Job ID = 1290658 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 12,081,024 reads read : 24,162,048 reads written : 12,081,024 reads 0-length : 12,081,024 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:46 12081024 reads; of these: 12081024 (100.00%) were unpaired; of these: 292231 (2.42%) aligned 0 times 10392278 (86.02%) aligned exactly 1 time 1396515 (11.56%) aligned >1 times 97.58% overall alignment rate Time searching: 00:02:47 Overall time: 00:02:47 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] 2679151 / 11788793 = 0.2273 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 22:00:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4082359/SRX4082359.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4082359/SRX4082359.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4082359/SRX4082359.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4082359/SRX4082359.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 22:00:40: #1 read tag files... INFO @ Sat, 01 Jun 2019 22:00:40: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 22:00:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4082359/SRX4082359.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4082359/SRX4082359.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4082359/SRX4082359.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4082359/SRX4082359.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 22:00:40: #1 read tag files... INFO @ Sat, 01 Jun 2019 22:00:40: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 22:00:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4082359/SRX4082359.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4082359/SRX4082359.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4082359/SRX4082359.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4082359/SRX4082359.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 22:00:40: #1 read tag files... INFO @ Sat, 01 Jun 2019 22:00:40: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 22:00:47: 1000000 INFO @ Sat, 01 Jun 2019 22:00:50: 1000000 INFO @ Sat, 01 Jun 2019 22:00:50: 1000000 INFO @ Sat, 01 Jun 2019 22:00:54: 2000000 INFO @ Sat, 01 Jun 2019 22:00:58: 2000000 INFO @ Sat, 01 Jun 2019 22:00:59: 2000000 INFO @ Sat, 01 Jun 2019 22:01:01: 3000000 INFO @ Sat, 01 Jun 2019 22:01:07: 3000000 INFO @ Sat, 01 Jun 2019 22:01:07: 3000000 INFO @ Sat, 01 Jun 2019 22:01:08: 4000000 INFO @ Sat, 01 Jun 2019 22:01:15: 5000000 INFO @ Sat, 01 Jun 2019 22:01:15: 4000000 INFO @ Sat, 01 Jun 2019 22:01:16: 4000000 INFO @ Sat, 01 Jun 2019 22:01:21: 6000000 INFO @ Sat, 01 Jun 2019 22:01:24: 5000000 INFO @ Sat, 01 Jun 2019 22:01:25: 5000000 INFO @ Sat, 01 Jun 2019 22:01:28: 7000000 INFO @ Sat, 01 Jun 2019 22:01:32: 6000000 INFO @ Sat, 01 Jun 2019 22:01:34: 6000000 INFO @ Sat, 01 Jun 2019 22:01:35: 8000000 INFO @ Sat, 01 Jun 2019 22:01:40: 7000000 INFO @ Sat, 01 Jun 2019 22:01:42: 9000000 INFO @ Sat, 01 Jun 2019 22:01:42: 7000000 INFO @ Sat, 01 Jun 2019 22:01:43: #1 tag size is determined as 50 bps INFO @ Sat, 01 Jun 2019 22:01:43: #1 tag size = 50 INFO @ Sat, 01 Jun 2019 22:01:43: #1 total tags in treatment: 9109642 INFO @ Sat, 01 Jun 2019 22:01:43: #1 user defined the maximum tags... INFO @ Sat, 01 Jun 2019 22:01:43: #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 22:01:43: #1 tags after filtering in treatment: 9109642 INFO @ Sat, 01 Jun 2019 22:01:43: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 01 Jun 2019 22:01:43: #1 finished! INFO @ Sat, 01 Jun 2019 22:01:43: #2 Build Peak Model... INFO @ Sat, 01 Jun 2019 22:01:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 01 Jun 2019 22:01:44: #2 number of paired peaks: 2582 INFO @ Sat, 01 Jun 2019 22:01:44: start model_add_line... INFO @ Sat, 01 Jun 2019 22:01:44: start X-correlation... INFO @ Sat, 01 Jun 2019 22:01:44: end of X-cor INFO @ Sat, 01 Jun 2019 22:01:44: #2 finished! INFO @ Sat, 01 Jun 2019 22:01:44: #2 predicted fragment length is 155 bps INFO @ Sat, 01 Jun 2019 22:01:44: #2 alternative fragment length(s) may be 4,155 bps INFO @ Sat, 01 Jun 2019 22:01:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4082359/SRX4082359.10_model.r INFO @ Sat, 01 Jun 2019 22:01:44: #3 Call peaks... INFO @ Sat, 01 Jun 2019 22:01:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 01 Jun 2019 22:01:49: 8000000 INFO @ Sat, 01 Jun 2019 22:01:51: 8000000 INFO @ Sat, 01 Jun 2019 22:01:57: 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: 9109642 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: 9109642 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 22:01:59: #2 number of paired peaks: 2582 INFO @ Sat, 01 Jun 2019 22:01:59: start model_add_line... INFO @ Sat, 01 Jun 2019 22:01:59: 9000000 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 155 bps INFO @ Sat, 01 Jun 2019 22:01:59: #2 alternative fragment length(s) may be 4,155 bps INFO @ Sat, 01 Jun 2019 22:01:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4082359/SRX4082359.05_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: #1 tag size is determined as 50 bps INFO @ Sat, 01 Jun 2019 22:02:00: #1 tag size = 50 INFO @ Sat, 01 Jun 2019 22:02:00: #1 total tags in treatment: 9109642 INFO @ Sat, 01 Jun 2019 22:02:00: #1 user defined the maximum tags... INFO @ Sat, 01 Jun 2019 22:02:00: #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 22:02:00: #1 tags after filtering in treatment: 9109642 INFO @ Sat, 01 Jun 2019 22:02:00: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 01 Jun 2019 22:02:00: #1 finished! INFO @ Sat, 01 Jun 2019 22:02:00: #2 Build Peak Model... INFO @ Sat, 01 Jun 2019 22:02:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 01 Jun 2019 22:02:01: #2 number of paired peaks: 2582 INFO @ Sat, 01 Jun 2019 22:02:01: start model_add_line... INFO @ Sat, 01 Jun 2019 22:02:01: start X-correlation... INFO @ Sat, 01 Jun 2019 22:02:01: end of X-cor INFO @ Sat, 01 Jun 2019 22:02:01: #2 finished! INFO @ Sat, 01 Jun 2019 22:02:01: #2 predicted fragment length is 155 bps INFO @ Sat, 01 Jun 2019 22:02:01: #2 alternative fragment length(s) may be 4,155 bps INFO @ Sat, 01 Jun 2019 22:02:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4082359/SRX4082359.20_model.r INFO @ Sat, 01 Jun 2019 22:02:02: #3 Call peaks... INFO @ Sat, 01 Jun 2019 22:02:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 01 Jun 2019 22:02:12: #3 Call peaks for each chromosome... INFO @ Sat, 01 Jun 2019 22:02:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4082359/SRX4082359.10_peaks.xls INFO @ Sat, 01 Jun 2019 22:02:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4082359/SRX4082359.10_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 22:02:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4082359/SRX4082359.10_summits.bed INFO @ Sat, 01 Jun 2019 22:02:24: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (3455 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sat, 01 Jun 2019 22:02:27: #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 22:02:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4082359/SRX4082359.05_peaks.xls INFO @ Sat, 01 Jun 2019 22:02:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4082359/SRX4082359.05_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 22:02:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4082359/SRX4082359.05_summits.bed INFO @ Sat, 01 Jun 2019 22:02:40: Done! pass1 - making usageList (7 chroms): 4 millis pass2 - checking and writing primary data (6733 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sat, 01 Jun 2019 22:02:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4082359/SRX4082359.20_peaks.xls INFO @ Sat, 01 Jun 2019 22:02:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4082359/SRX4082359.20_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 22:02:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4082359/SRX4082359.20_summits.bed INFO @ Sat, 01 Jun 2019 22:02:41: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (938 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。