Job ID = 1292003 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 22,272,822 reads read : 44,545,644 reads written : 44,545,644 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: 00:26:43 22272822 reads; of these: 22272822 (100.00%) were paired; of these: 10407087 (46.73%) aligned concordantly 0 times 10040370 (45.08%) aligned concordantly exactly 1 time 1825365 (8.20%) aligned concordantly >1 times ---- 10407087 pairs aligned concordantly 0 times; of these: 1491769 (14.33%) aligned discordantly 1 time ---- 8915318 pairs aligned 0 times concordantly or discordantly; of these: 17830636 mates make up the pairs; of these: 16252563 (91.15%) aligned 0 times 987508 (5.54%) aligned exactly 1 time 590565 (3.31%) aligned >1 times 63.51% overall alignment rate Time searching: 00:26:43 Overall time: 00:26:43 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 12 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 11629749 / 13352796 = 0.8710 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 17:58:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2978699/SRX2978699.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2978699/SRX2978699.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2978699/SRX2978699.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2978699/SRX2978699.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 17:58:50: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:58:50: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:58:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2978699/SRX2978699.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2978699/SRX2978699.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2978699/SRX2978699.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2978699/SRX2978699.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 17:58:50: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:58:50: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:58:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2978699/SRX2978699.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2978699/SRX2978699.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2978699/SRX2978699.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2978699/SRX2978699.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 17:58:50: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:58:50: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:59:01: 1000000 INFO @ Sun, 02 Jun 2019 17:59:02: 1000000 INFO @ Sun, 02 Jun 2019 17:59:02: 1000000 INFO @ Sun, 02 Jun 2019 17:59:12: 2000000 INFO @ Sun, 02 Jun 2019 17:59:13: 2000000 INFO @ Sun, 02 Jun 2019 17:59:13: 2000000 INFO @ Sun, 02 Jun 2019 17:59:23: 3000000 INFO @ Sun, 02 Jun 2019 17:59:25: 3000000 INFO @ Sun, 02 Jun 2019 17:59:26: 3000000 INFO @ Sun, 02 Jun 2019 17:59:33: 4000000 INFO @ Sun, 02 Jun 2019 17:59:37: 4000000 INFO @ Sun, 02 Jun 2019 17:59:38: 4000000 INFO @ Sun, 02 Jun 2019 17:59:44: 5000000 INFO @ Sun, 02 Jun 2019 17:59:44: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 17:59:44: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 17:59:44: #1 total tags in treatment: 1456772 INFO @ Sun, 02 Jun 2019 17:59:44: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:59:44: #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 17:59:44: #1 tags after filtering in treatment: 1288099 INFO @ Sun, 02 Jun 2019 17:59:44: #1 Redundant rate of treatment: 0.12 INFO @ Sun, 02 Jun 2019 17:59:44: #1 finished! INFO @ Sun, 02 Jun 2019 17:59:44: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:59:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:59:45: #2 number of paired peaks: 1269 INFO @ Sun, 02 Jun 2019 17:59:45: start model_add_line... INFO @ Sun, 02 Jun 2019 17:59:45: start X-correlation... INFO @ Sun, 02 Jun 2019 17:59:45: end of X-cor INFO @ Sun, 02 Jun 2019 17:59:45: #2 finished! INFO @ Sun, 02 Jun 2019 17:59:45: #2 predicted fragment length is 196 bps INFO @ Sun, 02 Jun 2019 17:59:45: #2 alternative fragment length(s) may be 196 bps INFO @ Sun, 02 Jun 2019 17:59:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2978699/SRX2978699.05_model.r INFO @ Sun, 02 Jun 2019 17:59:45: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:59:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:59:48: 5000000 INFO @ Sun, 02 Jun 2019 17:59:48: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 17:59:48: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 17:59:48: #1 total tags in treatment: 1456772 INFO @ Sun, 02 Jun 2019 17:59:48: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:59:48: #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 17:59:48: #1 tags after filtering in treatment: 1288099 INFO @ Sun, 02 Jun 2019 17:59:48: #1 Redundant rate of treatment: 0.12 INFO @ Sun, 02 Jun 2019 17:59:48: #1 finished! INFO @ Sun, 02 Jun 2019 17:59:48: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:59:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:59:48: #2 number of paired peaks: 1269 INFO @ Sun, 02 Jun 2019 17:59:48: start model_add_line... INFO @ Sun, 02 Jun 2019 17:59:48: start X-correlation... INFO @ Sun, 02 Jun 2019 17:59:48: end of X-cor INFO @ Sun, 02 Jun 2019 17:59:48: #2 finished! INFO @ Sun, 02 Jun 2019 17:59:48: #2 predicted fragment length is 196 bps INFO @ Sun, 02 Jun 2019 17:59:48: #2 alternative fragment length(s) may be 196 bps INFO @ Sun, 02 Jun 2019 17:59:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2978699/SRX2978699.10_model.r INFO @ Sun, 02 Jun 2019 17:59:48: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:59:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:59:51: 5000000 INFO @ Sun, 02 Jun 2019 17:59:51: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 17:59:51: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 17:59:51: #1 total tags in treatment: 1456772 INFO @ Sun, 02 Jun 2019 17:59:51: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:59:51: #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 17:59:51: #1 tags after filtering in treatment: 1288099 INFO @ Sun, 02 Jun 2019 17:59:51: #1 Redundant rate of treatment: 0.12 INFO @ Sun, 02 Jun 2019 17:59:51: #1 finished! INFO @ Sun, 02 Jun 2019 17:59:51: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:59:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:59:52: #2 number of paired peaks: 1269 INFO @ Sun, 02 Jun 2019 17:59:52: start model_add_line... INFO @ Sun, 02 Jun 2019 17:59:52: start X-correlation... INFO @ Sun, 02 Jun 2019 17:59:52: end of X-cor INFO @ Sun, 02 Jun 2019 17:59:52: #2 finished! INFO @ Sun, 02 Jun 2019 17:59:52: #2 predicted fragment length is 196 bps INFO @ Sun, 02 Jun 2019 17:59:52: #2 alternative fragment length(s) may be 196 bps INFO @ Sun, 02 Jun 2019 17:59:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2978699/SRX2978699.20_model.r INFO @ Sun, 02 Jun 2019 17:59:52: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:59:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:59:52: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:59:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2978699/SRX2978699.05_peaks.xls INFO @ Sun, 02 Jun 2019 17:59:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2978699/SRX2978699.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:59:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2978699/SRX2978699.05_summits.bed INFO @ Sun, 02 Jun 2019 17:59:55: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (777 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 17:59:56: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:59:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2978699/SRX2978699.10_peaks.xls INFO @ Sun, 02 Jun 2019 17:59:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2978699/SRX2978699.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:59:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2978699/SRX2978699.10_summits.bed INFO @ Sun, 02 Jun 2019 17:59:58: Done! INFO @ Sun, 02 Jun 2019 17:59:59: #3 Call peaks for each chromosome... pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (440 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:00:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2978699/SRX2978699.20_peaks.xls INFO @ Sun, 02 Jun 2019 18:00:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2978699/SRX2978699.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:00:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2978699/SRX2978699.20_summits.bed INFO @ Sun, 02 Jun 2019 18:00:01: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (210 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。