Job ID = 8071500 SRX = SRX7917566 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-08-08T04:28:17 prefetch.2.10.7: 1) Downloading 'SRR11313147'... 2020-08-08T04:28:17 prefetch.2.10.7: Downloading via HTTPS... 2020-08-08T04:32:01 prefetch.2.10.7: HTTPS download succeed 2020-08-08T04:32:01 prefetch.2.10.7: 'SRR11313147' is valid 2020-08-08T04:32:01 prefetch.2.10.7: 1) 'SRR11313147' was downloaded successfully Read 2429603 spots for SRR11313147/SRR11313147.sra Written 2429603 spots for SRR11313147/SRR11313147.sra fastq に変換しました。 bowtie でマッピング中... Your job 8072615 ("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: 00:03:00 2429603 reads; of these: 2429603 (100.00%) were paired; of these: 718660 (29.58%) aligned concordantly 0 times 1469533 (60.48%) aligned concordantly exactly 1 time 241410 (9.94%) aligned concordantly >1 times ---- 718660 pairs aligned concordantly 0 times; of these: 206613 (28.75%) aligned discordantly 1 time ---- 512047 pairs aligned 0 times concordantly or discordantly; of these: 1024094 mates make up the pairs; of these: 851235 (83.12%) aligned 0 times 90221 (8.81%) aligned exactly 1 time 82638 (8.07%) aligned >1 times 82.48% overall alignment rate Time searching: 00:03:00 Overall time: 00:03:00 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] 863157 / 1910814 = 0.4517 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 13:36:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7917566/SRX7917566.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7917566/SRX7917566.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7917566/SRX7917566.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7917566/SRX7917566.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 13:36:33: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:36:33: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:36:39: 1000000 INFO @ Sat, 08 Aug 2020 13:36:45: 2000000 INFO @ Sat, 08 Aug 2020 13:36:46: #1 tag size is determined as 62 bps INFO @ Sat, 08 Aug 2020 13:36:46: #1 tag size = 62 INFO @ Sat, 08 Aug 2020 13:36:46: #1 total tags in treatment: 898788 INFO @ Sat, 08 Aug 2020 13:36:46: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:36:46: #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 13:36:47: #1 tags after filtering in treatment: 646393 INFO @ Sat, 08 Aug 2020 13:36:47: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 08 Aug 2020 13:36:47: #1 finished! INFO @ Sat, 08 Aug 2020 13:36:47: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:36:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:36:47: #2 number of paired peaks: 3733 INFO @ Sat, 08 Aug 2020 13:36:47: start model_add_line... INFO @ Sat, 08 Aug 2020 13:36:47: start X-correlation... INFO @ Sat, 08 Aug 2020 13:36:47: end of X-cor INFO @ Sat, 08 Aug 2020 13:36:47: #2 finished! INFO @ Sat, 08 Aug 2020 13:36:47: #2 predicted fragment length is 166 bps INFO @ Sat, 08 Aug 2020 13:36:47: #2 alternative fragment length(s) may be 3,44,88,156,166 bps INFO @ Sat, 08 Aug 2020 13:36:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7917566/SRX7917566.05_model.r INFO @ Sat, 08 Aug 2020 13:36:47: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:36:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:36:48: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:36:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7917566/SRX7917566.05_peaks.xls INFO @ Sat, 08 Aug 2020 13:36:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7917566/SRX7917566.05_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:36:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7917566/SRX7917566.05_summits.bed INFO @ Sat, 08 Aug 2020 13:36:49: Done! pass1 - making usageList (2 chroms): 1 millis pass2 - checking and writing primary data (4 records, 4 fields): 1 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 13:37:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7917566/SRX7917566.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7917566/SRX7917566.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7917566/SRX7917566.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7917566/SRX7917566.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 13:37:04: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:37:04: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:37:09: 1000000 INFO @ Sat, 08 Aug 2020 13:37:15: 2000000 INFO @ Sat, 08 Aug 2020 13:37:16: #1 tag size is determined as 62 bps INFO @ Sat, 08 Aug 2020 13:37:16: #1 tag size = 62 INFO @ Sat, 08 Aug 2020 13:37:16: #1 total tags in treatment: 898788 INFO @ Sat, 08 Aug 2020 13:37:16: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:37:16: #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 13:37:16: #1 tags after filtering in treatment: 646393 INFO @ Sat, 08 Aug 2020 13:37:16: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 08 Aug 2020 13:37:16: #1 finished! INFO @ Sat, 08 Aug 2020 13:37:16: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:37:16: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:37:17: #2 number of paired peaks: 3733 INFO @ Sat, 08 Aug 2020 13:37:17: start model_add_line... INFO @ Sat, 08 Aug 2020 13:37:17: start X-correlation... INFO @ Sat, 08 Aug 2020 13:37:17: end of X-cor INFO @ Sat, 08 Aug 2020 13:37:17: #2 finished! INFO @ Sat, 08 Aug 2020 13:37:17: #2 predicted fragment length is 166 bps INFO @ Sat, 08 Aug 2020 13:37:17: #2 alternative fragment length(s) may be 3,44,88,156,166 bps INFO @ Sat, 08 Aug 2020 13:37:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7917566/SRX7917566.10_model.r INFO @ Sat, 08 Aug 2020 13:37:17: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:37:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:37:18: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:37:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7917566/SRX7917566.10_peaks.xls INFO @ Sat, 08 Aug 2020 13:37:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7917566/SRX7917566.10_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:37:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7917566/SRX7917566.10_summits.bed INFO @ Sat, 08 Aug 2020 13:37:18: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) 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 13:37:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7917566/SRX7917566.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7917566/SRX7917566.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7917566/SRX7917566.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7917566/SRX7917566.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 13:37:34: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:37:34: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:37:39: 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 13:37:45: 2000000 INFO @ Sat, 08 Aug 2020 13:37:47: #1 tag size is determined as 62 bps INFO @ Sat, 08 Aug 2020 13:37:47: #1 tag size = 62 INFO @ Sat, 08 Aug 2020 13:37:47: #1 total tags in treatment: 898788 INFO @ Sat, 08 Aug 2020 13:37:47: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:37:47: #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 13:37:47: #1 tags after filtering in treatment: 646393 INFO @ Sat, 08 Aug 2020 13:37:47: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 08 Aug 2020 13:37:47: #1 finished! INFO @ Sat, 08 Aug 2020 13:37:47: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:37:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:37:47: #2 number of paired peaks: 3733 INFO @ Sat, 08 Aug 2020 13:37:47: start model_add_line... INFO @ Sat, 08 Aug 2020 13:37:47: start X-correlation... INFO @ Sat, 08 Aug 2020 13:37:47: end of X-cor INFO @ Sat, 08 Aug 2020 13:37:47: #2 finished! INFO @ Sat, 08 Aug 2020 13:37:47: #2 predicted fragment length is 166 bps INFO @ Sat, 08 Aug 2020 13:37:47: #2 alternative fragment length(s) may be 3,44,88,156,166 bps INFO @ Sat, 08 Aug 2020 13:37:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7917566/SRX7917566.20_model.r INFO @ Sat, 08 Aug 2020 13:37:47: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:37:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:37:48: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:37:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7917566/SRX7917566.20_peaks.xls INFO @ Sat, 08 Aug 2020 13:37:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7917566/SRX7917566.20_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:37:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7917566/SRX7917566.20_summits.bed INFO @ Sat, 08 Aug 2020 13:37:49: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling