Job ID = 1293152 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 42,267,115 reads read : 42,267,115 reads written : 42,267,115 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: 00:10:29 42267115 reads; of these: 42267115 (100.00%) were unpaired; of these: 10923317 (25.84%) aligned 0 times 28777424 (68.08%) aligned exactly 1 time 2566374 (6.07%) aligned >1 times 74.16% overall alignment rate Time searching: 00:10:29 Overall time: 00:10:29 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 16 files... [bam_rmdupse_core] 10609101 / 31343798 = 0.3385 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 22:41:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402720/SRX5402720.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402720/SRX5402720.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402720/SRX5402720.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402720/SRX5402720.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 22:41:39: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:41:39: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:41:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402720/SRX5402720.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402720/SRX5402720.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402720/SRX5402720.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402720/SRX5402720.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 22:41:39: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:41:39: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:41:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402720/SRX5402720.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402720/SRX5402720.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402720/SRX5402720.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402720/SRX5402720.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 22:41:39: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:41:39: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:41:48: 1000000 INFO @ Sun, 02 Jun 2019 22:41:49: 1000000 INFO @ Sun, 02 Jun 2019 22:41:49: 1000000 INFO @ Sun, 02 Jun 2019 22:41:56: 2000000 INFO @ Sun, 02 Jun 2019 22:41:58: 2000000 INFO @ Sun, 02 Jun 2019 22:41:59: 2000000 INFO @ Sun, 02 Jun 2019 22:42:04: 3000000 INFO @ Sun, 02 Jun 2019 22:42:08: 3000000 INFO @ Sun, 02 Jun 2019 22:42:09: 3000000 INFO @ Sun, 02 Jun 2019 22:42:13: 4000000 INFO @ Sun, 02 Jun 2019 22:42:17: 4000000 INFO @ Sun, 02 Jun 2019 22:42:19: 4000000 INFO @ Sun, 02 Jun 2019 22:42:21: 5000000 INFO @ Sun, 02 Jun 2019 22:42:27: 5000000 INFO @ Sun, 02 Jun 2019 22:42:29: 5000000 INFO @ Sun, 02 Jun 2019 22:42:30: 6000000 INFO @ Sun, 02 Jun 2019 22:42:36: 6000000 INFO @ Sun, 02 Jun 2019 22:42:38: 7000000 INFO @ Sun, 02 Jun 2019 22:42:39: 6000000 INFO @ Sun, 02 Jun 2019 22:42:45: 7000000 INFO @ Sun, 02 Jun 2019 22:42:46: 8000000 INFO @ Sun, 02 Jun 2019 22:42:49: 7000000 INFO @ Sun, 02 Jun 2019 22:42:54: 8000000 INFO @ Sun, 02 Jun 2019 22:42:54: 9000000 INFO @ Sun, 02 Jun 2019 22:42:59: 8000000 INFO @ Sun, 02 Jun 2019 22:43:03: 10000000 INFO @ Sun, 02 Jun 2019 22:43:03: 9000000 INFO @ Sun, 02 Jun 2019 22:43:09: 9000000 INFO @ Sun, 02 Jun 2019 22:43:11: 11000000 INFO @ Sun, 02 Jun 2019 22:43:12: 10000000 INFO @ Sun, 02 Jun 2019 22:43:18: 10000000 INFO @ Sun, 02 Jun 2019 22:43:19: 12000000 INFO @ Sun, 02 Jun 2019 22:43:21: 11000000 INFO @ Sun, 02 Jun 2019 22:43:28: 13000000 INFO @ Sun, 02 Jun 2019 22:43:28: 11000000 INFO @ Sun, 02 Jun 2019 22:43:30: 12000000 INFO @ Sun, 02 Jun 2019 22:43:36: 14000000 INFO @ Sun, 02 Jun 2019 22:43:38: 12000000 INFO @ Sun, 02 Jun 2019 22:43:40: 13000000 INFO @ Sun, 02 Jun 2019 22:43:44: 15000000 INFO @ Sun, 02 Jun 2019 22:43:48: 13000000 INFO @ Sun, 02 Jun 2019 22:43:49: 14000000 INFO @ Sun, 02 Jun 2019 22:43:52: 16000000 INFO @ Sun, 02 Jun 2019 22:43:58: 14000000 INFO @ Sun, 02 Jun 2019 22:43:58: 15000000 INFO @ Sun, 02 Jun 2019 22:44:01: 17000000 INFO @ Sun, 02 Jun 2019 22:44:07: 16000000 INFO @ Sun, 02 Jun 2019 22:44:07: 15000000 INFO @ Sun, 02 Jun 2019 22:44:09: 18000000 INFO @ Sun, 02 Jun 2019 22:44:16: 17000000 INFO @ Sun, 02 Jun 2019 22:44:17: 16000000 INFO @ Sun, 02 Jun 2019 22:44:17: 19000000 INFO @ Sun, 02 Jun 2019 22:44:25: 18000000 INFO @ Sun, 02 Jun 2019 22:44:25: 20000000 INFO @ Sun, 02 Jun 2019 22:44:26: 17000000 INFO @ Sun, 02 Jun 2019 22:44:31: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:44:31: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:44:31: #1 total tags in treatment: 20734697 INFO @ Sun, 02 Jun 2019 22:44:31: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:44:31: #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 22:44:32: #1 tags after filtering in treatment: 20734697 INFO @ Sun, 02 Jun 2019 22:44:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:44:32: #1 finished! INFO @ Sun, 02 Jun 2019 22:44:32: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:44:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:44:34: 19000000 INFO @ Sun, 02 Jun 2019 22:44:35: #2 number of paired peaks: 5451 INFO @ Sun, 02 Jun 2019 22:44:35: start model_add_line... INFO @ Sun, 02 Jun 2019 22:44:35: start X-correlation... INFO @ Sun, 02 Jun 2019 22:44:35: end of X-cor INFO @ Sun, 02 Jun 2019 22:44:35: #2 finished! INFO @ Sun, 02 Jun 2019 22:44:35: #2 predicted fragment length is 101 bps INFO @ Sun, 02 Jun 2019 22:44:35: #2 alternative fragment length(s) may be 3,101 bps INFO @ Sun, 02 Jun 2019 22:44:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402720/SRX5402720.20_model.r INFO @ Sun, 02 Jun 2019 22:44:35: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:44:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:44:36: 18000000 INFO @ Sun, 02 Jun 2019 22:44:43: 20000000 INFO @ Sun, 02 Jun 2019 22:44:45: 19000000 INFO @ Sun, 02 Jun 2019 22:44:50: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:44:50: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:44:50: #1 total tags in treatment: 20734697 INFO @ Sun, 02 Jun 2019 22:44:50: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:44:50: #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 22:44:50: #1 tags after filtering in treatment: 20734697 INFO @ Sun, 02 Jun 2019 22:44:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:44:50: #1 finished! INFO @ Sun, 02 Jun 2019 22:44:50: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:44:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:44:53: #2 number of paired peaks: 5451 INFO @ Sun, 02 Jun 2019 22:44:53: start model_add_line... INFO @ Sun, 02 Jun 2019 22:44:54: start X-correlation... INFO @ Sun, 02 Jun 2019 22:44:54: end of X-cor INFO @ Sun, 02 Jun 2019 22:44:54: #2 finished! INFO @ Sun, 02 Jun 2019 22:44:54: #2 predicted fragment length is 101 bps INFO @ Sun, 02 Jun 2019 22:44:54: #2 alternative fragment length(s) may be 3,101 bps INFO @ Sun, 02 Jun 2019 22:44:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402720/SRX5402720.05_model.r INFO @ Sun, 02 Jun 2019 22:44:54: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:44:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:44:55: 20000000 INFO @ Sun, 02 Jun 2019 22:45:02: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:45:02: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:45:02: #1 total tags in treatment: 20734697 INFO @ Sun, 02 Jun 2019 22:45:02: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:45:02: #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 22:45:02: #1 tags after filtering in treatment: 20734697 INFO @ Sun, 02 Jun 2019 22:45:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:45:02: #1 finished! INFO @ Sun, 02 Jun 2019 22:45:02: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:45:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:45:05: #2 number of paired peaks: 5451 INFO @ Sun, 02 Jun 2019 22:45:05: start model_add_line... INFO @ Sun, 02 Jun 2019 22:45:06: start X-correlation... INFO @ Sun, 02 Jun 2019 22:45:06: end of X-cor INFO @ Sun, 02 Jun 2019 22:45:06: #2 finished! INFO @ Sun, 02 Jun 2019 22:45:06: #2 predicted fragment length is 101 bps INFO @ Sun, 02 Jun 2019 22:45:06: #2 alternative fragment length(s) may be 3,101 bps INFO @ Sun, 02 Jun 2019 22:45:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402720/SRX5402720.10_model.r INFO @ Sun, 02 Jun 2019 22:45:06: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:45:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:45:33: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:45:52: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:45:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402720/SRX5402720.20_peaks.xls INFO @ Sun, 02 Jun 2019 22:45:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402720/SRX5402720.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:45:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402720/SRX5402720.20_summits.bed INFO @ Sun, 02 Jun 2019 22:45:57: Done! pass1 - making usageList (6 chroms): 4 millis pass2 - checking and writing primary data (6931 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:46:03: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 02 Jun 2019 22:46:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402720/SRX5402720.05_peaks.xls INFO @ Sun, 02 Jun 2019 22:46:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402720/SRX5402720.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:46:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402720/SRX5402720.05_summits.bed INFO @ Sun, 02 Jun 2019 22:46:17: Done! pass1 - making usageList (6 chroms): 7 millis pass2 - checking and writing primary data (17494 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:46:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402720/SRX5402720.10_peaks.xls INFO @ Sun, 02 Jun 2019 22:46:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402720/SRX5402720.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:46:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402720/SRX5402720.10_summits.bed INFO @ Sun, 02 Jun 2019 22:46:25: Done! pass1 - making usageList (6 chroms): 5 millis pass2 - checking and writing primary data (13170 records, 4 fields): 20 millis CompletedMACS2peakCalling BigWig に変換しました。