Job ID = 8069547 SRX = SRX7917378 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-08-08T03:34:46 prefetch.2.10.7: 1) Downloading 'SRR11312925'... 2020-08-08T03:34:46 prefetch.2.10.7: Downloading via HTTPS... 2020-08-08T03:35:14 prefetch.2.10.7: HTTPS download succeed 2020-08-08T03:35:14 prefetch.2.10.7: 'SRR11312925' is valid 2020-08-08T03:35:14 prefetch.2.10.7: 1) 'SRR11312925' was downloaded successfully Read 2446436 spots for SRR11312925/SRR11312925.sra Written 2446436 spots for SRR11312925/SRR11312925.sra fastq に変換しました。 bowtie でマッピング中... Your job 8069794 ("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: 00:02:28 2446436 reads; of these: 2446436 (100.00%) were paired; of these: 743708 (30.40%) aligned concordantly 0 times 1486566 (60.76%) aligned concordantly exactly 1 time 216162 (8.84%) aligned concordantly >1 times ---- 743708 pairs aligned concordantly 0 times; of these: 196211 (26.38%) aligned discordantly 1 time ---- 547497 pairs aligned 0 times concordantly or discordantly; of these: 1094994 mates make up the pairs; of these: 919759 (84.00%) aligned 0 times 94656 (8.64%) aligned exactly 1 time 80579 (7.36%) aligned >1 times 81.20% overall alignment rate Time searching: 00:02:28 Overall time: 00:02:28 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] 836794 / 1891778 = 0.4423 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 12:39:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7917378/SRX7917378.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7917378/SRX7917378.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7917378/SRX7917378.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7917378/SRX7917378.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 12:39:13: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:39:13: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:39:19: 1000000 INFO @ Sat, 08 Aug 2020 12:39:24: 2000000 INFO @ Sat, 08 Aug 2020 12:39:26: #1 tag size is determined as 62 bps INFO @ Sat, 08 Aug 2020 12:39:26: #1 tag size = 62 INFO @ Sat, 08 Aug 2020 12:39:26: #1 total tags in treatment: 898883 INFO @ Sat, 08 Aug 2020 12:39:26: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:39:26: #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 12:39:26: #1 tags after filtering in treatment: 624986 INFO @ Sat, 08 Aug 2020 12:39:26: #1 Redundant rate of treatment: 0.30 INFO @ Sat, 08 Aug 2020 12:39:26: #1 finished! INFO @ Sat, 08 Aug 2020 12:39:26: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:39:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:39:26: #2 number of paired peaks: 5034 INFO @ Sat, 08 Aug 2020 12:39:26: start model_add_line... INFO @ Sat, 08 Aug 2020 12:39:26: start X-correlation... INFO @ Sat, 08 Aug 2020 12:39:26: end of X-cor INFO @ Sat, 08 Aug 2020 12:39:26: #2 finished! INFO @ Sat, 08 Aug 2020 12:39:26: #2 predicted fragment length is 188 bps INFO @ Sat, 08 Aug 2020 12:39:26: #2 alternative fragment length(s) may be 2,65,188 bps INFO @ Sat, 08 Aug 2020 12:39:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7917378/SRX7917378.05_model.r INFO @ Sat, 08 Aug 2020 12:39:26: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:39:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:39:27: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:39:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7917378/SRX7917378.05_peaks.xls INFO @ Sat, 08 Aug 2020 12:39:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7917378/SRX7917378.05_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:39:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7917378/SRX7917378.05_summits.bed INFO @ Sat, 08 Aug 2020 12:39:28: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (18 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 @ Sat, 08 Aug 2020 12:39:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7917378/SRX7917378.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7917378/SRX7917378.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7917378/SRX7917378.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7917378/SRX7917378.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 12:39:43: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:39:43: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:39:48: 1000000 INFO @ Sat, 08 Aug 2020 12:39:54: 2000000 INFO @ Sat, 08 Aug 2020 12:39:55: #1 tag size is determined as 62 bps INFO @ Sat, 08 Aug 2020 12:39:55: #1 tag size = 62 INFO @ Sat, 08 Aug 2020 12:39:55: #1 total tags in treatment: 898883 INFO @ Sat, 08 Aug 2020 12:39:55: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:39:55: #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 12:39:56: #1 tags after filtering in treatment: 624986 INFO @ Sat, 08 Aug 2020 12:39:56: #1 Redundant rate of treatment: 0.30 INFO @ Sat, 08 Aug 2020 12:39:56: #1 finished! INFO @ Sat, 08 Aug 2020 12:39:56: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:39:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:39:56: #2 number of paired peaks: 5034 INFO @ Sat, 08 Aug 2020 12:39:56: start model_add_line... INFO @ Sat, 08 Aug 2020 12:39:56: start X-correlation... INFO @ Sat, 08 Aug 2020 12:39:56: end of X-cor INFO @ Sat, 08 Aug 2020 12:39:56: #2 finished! INFO @ Sat, 08 Aug 2020 12:39:56: #2 predicted fragment length is 188 bps INFO @ Sat, 08 Aug 2020 12:39:56: #2 alternative fragment length(s) may be 2,65,188 bps INFO @ Sat, 08 Aug 2020 12:39:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7917378/SRX7917378.10_model.r INFO @ Sat, 08 Aug 2020 12:39:56: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:39:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:39:57: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:39:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7917378/SRX7917378.10_peaks.xls INFO @ Sat, 08 Aug 2020 12:39:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7917378/SRX7917378.10_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:39:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7917378/SRX7917378.10_summits.bed INFO @ Sat, 08 Aug 2020 12:39:58: Done! pass1 - making usageList (2 chroms): 0 millis pass2 - checking and writing primary data (3 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 12:40:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7917378/SRX7917378.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7917378/SRX7917378.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7917378/SRX7917378.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7917378/SRX7917378.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 12:40:13: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:40:13: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:40:19: 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 12:40:25: 2000000 INFO @ Sat, 08 Aug 2020 12:40:27: #1 tag size is determined as 62 bps INFO @ Sat, 08 Aug 2020 12:40:27: #1 tag size = 62 INFO @ Sat, 08 Aug 2020 12:40:27: #1 total tags in treatment: 898883 INFO @ Sat, 08 Aug 2020 12:40:27: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:40:27: #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 12:40:27: #1 tags after filtering in treatment: 624986 INFO @ Sat, 08 Aug 2020 12:40:27: #1 Redundant rate of treatment: 0.30 INFO @ Sat, 08 Aug 2020 12:40:27: #1 finished! INFO @ Sat, 08 Aug 2020 12:40:27: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:40:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:40:27: #2 number of paired peaks: 5034 INFO @ Sat, 08 Aug 2020 12:40:27: start model_add_line... INFO @ Sat, 08 Aug 2020 12:40:27: start X-correlation... INFO @ Sat, 08 Aug 2020 12:40:27: end of X-cor INFO @ Sat, 08 Aug 2020 12:40:27: #2 finished! INFO @ Sat, 08 Aug 2020 12:40:27: #2 predicted fragment length is 188 bps INFO @ Sat, 08 Aug 2020 12:40:27: #2 alternative fragment length(s) may be 2,65,188 bps INFO @ Sat, 08 Aug 2020 12:40:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7917378/SRX7917378.20_model.r INFO @ Sat, 08 Aug 2020 12:40:27: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:40:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:40:28: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:40:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7917378/SRX7917378.20_peaks.xls INFO @ Sat, 08 Aug 2020 12:40:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7917378/SRX7917378.20_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:40:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7917378/SRX7917378.20_summits.bed INFO @ Sat, 08 Aug 2020 12:40:29: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling