Job ID = 1292490 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 16,986,480 reads read : 16,986,480 reads written : 16,986,480 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: 00:03:55 16986480 reads; of these: 16986480 (100.00%) were unpaired; of these: 316287 (1.86%) aligned 0 times 15015074 (88.39%) aligned exactly 1 time 1655119 (9.74%) aligned >1 times 98.14% overall alignment rate Time searching: 00:03:55 Overall time: 00:03:55 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] 3292080 / 16670193 = 0.1975 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 19:15:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466474/SRX466474.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466474/SRX466474.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466474/SRX466474.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466474/SRX466474.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 19:15:50: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:15:50: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:15:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466474/SRX466474.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466474/SRX466474.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466474/SRX466474.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466474/SRX466474.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 19:15:50: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:15:50: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:15:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466474/SRX466474.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466474/SRX466474.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466474/SRX466474.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466474/SRX466474.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 19:15:50: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:15:50: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:15:58: 1000000 INFO @ Sun, 02 Jun 2019 19:15:59: 1000000 INFO @ Sun, 02 Jun 2019 19:15:59: 1000000 INFO @ Sun, 02 Jun 2019 19:16:05: 2000000 INFO @ Sun, 02 Jun 2019 19:16:07: 2000000 INFO @ Sun, 02 Jun 2019 19:16:07: 2000000 INFO @ Sun, 02 Jun 2019 19:16:11: 3000000 INFO @ Sun, 02 Jun 2019 19:16:15: 3000000 INFO @ Sun, 02 Jun 2019 19:16:15: 3000000 INFO @ Sun, 02 Jun 2019 19:16:18: 4000000 INFO @ Sun, 02 Jun 2019 19:16:23: 4000000 INFO @ Sun, 02 Jun 2019 19:16:23: 4000000 INFO @ Sun, 02 Jun 2019 19:16:25: 5000000 INFO @ Sun, 02 Jun 2019 19:16:31: 5000000 INFO @ Sun, 02 Jun 2019 19:16:31: 5000000 INFO @ Sun, 02 Jun 2019 19:16:32: 6000000 INFO @ Sun, 02 Jun 2019 19:16:39: 7000000 INFO @ Sun, 02 Jun 2019 19:16:39: 6000000 INFO @ Sun, 02 Jun 2019 19:16:39: 6000000 INFO @ Sun, 02 Jun 2019 19:16:46: 8000000 INFO @ Sun, 02 Jun 2019 19:16:47: 7000000 INFO @ Sun, 02 Jun 2019 19:16:48: 7000000 INFO @ Sun, 02 Jun 2019 19:16:53: 9000000 INFO @ Sun, 02 Jun 2019 19:16:55: 8000000 INFO @ Sun, 02 Jun 2019 19:16:56: 8000000 INFO @ Sun, 02 Jun 2019 19:17:00: 10000000 INFO @ Sun, 02 Jun 2019 19:17:03: 9000000 INFO @ Sun, 02 Jun 2019 19:17:04: 9000000 INFO @ Sun, 02 Jun 2019 19:17:06: 11000000 INFO @ Sun, 02 Jun 2019 19:17:11: 10000000 INFO @ Sun, 02 Jun 2019 19:17:12: 10000000 INFO @ Sun, 02 Jun 2019 19:17:13: 12000000 INFO @ Sun, 02 Jun 2019 19:17:19: 11000000 INFO @ Sun, 02 Jun 2019 19:17:20: 11000000 INFO @ Sun, 02 Jun 2019 19:17:20: 13000000 INFO @ Sun, 02 Jun 2019 19:17:23: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 19:17:23: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 19:17:23: #1 total tags in treatment: 13378113 INFO @ Sun, 02 Jun 2019 19:17:23: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:17:23: #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 19:17:23: #1 tags after filtering in treatment: 13378113 INFO @ Sun, 02 Jun 2019 19:17:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:17:23: #1 finished! INFO @ Sun, 02 Jun 2019 19:17:23: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:17:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:17:25: #2 number of paired peaks: 644 WARNING @ Sun, 02 Jun 2019 19:17:25: Fewer paired peaks (644) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 644 pairs to build model! INFO @ Sun, 02 Jun 2019 19:17:25: start model_add_line... INFO @ Sun, 02 Jun 2019 19:17:25: start X-correlation... INFO @ Sun, 02 Jun 2019 19:17:25: end of X-cor INFO @ Sun, 02 Jun 2019 19:17:25: #2 finished! INFO @ Sun, 02 Jun 2019 19:17:25: #2 predicted fragment length is 137 bps INFO @ Sun, 02 Jun 2019 19:17:25: #2 alternative fragment length(s) may be 3,137 bps INFO @ Sun, 02 Jun 2019 19:17:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466474/SRX466474.20_model.r INFO @ Sun, 02 Jun 2019 19:17:25: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:17:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:17:27: 12000000 INFO @ Sun, 02 Jun 2019 19:17:28: 12000000 INFO @ Sun, 02 Jun 2019 19:17:35: 13000000 INFO @ Sun, 02 Jun 2019 19:17:36: 13000000 INFO @ Sun, 02 Jun 2019 19:17:38: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 19:17:38: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 19:17:38: #1 total tags in treatment: 13378113 INFO @ Sun, 02 Jun 2019 19:17:38: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:17:38: #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 19:17:38: #1 tags after filtering in treatment: 13378113 INFO @ Sun, 02 Jun 2019 19:17:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:17:38: #1 finished! INFO @ Sun, 02 Jun 2019 19:17:38: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:17:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:17:39: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 19:17:39: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 19:17:39: #1 total tags in treatment: 13378113 INFO @ Sun, 02 Jun 2019 19:17:39: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:17:39: #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 19:17:39: #1 tags after filtering in treatment: 13378113 INFO @ Sun, 02 Jun 2019 19:17:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:17:39: #1 finished! INFO @ Sun, 02 Jun 2019 19:17:39: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:17:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:17:40: #2 number of paired peaks: 644 WARNING @ Sun, 02 Jun 2019 19:17:40: Fewer paired peaks (644) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 644 pairs to build model! INFO @ Sun, 02 Jun 2019 19:17:40: start model_add_line... INFO @ Sun, 02 Jun 2019 19:17:40: start X-correlation... INFO @ Sun, 02 Jun 2019 19:17:40: end of X-cor INFO @ Sun, 02 Jun 2019 19:17:40: #2 finished! INFO @ Sun, 02 Jun 2019 19:17:40: #2 predicted fragment length is 137 bps INFO @ Sun, 02 Jun 2019 19:17:40: #2 alternative fragment length(s) may be 3,137 bps INFO @ Sun, 02 Jun 2019 19:17:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466474/SRX466474.05_model.r INFO @ Sun, 02 Jun 2019 19:17:40: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:17:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:17:40: #2 number of paired peaks: 644 WARNING @ Sun, 02 Jun 2019 19:17:40: Fewer paired peaks (644) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 644 pairs to build model! INFO @ Sun, 02 Jun 2019 19:17:40: start model_add_line... INFO @ Sun, 02 Jun 2019 19:17:40: start X-correlation... INFO @ Sun, 02 Jun 2019 19:17:40: end of X-cor INFO @ Sun, 02 Jun 2019 19:17:40: #2 finished! INFO @ Sun, 02 Jun 2019 19:17:40: #2 predicted fragment length is 137 bps INFO @ Sun, 02 Jun 2019 19:17:40: #2 alternative fragment length(s) may be 3,137 bps INFO @ Sun, 02 Jun 2019 19:17:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466474/SRX466474.10_model.r INFO @ Sun, 02 Jun 2019 19:17:40: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:17:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:18:03: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:18:17: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:18:18: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:18:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466474/SRX466474.20_peaks.xls INFO @ Sun, 02 Jun 2019 19:18:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466474/SRX466474.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:18:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466474/SRX466474.20_summits.bed INFO @ Sun, 02 Jun 2019 19:18:21: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (1617 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:18:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466474/SRX466474.05_peaks.xls INFO @ Sun, 02 Jun 2019 19:18:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466474/SRX466474.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:18:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466474/SRX466474.05_summits.bed INFO @ Sun, 02 Jun 2019 19:18:36: Done! INFO @ Sun, 02 Jun 2019 19:18:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466474/SRX466474.10_peaks.xls INFO @ Sun, 02 Jun 2019 19:18:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466474/SRX466474.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:18:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466474/SRX466474.10_summits.bed INFO @ Sun, 02 Jun 2019 19:18:36: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (11975 records, 4 fields): 16 millis CompletedMACS2peakCalling pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (5633 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。