Job ID = 1296401 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-06-03T07:15:47 fasterq-dump.2.9.6 fatal: SIGNAL - Segmentation fault spots read : 35,115,748 reads read : 70,231,496 reads written : 70,231,496 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: 00:10:51 35115748 reads; of these: 35115748 (100.00%) were paired; of these: 33622577 (95.75%) aligned concordantly 0 times 1174463 (3.34%) aligned concordantly exactly 1 time 318708 (0.91%) aligned concordantly >1 times ---- 33622577 pairs aligned concordantly 0 times; of these: 3017 (0.01%) aligned discordantly 1 time ---- 33619560 pairs aligned 0 times concordantly or discordantly; of these: 67239120 mates make up the pairs; of these: 66670361 (99.15%) aligned 0 times 166977 (0.25%) aligned exactly 1 time 401782 (0.60%) aligned >1 times 5.07% overall alignment rate Time searching: 00:10:51 Overall time: 00:10:51 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 73453 / 1493557 = 0.0492 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 @ Mon, 03 Jun 2019 16:30:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650754/SRX4650754.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650754/SRX4650754.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650754/SRX4650754.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650754/SRX4650754.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 16:30:06: #1 read tag files... INFO @ Mon, 03 Jun 2019 16:30:06: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 16:30:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650754/SRX4650754.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650754/SRX4650754.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650754/SRX4650754.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650754/SRX4650754.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 16:30:06: #1 read tag files... INFO @ Mon, 03 Jun 2019 16:30:06: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 16:30:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650754/SRX4650754.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650754/SRX4650754.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650754/SRX4650754.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650754/SRX4650754.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 16:30:06: #1 read tag files... INFO @ Mon, 03 Jun 2019 16:30:06: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 16:30:14: 1000000 INFO @ Mon, 03 Jun 2019 16:30:16: 1000000 INFO @ Mon, 03 Jun 2019 16:30:16: 1000000 INFO @ Mon, 03 Jun 2019 16:30:21: 2000000 INFO @ Mon, 03 Jun 2019 16:30:25: 2000000 INFO @ Mon, 03 Jun 2019 16:30:25: 2000000 INFO @ Mon, 03 Jun 2019 16:30:29: 3000000 INFO @ Mon, 03 Jun 2019 16:30:32: #1 tag size is determined as 38 bps INFO @ Mon, 03 Jun 2019 16:30:32: #1 tag size = 38 INFO @ Mon, 03 Jun 2019 16:30:32: #1 total tags in treatment: 1419878 INFO @ Mon, 03 Jun 2019 16:30:32: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 16:30:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 16:30:32: #1 tags after filtering in treatment: 1372554 INFO @ Mon, 03 Jun 2019 16:30:32: #1 Redundant rate of treatment: 0.03 INFO @ Mon, 03 Jun 2019 16:30:32: #1 finished! INFO @ Mon, 03 Jun 2019 16:30:32: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 16:30:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 16:30:32: #2 number of paired peaks: 3078 INFO @ Mon, 03 Jun 2019 16:30:32: start model_add_line... INFO @ Mon, 03 Jun 2019 16:30:32: start X-correlation... INFO @ Mon, 03 Jun 2019 16:30:32: end of X-cor INFO @ Mon, 03 Jun 2019 16:30:32: #2 finished! INFO @ Mon, 03 Jun 2019 16:30:32: #2 predicted fragment length is 147 bps INFO @ Mon, 03 Jun 2019 16:30:32: #2 alternative fragment length(s) may be 4,147 bps INFO @ Mon, 03 Jun 2019 16:30:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650754/SRX4650754.05_model.r INFO @ Mon, 03 Jun 2019 16:30:32: #3 Call peaks... INFO @ Mon, 03 Jun 2019 16:30:32: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 16:30:33: 3000000 INFO @ Mon, 03 Jun 2019 16:30:34: 3000000 INFO @ Mon, 03 Jun 2019 16:30:37: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 16:30:37: #1 tag size is determined as 38 bps INFO @ Mon, 03 Jun 2019 16:30:37: #1 tag size = 38 INFO @ Mon, 03 Jun 2019 16:30:37: #1 total tags in treatment: 1419878 INFO @ Mon, 03 Jun 2019 16:30:37: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 16:30:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 16:30:37: #1 tags after filtering in treatment: 1372554 INFO @ Mon, 03 Jun 2019 16:30:37: #1 Redundant rate of treatment: 0.03 INFO @ Mon, 03 Jun 2019 16:30:37: #1 finished! INFO @ Mon, 03 Jun 2019 16:30:37: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 16:30:37: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 16:30:37: #2 number of paired peaks: 3078 INFO @ Mon, 03 Jun 2019 16:30:37: start model_add_line... INFO @ Mon, 03 Jun 2019 16:30:37: start X-correlation... INFO @ Mon, 03 Jun 2019 16:30:37: end of X-cor INFO @ Mon, 03 Jun 2019 16:30:37: #2 finished! INFO @ Mon, 03 Jun 2019 16:30:37: #2 predicted fragment length is 147 bps INFO @ Mon, 03 Jun 2019 16:30:37: #2 alternative fragment length(s) may be 4,147 bps INFO @ Mon, 03 Jun 2019 16:30:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650754/SRX4650754.20_model.r INFO @ Mon, 03 Jun 2019 16:30:37: #3 Call peaks... INFO @ Mon, 03 Jun 2019 16:30:37: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 16:30:38: #1 tag size is determined as 38 bps INFO @ Mon, 03 Jun 2019 16:30:38: #1 tag size = 38 INFO @ Mon, 03 Jun 2019 16:30:38: #1 total tags in treatment: 1419878 INFO @ Mon, 03 Jun 2019 16:30:38: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 16:30:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 16:30:38: #1 tags after filtering in treatment: 1372554 INFO @ Mon, 03 Jun 2019 16:30:38: #1 Redundant rate of treatment: 0.03 INFO @ Mon, 03 Jun 2019 16:30:38: #1 finished! INFO @ Mon, 03 Jun 2019 16:30:38: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 16:30:38: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 16:30:38: #2 number of paired peaks: 3078 INFO @ Mon, 03 Jun 2019 16:30:38: start model_add_line... INFO @ Mon, 03 Jun 2019 16:30:38: start X-correlation... INFO @ Mon, 03 Jun 2019 16:30:38: end of X-cor INFO @ Mon, 03 Jun 2019 16:30:38: #2 finished! INFO @ Mon, 03 Jun 2019 16:30:38: #2 predicted fragment length is 147 bps INFO @ Mon, 03 Jun 2019 16:30:38: #2 alternative fragment length(s) may be 4,147 bps INFO @ Mon, 03 Jun 2019 16:30:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650754/SRX4650754.10_model.r INFO @ Mon, 03 Jun 2019 16:30:38: #3 Call peaks... INFO @ Mon, 03 Jun 2019 16:30:38: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 16:30:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650754/SRX4650754.05_peaks.xls INFO @ Mon, 03 Jun 2019 16:30:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650754/SRX4650754.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 16:30:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650754/SRX4650754.05_summits.bed INFO @ Mon, 03 Jun 2019 16:30:39: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (273 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 16:30:42: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 16:30:43: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 16:30:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650754/SRX4650754.20_peaks.xls INFO @ Mon, 03 Jun 2019 16:30:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650754/SRX4650754.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 16:30:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650754/SRX4650754.20_summits.bed INFO @ Mon, 03 Jun 2019 16:30:45: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (60 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 16:30:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650754/SRX4650754.10_peaks.xls INFO @ Mon, 03 Jun 2019 16:30:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650754/SRX4650754.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 16:30:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650754/SRX4650754.10_summits.bed INFO @ Mon, 03 Jun 2019 16:30:46: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (125 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。