Job ID = 5721141 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 2,343,617 reads read : 4,687,234 reads written : 4,687,234 rm: cannot remove ‘[DSE]RR*’: 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: 00:03:37 2343617 reads; of these: 2343617 (100.00%) were paired; of these: 617129 (26.33%) aligned concordantly 0 times 1459857 (62.29%) aligned concordantly exactly 1 time 266631 (11.38%) aligned concordantly >1 times ---- 617129 pairs aligned concordantly 0 times; of these: 316971 (51.36%) aligned discordantly 1 time ---- 300158 pairs aligned 0 times concordantly or discordantly; of these: 600316 mates make up the pairs; of these: 286401 (47.71%) aligned 0 times 173907 (28.97%) aligned exactly 1 time 140008 (23.32%) aligned >1 times 93.89% overall alignment rate Time searching: 00:03:37 Overall time: 00:03:37 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] 94713 / 2033828 = 0.0466 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 16 Apr 2020 05:21:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708280/SRX6708280.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708280/SRX6708280.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708280/SRX6708280.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708280/SRX6708280.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 @ Thu, 16 Apr 2020 05:21:24: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:21:24: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:21:29: 1000000 INFO @ Thu, 16 Apr 2020 05:21:34: 2000000 INFO @ Thu, 16 Apr 2020 05:21:39: 3000000 INFO @ Thu, 16 Apr 2020 05:21:43: 4000000 INFO @ Thu, 16 Apr 2020 05:21:44: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:21:44: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:21:44: #1 total tags in treatment: 1639660 INFO @ Thu, 16 Apr 2020 05:21:44: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:21:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 05:21:44: #1 tags after filtering in treatment: 1587071 INFO @ Thu, 16 Apr 2020 05:21:44: #1 Redundant rate of treatment: 0.03 INFO @ Thu, 16 Apr 2020 05:21:44: #1 finished! INFO @ Thu, 16 Apr 2020 05:21:44: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:21:44: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:21:44: #2 number of paired peaks: 4486 INFO @ Thu, 16 Apr 2020 05:21:44: start model_add_line... INFO @ Thu, 16 Apr 2020 05:21:44: start X-correlation... INFO @ Thu, 16 Apr 2020 05:21:44: end of X-cor INFO @ Thu, 16 Apr 2020 05:21:44: #2 finished! INFO @ Thu, 16 Apr 2020 05:21:44: #2 predicted fragment length is 240 bps INFO @ Thu, 16 Apr 2020 05:21:44: #2 alternative fragment length(s) may be 240 bps INFO @ Thu, 16 Apr 2020 05:21:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708280/SRX6708280.05_model.r INFO @ Thu, 16 Apr 2020 05:21:44: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:21:44: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:21:48: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:21:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708280/SRX6708280.05_peaks.xls INFO @ Thu, 16 Apr 2020 05:21:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708280/SRX6708280.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:21:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708280/SRX6708280.05_summits.bed INFO @ Thu, 16 Apr 2020 05:21:50: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1319 records, 4 fields): 2 millis CompletedMACS2peakCalling WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 16 Apr 2020 05:21:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708280/SRX6708280.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708280/SRX6708280.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708280/SRX6708280.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708280/SRX6708280.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 @ Thu, 16 Apr 2020 05:21:54: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:21:54: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:21:59: 1000000 INFO @ Thu, 16 Apr 2020 05:22:04: 2000000 INFO @ Thu, 16 Apr 2020 05:22:08: 3000000 INFO @ Thu, 16 Apr 2020 05:22:13: 4000000 INFO @ Thu, 16 Apr 2020 05:22:14: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:22:14: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:22:14: #1 total tags in treatment: 1639660 INFO @ Thu, 16 Apr 2020 05:22:14: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:22:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 05:22:14: #1 tags after filtering in treatment: 1587071 INFO @ Thu, 16 Apr 2020 05:22:14: #1 Redundant rate of treatment: 0.03 INFO @ Thu, 16 Apr 2020 05:22:14: #1 finished! INFO @ Thu, 16 Apr 2020 05:22:14: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:22:14: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:22:14: #2 number of paired peaks: 4486 INFO @ Thu, 16 Apr 2020 05:22:14: start model_add_line... INFO @ Thu, 16 Apr 2020 05:22:14: start X-correlation... INFO @ Thu, 16 Apr 2020 05:22:14: end of X-cor INFO @ Thu, 16 Apr 2020 05:22:14: #2 finished! INFO @ Thu, 16 Apr 2020 05:22:14: #2 predicted fragment length is 240 bps INFO @ Thu, 16 Apr 2020 05:22:14: #2 alternative fragment length(s) may be 240 bps INFO @ Thu, 16 Apr 2020 05:22:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708280/SRX6708280.10_model.r INFO @ Thu, 16 Apr 2020 05:22:14: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:22:14: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:22:18: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:22:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708280/SRX6708280.10_peaks.xls INFO @ Thu, 16 Apr 2020 05:22:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708280/SRX6708280.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:22:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708280/SRX6708280.10_summits.bed INFO @ Thu, 16 Apr 2020 05:22:20: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (377 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 16 Apr 2020 05:22:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708280/SRX6708280.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708280/SRX6708280.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708280/SRX6708280.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708280/SRX6708280.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 @ Thu, 16 Apr 2020 05:22:24: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:22:24: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:22:29: 1000000 INFO @ Thu, 16 Apr 2020 05:22:34: 2000000 INFO @ Thu, 16 Apr 2020 05:22:39: 3000000 INFO @ Thu, 16 Apr 2020 05:22:43: 4000000 INFO @ Thu, 16 Apr 2020 05:22:44: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:22:44: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:22:44: #1 total tags in treatment: 1639660 INFO @ Thu, 16 Apr 2020 05:22:44: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:22:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 05:22:44: #1 tags after filtering in treatment: 1587071 INFO @ Thu, 16 Apr 2020 05:22:44: #1 Redundant rate of treatment: 0.03 INFO @ Thu, 16 Apr 2020 05:22:44: #1 finished! INFO @ Thu, 16 Apr 2020 05:22:44: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:22:44: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:22:45: #2 number of paired peaks: 4486 INFO @ Thu, 16 Apr 2020 05:22:45: start model_add_line... INFO @ Thu, 16 Apr 2020 05:22:45: start X-correlation... INFO @ Thu, 16 Apr 2020 05:22:45: end of X-cor INFO @ Thu, 16 Apr 2020 05:22:45: #2 finished! INFO @ Thu, 16 Apr 2020 05:22:45: #2 predicted fragment length is 240 bps INFO @ Thu, 16 Apr 2020 05:22:45: #2 alternative fragment length(s) may be 240 bps INFO @ Thu, 16 Apr 2020 05:22:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708280/SRX6708280.20_model.r INFO @ Thu, 16 Apr 2020 05:22:45: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:22:45: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:22:48: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:22:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708280/SRX6708280.20_peaks.xls INFO @ Thu, 16 Apr 2020 05:22:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708280/SRX6708280.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:22:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708280/SRX6708280.20_summits.bed INFO @ Thu, 16 Apr 2020 05:22:50: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (153 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。