:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4082360/SRX4082360.20_peaks.xls INFO @ Sat, 01 Jun 2019 22:02:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4082360/SRX4082360.20_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 22:02:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4082360/SRX4082360.20_summits.bed INFO @ Sat, 01 Jun 2019 22:02:31: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (2041 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 01 Jun 2019 22:02:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4082360/SRX4082360.05_peaks.xls INFO @ Sat, 01 Jun 2019 22:02:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4082360/SRX4082360.05_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 22:02:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4082360/SRX4082360.10_peaks.xls INFO @ Sat, 01 Jun 2019 22:02:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4082360/SRX4082360.05_summits.bed INFO @ Sat, 01 Jun 2019 22:02:43: Done! INFO @ Sat, 01 Jun 2019 22:02:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4082360/SRX4082360.10_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 22:02:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4082360/SRX4082360.10_summits.bed INFO @ Sat, 01 Jun 2019 22:02:43: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (9267 records, 4 fields): 17 millis pass1 - making usageList (6 chroms): 4 millis CompletedMACS2peakCalling pass2 - checking and writing primary data (5698 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。