Job ID = 1293154 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 11,328,065 reads read : 22,656,130 reads written : 11,328,065 reads 0-length : 11,328,065 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: 00:02:21 11328065 reads; of these: 11328065 (100.00%) were unpaired; of these: 313971 (2.77%) aligned 0 times 10002788 (88.30%) aligned exactly 1 time 1011306 (8.93%) aligned >1 times 97.23% overall alignment rate Time searching: 00:02:21 Overall time: 00:02:21 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] 2406449 / 11014094 = 0.2185 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 22:07:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402722/SRX5402722.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402722/SRX5402722.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402722/SRX5402722.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402722/SRX5402722.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 22:07:52: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:07:52: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:07:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402722/SRX5402722.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402722/SRX5402722.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402722/SRX5402722.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402722/SRX5402722.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 22:07:52: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:07:52: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:07:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402722/SRX5402722.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402722/SRX5402722.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402722/SRX5402722.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402722/SRX5402722.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 22:07:52: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:07:52: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:08:01: 1000000 INFO @ Sun, 02 Jun 2019 22:08:02: 1000000 INFO @ Sun, 02 Jun 2019 22:08:02: 1000000 INFO @ Sun, 02 Jun 2019 22:08:08: 2000000 INFO @ Sun, 02 Jun 2019 22:08:10: 2000000 INFO @ Sun, 02 Jun 2019 22:08:11: 2000000 INFO @ Sun, 02 Jun 2019 22:08:16: 3000000 INFO @ Sun, 02 Jun 2019 22:08:19: 3000000 INFO @ Sun, 02 Jun 2019 22:08:19: 3000000 INFO @ Sun, 02 Jun 2019 22:08:23: 4000000 INFO @ Sun, 02 Jun 2019 22:08:27: 4000000 INFO @ Sun, 02 Jun 2019 22:08:28: 4000000 INFO @ Sun, 02 Jun 2019 22:08:31: 5000000 INFO @ Sun, 02 Jun 2019 22:08:36: 5000000 INFO @ Sun, 02 Jun 2019 22:08:37: 5000000 INFO @ Sun, 02 Jun 2019 22:08:39: 6000000 INFO @ Sun, 02 Jun 2019 22:08:44: 6000000 INFO @ Sun, 02 Jun 2019 22:08:45: 6000000 INFO @ Sun, 02 Jun 2019 22:08:46: 7000000 INFO @ Sun, 02 Jun 2019 22:08:53: 7000000 INFO @ Sun, 02 Jun 2019 22:08:54: 8000000 INFO @ Sun, 02 Jun 2019 22:08:54: 7000000 INFO @ Sun, 02 Jun 2019 22:08:58: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 22:08:58: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 22:08:58: #1 total tags in treatment: 8607645 INFO @ Sun, 02 Jun 2019 22:08:58: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:08:58: #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 22:08:59: #1 tags after filtering in treatment: 8607645 INFO @ Sun, 02 Jun 2019 22:08:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:08:59: #1 finished! INFO @ Sun, 02 Jun 2019 22:08:59: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:08:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:09:00: #2 number of paired peaks: 2579 INFO @ Sun, 02 Jun 2019 22:09:00: start model_add_line... INFO @ Sun, 02 Jun 2019 22:09:00: start X-correlation... INFO @ Sun, 02 Jun 2019 22:09:00: end of X-cor INFO @ Sun, 02 Jun 2019 22:09:00: #2 finished! INFO @ Sun, 02 Jun 2019 22:09:00: #2 predicted fragment length is 152 bps INFO @ Sun, 02 Jun 2019 22:09:00: #2 alternative fragment length(s) may be 3,152 bps INFO @ Sun, 02 Jun 2019 22:09:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402722/SRX5402722.20_model.r INFO @ Sun, 02 Jun 2019 22:09:00: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:09:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:09:01: 8000000 INFO @ Sun, 02 Jun 2019 22:09:03: 8000000 INFO @ Sun, 02 Jun 2019 22:09:07: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 22:09:07: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 22:09:07: #1 total tags in treatment: 8607645 INFO @ Sun, 02 Jun 2019 22:09:07: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:09:07: #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 22:09:07: #1 tags after filtering in treatment: 8607645 INFO @ Sun, 02 Jun 2019 22:09:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:09:07: #1 finished! INFO @ Sun, 02 Jun 2019 22:09:07: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:09:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:09:08: #2 number of paired peaks: 2579 INFO @ Sun, 02 Jun 2019 22:09:08: start model_add_line... INFO @ Sun, 02 Jun 2019 22:09:08: start X-correlation... INFO @ Sun, 02 Jun 2019 22:09:08: end of X-cor INFO @ Sun, 02 Jun 2019 22:09:08: #2 finished! INFO @ Sun, 02 Jun 2019 22:09:08: #2 predicted fragment length is 152 bps INFO @ Sun, 02 Jun 2019 22:09:08: #2 alternative fragment length(s) may be 3,152 bps INFO @ Sun, 02 Jun 2019 22:09:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402722/SRX5402722.10_model.r INFO @ Sun, 02 Jun 2019 22:09:08: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:09:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:09:08: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 22:09:08: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 22:09:08: #1 total tags in treatment: 8607645 INFO @ Sun, 02 Jun 2019 22:09:08: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:09:08: #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 22:09:08: #1 tags after filtering in treatment: 8607645 INFO @ Sun, 02 Jun 2019 22:09:08: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:09:08: #1 finished! INFO @ Sun, 02 Jun 2019 22:09:08: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:09:08: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:09:09: #2 number of paired peaks: 2579 INFO @ Sun, 02 Jun 2019 22:09:09: start model_add_line... INFO @ Sun, 02 Jun 2019 22:09:09: start X-correlation... INFO @ Sun, 02 Jun 2019 22:09:09: end of X-cor INFO @ Sun, 02 Jun 2019 22:09:09: #2 finished! INFO @ Sun, 02 Jun 2019 22:09:09: #2 predicted fragment length is 152 bps INFO @ Sun, 02 Jun 2019 22:09:09: #2 alternative fragment length(s) may be 3,152 bps INFO @ Sun, 02 Jun 2019 22:09:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402722/SRX5402722.05_model.r INFO @ Sun, 02 Jun 2019 22:09:09: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:09:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:09:26: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:09:34: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:09:36: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:09:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402722/SRX5402722.20_peaks.xls INFO @ Sun, 02 Jun 2019 22:09:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402722/SRX5402722.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:09:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402722/SRX5402722.20_summits.bed INFO @ Sun, 02 Jun 2019 22:09:39: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (591 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:09:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402722/SRX5402722.10_peaks.xls INFO @ Sun, 02 Jun 2019 22:09:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402722/SRX5402722.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:09:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402722/SRX5402722.10_summits.bed INFO @ Sun, 02 Jun 2019 22:09:47: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3369 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:09:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402722/SRX5402722.05_peaks.xls INFO @ Sun, 02 Jun 2019 22:09:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402722/SRX5402722.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:09:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402722/SRX5402722.05_summits.bed INFO @ Sun, 02 Jun 2019 22:09:50: Done! pass1 - making usageList (7 chroms): 5 millis pass2 - checking and writing primary data (7887 records, 4 fields): 16 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。