Job ID = 8071264 SRX = SRX7917538 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-08-08T04:26:02 prefetch.2.10.7: 1) Downloading 'SRR11313119'... 2020-08-08T04:26:02 prefetch.2.10.7: Downloading via HTTPS... 2020-08-08T04:26:30 prefetch.2.10.7: HTTPS download succeed 2020-08-08T04:26:30 prefetch.2.10.7: 'SRR11313119' is valid 2020-08-08T04:26:30 prefetch.2.10.7: 1) 'SRR11313119' was downloaded successfully Read 1889478 spots for SRR11313119/SRR11313119.sra Written 1889478 spots for SRR11313119/SRR11313119.sra fastq に変換しました。 bowtie でマッピング中... Your job 8072294 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:10 1889478 reads; of these: 1889478 (100.00%) were paired; of these: 445752 (23.59%) aligned concordantly 0 times 1268006 (67.11%) aligned concordantly exactly 1 time 175720 (9.30%) aligned concordantly >1 times ---- 445752 pairs aligned concordantly 0 times; of these: 168399 (37.78%) aligned discordantly 1 time ---- 277353 pairs aligned 0 times concordantly or discordantly; of these: 554706 mates make up the pairs; of these: 412949 (74.44%) aligned 0 times 74967 (13.51%) aligned exactly 1 time 66790 (12.04%) aligned >1 times 89.07% overall alignment rate Time searching: 00:02:10 Overall time: 00:02:10 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] 713278 / 1606310 = 0.4440 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 @ Sat, 08 Aug 2020 13:30:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7917538/SRX7917538.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7917538/SRX7917538.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7917538/SRX7917538.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7917538/SRX7917538.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 @ Sat, 08 Aug 2020 13:30:01: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:30:01: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:30:06: 1000000 INFO @ Sat, 08 Aug 2020 13:30:11: #1 tag size is determined as 62 bps INFO @ Sat, 08 Aug 2020 13:30:11: #1 tag size = 62 INFO @ Sat, 08 Aug 2020 13:30:11: #1 total tags in treatment: 758846 INFO @ Sat, 08 Aug 2020 13:30:11: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:30:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Aug 2020 13:30:11: #1 tags after filtering in treatment: 529666 INFO @ Sat, 08 Aug 2020 13:30:11: #1 Redundant rate of treatment: 0.30 INFO @ Sat, 08 Aug 2020 13:30:11: #1 finished! INFO @ Sat, 08 Aug 2020 13:30:11: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:30:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:30:11: #2 number of paired peaks: 5691 INFO @ Sat, 08 Aug 2020 13:30:11: start model_add_line... INFO @ Sat, 08 Aug 2020 13:30:11: start X-correlation... INFO @ Sat, 08 Aug 2020 13:30:11: end of X-cor INFO @ Sat, 08 Aug 2020 13:30:11: #2 finished! INFO @ Sat, 08 Aug 2020 13:30:11: #2 predicted fragment length is 192 bps INFO @ Sat, 08 Aug 2020 13:30:11: #2 alternative fragment length(s) may be 3,180,192 bps INFO @ Sat, 08 Aug 2020 13:30:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7917538/SRX7917538.05_model.r INFO @ Sat, 08 Aug 2020 13:30:11: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:30:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:30:12: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:30:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7917538/SRX7917538.05_peaks.xls INFO @ Sat, 08 Aug 2020 13:30:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7917538/SRX7917538.05_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:30:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7917538/SRX7917538.05_summits.bed INFO @ Sat, 08 Aug 2020 13:30:13: Done! pass1 - making usageList (2 chroms): 1 millis pass2 - checking and writing primary data (13 records, 4 fields): 12 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 @ Sat, 08 Aug 2020 13:30:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7917538/SRX7917538.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7917538/SRX7917538.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7917538/SRX7917538.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7917538/SRX7917538.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 @ Sat, 08 Aug 2020 13:30:31: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:30:31: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:30:36: 1000000 INFO @ Sat, 08 Aug 2020 13:30:41: #1 tag size is determined as 62 bps INFO @ Sat, 08 Aug 2020 13:30:41: #1 tag size = 62 INFO @ Sat, 08 Aug 2020 13:30:41: #1 total tags in treatment: 758846 INFO @ Sat, 08 Aug 2020 13:30:41: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:30:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Aug 2020 13:30:41: #1 tags after filtering in treatment: 529666 INFO @ Sat, 08 Aug 2020 13:30:41: #1 Redundant rate of treatment: 0.30 INFO @ Sat, 08 Aug 2020 13:30:41: #1 finished! INFO @ Sat, 08 Aug 2020 13:30:41: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:30:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:30:41: #2 number of paired peaks: 5691 INFO @ Sat, 08 Aug 2020 13:30:41: start model_add_line... INFO @ Sat, 08 Aug 2020 13:30:41: start X-correlation... INFO @ Sat, 08 Aug 2020 13:30:41: end of X-cor INFO @ Sat, 08 Aug 2020 13:30:41: #2 finished! INFO @ Sat, 08 Aug 2020 13:30:41: #2 predicted fragment length is 192 bps INFO @ Sat, 08 Aug 2020 13:30:41: #2 alternative fragment length(s) may be 3,180,192 bps INFO @ Sat, 08 Aug 2020 13:30:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7917538/SRX7917538.10_model.r INFO @ Sat, 08 Aug 2020 13:30:41: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:30:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:30:42: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:30:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7917538/SRX7917538.10_peaks.xls INFO @ Sat, 08 Aug 2020 13:30:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7917538/SRX7917538.10_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:30:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7917538/SRX7917538.10_summits.bed INFO @ Sat, 08 Aug 2020 13:30:42: Done! pass1 - making usageList (1 chroms): 0 millis pass2 - checking and writing primary data (2 records, 4 fields): 1 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 @ Sat, 08 Aug 2020 13:31:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7917538/SRX7917538.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7917538/SRX7917538.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7917538/SRX7917538.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7917538/SRX7917538.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 @ Sat, 08 Aug 2020 13:31:01: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:31:01: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:31:06: 1000000 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Sat, 08 Aug 2020 13:31:11: #1 tag size is determined as 62 bps INFO @ Sat, 08 Aug 2020 13:31:11: #1 tag size = 62 INFO @ Sat, 08 Aug 2020 13:31:11: #1 total tags in treatment: 758846 INFO @ Sat, 08 Aug 2020 13:31:11: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:31:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Aug 2020 13:31:11: #1 tags after filtering in treatment: 529666 INFO @ Sat, 08 Aug 2020 13:31:11: #1 Redundant rate of treatment: 0.30 INFO @ Sat, 08 Aug 2020 13:31:11: #1 finished! INFO @ Sat, 08 Aug 2020 13:31:11: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:31:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:31:11: #2 number of paired peaks: 5691 INFO @ Sat, 08 Aug 2020 13:31:11: start model_add_line... INFO @ Sat, 08 Aug 2020 13:31:11: start X-correlation... INFO @ Sat, 08 Aug 2020 13:31:11: end of X-cor INFO @ Sat, 08 Aug 2020 13:31:11: #2 finished! INFO @ Sat, 08 Aug 2020 13:31:11: #2 predicted fragment length is 192 bps INFO @ Sat, 08 Aug 2020 13:31:11: #2 alternative fragment length(s) may be 3,180,192 bps INFO @ Sat, 08 Aug 2020 13:31:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7917538/SRX7917538.20_model.r INFO @ Sat, 08 Aug 2020 13:31:11: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:31:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:31:12: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:31:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7917538/SRX7917538.20_peaks.xls INFO @ Sat, 08 Aug 2020 13:31:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7917538/SRX7917538.20_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:31:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7917538/SRX7917538.20_summits.bed INFO @ Sat, 08 Aug 2020 13:31:13: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling