Job ID = 6528427 SRX = SRX6441112 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-29T14:58:43 prefetch.2.10.7: 1) Downloading 'SRR9680910'... 2020-06-29T14:58:43 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T14:59:39 prefetch.2.10.7: HTTPS download succeed 2020-06-29T14:59:39 prefetch.2.10.7: 'SRR9680910' is valid 2020-06-29T14:59:39 prefetch.2.10.7: 1) 'SRR9680910' was downloaded successfully 2020-06-29T14:59:39 prefetch.2.10.7: 'SRR9680910' has 0 unresolved dependencies Read 3174617 spots for SRR9680910/SRR9680910.sra Written 3174617 spots for SRR9680910/SRR9680910.sra 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: 00:05:52 3174617 reads; of these: 3174617 (100.00%) were paired; of these: 702061 (22.11%) aligned concordantly 0 times 2007242 (63.23%) aligned concordantly exactly 1 time 465314 (14.66%) aligned concordantly >1 times ---- 702061 pairs aligned concordantly 0 times; of these: 383213 (54.58%) aligned discordantly 1 time ---- 318848 pairs aligned 0 times concordantly or discordantly; of these: 637696 mates make up the pairs; of these: 292527 (45.87%) aligned 0 times 144422 (22.65%) aligned exactly 1 time 200747 (31.48%) aligned >1 times 95.39% overall alignment rate Time searching: 00:05:52 Overall time: 00:05:52 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] 2361755 / 2847425 = 0.8294 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 @ Tue, 30 Jun 2020 00:09:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6441112/SRX6441112.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6441112/SRX6441112.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6441112/SRX6441112.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6441112/SRX6441112.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 @ Tue, 30 Jun 2020 00:09:55: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:09:55: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:10:01: 1000000 INFO @ Tue, 30 Jun 2020 00:10:02: #1 tag size is determined as 82 bps INFO @ Tue, 30 Jun 2020 00:10:02: #1 tag size = 82 INFO @ Tue, 30 Jun 2020 00:10:02: #1 total tags in treatment: 412044 INFO @ Tue, 30 Jun 2020 00:10:02: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:10:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 00:10:02: #1 tags after filtering in treatment: 326630 INFO @ Tue, 30 Jun 2020 00:10:02: #1 Redundant rate of treatment: 0.21 INFO @ Tue, 30 Jun 2020 00:10:02: #1 finished! INFO @ Tue, 30 Jun 2020 00:10:02: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:10:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:10:03: #2 number of paired peaks: 4390 INFO @ Tue, 30 Jun 2020 00:10:03: start model_add_line... INFO @ Tue, 30 Jun 2020 00:10:03: start X-correlation... INFO @ Tue, 30 Jun 2020 00:10:03: end of X-cor INFO @ Tue, 30 Jun 2020 00:10:03: #2 finished! INFO @ Tue, 30 Jun 2020 00:10:03: #2 predicted fragment length is 337 bps INFO @ Tue, 30 Jun 2020 00:10:03: #2 alternative fragment length(s) may be 5,241,337 bps INFO @ Tue, 30 Jun 2020 00:10:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6441112/SRX6441112.05_model.r INFO @ Tue, 30 Jun 2020 00:10:03: #3 Call peaks... INFO @ Tue, 30 Jun 2020 00:10:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 00:10:03: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 00:10:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6441112/SRX6441112.05_peaks.xls INFO @ Tue, 30 Jun 2020 00:10:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6441112/SRX6441112.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:10:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6441112/SRX6441112.05_summits.bed INFO @ Tue, 30 Jun 2020 00:10:04: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (121 records, 4 fields): 115 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 @ Tue, 30 Jun 2020 00:10:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6441112/SRX6441112.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6441112/SRX6441112.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6441112/SRX6441112.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6441112/SRX6441112.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 @ Tue, 30 Jun 2020 00:10:25: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:10:25: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:10:31: 1000000 INFO @ Tue, 30 Jun 2020 00:10:32: #1 tag size is determined as 82 bps INFO @ Tue, 30 Jun 2020 00:10:32: #1 tag size = 82 INFO @ Tue, 30 Jun 2020 00:10:32: #1 total tags in treatment: 412044 INFO @ Tue, 30 Jun 2020 00:10:32: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:10:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 00:10:32: #1 tags after filtering in treatment: 326630 INFO @ Tue, 30 Jun 2020 00:10:32: #1 Redundant rate of treatment: 0.21 INFO @ Tue, 30 Jun 2020 00:10:32: #1 finished! INFO @ Tue, 30 Jun 2020 00:10:32: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:10:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:10:33: #2 number of paired peaks: 4390 INFO @ Tue, 30 Jun 2020 00:10:33: start model_add_line... INFO @ Tue, 30 Jun 2020 00:10:33: start X-correlation... INFO @ Tue, 30 Jun 2020 00:10:33: end of X-cor INFO @ Tue, 30 Jun 2020 00:10:33: #2 finished! INFO @ Tue, 30 Jun 2020 00:10:33: #2 predicted fragment length is 337 bps INFO @ Tue, 30 Jun 2020 00:10:33: #2 alternative fragment length(s) may be 5,241,337 bps INFO @ Tue, 30 Jun 2020 00:10:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6441112/SRX6441112.10_model.r INFO @ Tue, 30 Jun 2020 00:10:33: #3 Call peaks... INFO @ Tue, 30 Jun 2020 00:10:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 00:10:33: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 00:10:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6441112/SRX6441112.10_peaks.xls INFO @ Tue, 30 Jun 2020 00:10:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6441112/SRX6441112.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:10:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6441112/SRX6441112.10_summits.bed INFO @ Tue, 30 Jun 2020 00:10:34: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (18 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 @ Tue, 30 Jun 2020 00:10:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6441112/SRX6441112.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6441112/SRX6441112.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6441112/SRX6441112.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6441112/SRX6441112.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 @ Tue, 30 Jun 2020 00:10:55: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:10:55: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 00:11:01: 1000000 INFO @ Tue, 30 Jun 2020 00:11:02: #1 tag size is determined as 82 bps INFO @ Tue, 30 Jun 2020 00:11:02: #1 tag size = 82 INFO @ Tue, 30 Jun 2020 00:11:02: #1 total tags in treatment: 412044 INFO @ Tue, 30 Jun 2020 00:11:02: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:11:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 00:11:02: #1 tags after filtering in treatment: 326630 INFO @ Tue, 30 Jun 2020 00:11:02: #1 Redundant rate of treatment: 0.21 INFO @ Tue, 30 Jun 2020 00:11:02: #1 finished! INFO @ Tue, 30 Jun 2020 00:11:02: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:11:02: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 00:11:03: #2 number of paired peaks: 4390 INFO @ Tue, 30 Jun 2020 00:11:03: start model_add_line... INFO @ Tue, 30 Jun 2020 00:11:03: start X-correlation... INFO @ Tue, 30 Jun 2020 00:11:03: end of X-cor INFO @ Tue, 30 Jun 2020 00:11:03: #2 finished! INFO @ Tue, 30 Jun 2020 00:11:03: #2 predicted fragment length is 337 bps INFO @ Tue, 30 Jun 2020 00:11:03: #2 alternative fragment length(s) may be 5,241,337 bps INFO @ Tue, 30 Jun 2020 00:11:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6441112/SRX6441112.20_model.r INFO @ Tue, 30 Jun 2020 00:11:03: #3 Call peaks... INFO @ Tue, 30 Jun 2020 00:11:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 00:11:03: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 00:11:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6441112/SRX6441112.20_peaks.xls INFO @ Tue, 30 Jun 2020 00:11:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6441112/SRX6441112.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:11:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6441112/SRX6441112.20_summits.bed INFO @ Tue, 30 Jun 2020 00:11:04: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling