Job ID = 6528426 SRX = SRX6441109 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-29T15:16:17 prefetch.2.10.7: 1) Downloading 'SRR9680907'... 2020-06-29T15:16:17 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T15:16:59 prefetch.2.10.7: HTTPS download succeed 2020-06-29T15:16:59 prefetch.2.10.7: 'SRR9680907' is valid 2020-06-29T15:16:59 prefetch.2.10.7: 1) 'SRR9680907' was downloaded successfully 2020-06-29T15:16:59 prefetch.2.10.7: 'SRR9680907' has 0 unresolved dependencies Read 1770097 spots for SRR9680907/SRR9680907.sra Written 1770097 spots for SRR9680907/SRR9680907.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: 00:06:05 1770097 reads; of these: 1770097 (100.00%) were paired; of these: 282605 (15.97%) aligned concordantly 0 times 411355 (23.24%) aligned concordantly exactly 1 time 1076137 (60.80%) aligned concordantly >1 times ---- 282605 pairs aligned concordantly 0 times; of these: 19783 (7.00%) aligned discordantly 1 time ---- 262822 pairs aligned 0 times concordantly or discordantly; of these: 525644 mates make up the pairs; of these: 251065 (47.76%) aligned 0 times 36558 (6.95%) aligned exactly 1 time 238021 (45.28%) aligned >1 times 92.91% overall alignment rate Time searching: 00:06:05 Overall time: 00:06:05 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] 1292907 / 1504192 = 0.8595 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 00:25:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6441109/SRX6441109.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6441109/SRX6441109.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6441109/SRX6441109.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6441109/SRX6441109.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 00:25:40: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:25:40: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:25:45: #1 tag size is determined as 81 bps INFO @ Tue, 30 Jun 2020 00:25:45: #1 tag size = 81 INFO @ Tue, 30 Jun 2020 00:25:45: #1 total tags in treatment: 208122 INFO @ Tue, 30 Jun 2020 00:25:45: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:25:45: #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 00:25:45: #1 tags after filtering in treatment: 162828 INFO @ Tue, 30 Jun 2020 00:25:45: #1 Redundant rate of treatment: 0.22 INFO @ Tue, 30 Jun 2020 00:25:45: #1 finished! INFO @ Tue, 30 Jun 2020 00:25:45: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:25:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:25:45: #2 number of paired peaks: 7793 INFO @ Tue, 30 Jun 2020 00:25:45: start model_add_line... INFO @ Tue, 30 Jun 2020 00:25:45: start X-correlation... INFO @ Tue, 30 Jun 2020 00:25:45: end of X-cor INFO @ Tue, 30 Jun 2020 00:25:45: #2 finished! INFO @ Tue, 30 Jun 2020 00:25:45: #2 predicted fragment length is 290 bps INFO @ Tue, 30 Jun 2020 00:25:45: #2 alternative fragment length(s) may be 4,111,290 bps INFO @ Tue, 30 Jun 2020 00:25:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6441109/SRX6441109.05_model.r INFO @ Tue, 30 Jun 2020 00:25:45: #3 Call peaks... INFO @ Tue, 30 Jun 2020 00:25:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 00:25:45: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 00:25:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6441109/SRX6441109.05_peaks.xls INFO @ Tue, 30 Jun 2020 00:25:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6441109/SRX6441109.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:25:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6441109/SRX6441109.05_summits.bed INFO @ Tue, 30 Jun 2020 00:25:46: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (48 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 @ Tue, 30 Jun 2020 00:26:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6441109/SRX6441109.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6441109/SRX6441109.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6441109/SRX6441109.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6441109/SRX6441109.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 00:26:10: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:26:10: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:26:14: #1 tag size is determined as 81 bps INFO @ Tue, 30 Jun 2020 00:26:14: #1 tag size = 81 INFO @ Tue, 30 Jun 2020 00:26:14: #1 total tags in treatment: 208122 INFO @ Tue, 30 Jun 2020 00:26:14: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:26:14: #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 00:26:14: #1 tags after filtering in treatment: 162828 INFO @ Tue, 30 Jun 2020 00:26:14: #1 Redundant rate of treatment: 0.22 INFO @ Tue, 30 Jun 2020 00:26:14: #1 finished! INFO @ Tue, 30 Jun 2020 00:26:14: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:26:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:26:15: #2 number of paired peaks: 7793 INFO @ Tue, 30 Jun 2020 00:26:15: start model_add_line... INFO @ Tue, 30 Jun 2020 00:26:15: start X-correlation... INFO @ Tue, 30 Jun 2020 00:26:15: end of X-cor INFO @ Tue, 30 Jun 2020 00:26:15: #2 finished! INFO @ Tue, 30 Jun 2020 00:26:15: #2 predicted fragment length is 290 bps INFO @ Tue, 30 Jun 2020 00:26:15: #2 alternative fragment length(s) may be 4,111,290 bps INFO @ Tue, 30 Jun 2020 00:26:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6441109/SRX6441109.10_model.r INFO @ Tue, 30 Jun 2020 00:26:15: #3 Call peaks... INFO @ Tue, 30 Jun 2020 00:26:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 00:26:15: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 00:26:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6441109/SRX6441109.10_peaks.xls INFO @ Tue, 30 Jun 2020 00:26:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6441109/SRX6441109.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:26:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6441109/SRX6441109.10_summits.bed INFO @ Tue, 30 Jun 2020 00:26:15: Done! pass1 - making usageList (5 chroms): 0 millis pass2 - checking and writing primary data (9 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 00:26:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6441109/SRX6441109.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6441109/SRX6441109.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6441109/SRX6441109.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6441109/SRX6441109.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 00:26:40: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:26:40: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 00:26:44: #1 tag size is determined as 81 bps INFO @ Tue, 30 Jun 2020 00:26:44: #1 tag size = 81 INFO @ Tue, 30 Jun 2020 00:26:44: #1 total tags in treatment: 208122 INFO @ Tue, 30 Jun 2020 00:26:44: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:26:44: #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 00:26:45: #1 tags after filtering in treatment: 162828 INFO @ Tue, 30 Jun 2020 00:26:45: #1 Redundant rate of treatment: 0.22 INFO @ Tue, 30 Jun 2020 00:26:45: #1 finished! INFO @ Tue, 30 Jun 2020 00:26:45: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:26:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:26:45: #2 number of paired peaks: 7793 INFO @ Tue, 30 Jun 2020 00:26:45: start model_add_line... INFO @ Tue, 30 Jun 2020 00:26:45: start X-correlation... INFO @ Tue, 30 Jun 2020 00:26:45: end of X-cor INFO @ Tue, 30 Jun 2020 00:26:45: #2 finished! INFO @ Tue, 30 Jun 2020 00:26:45: #2 predicted fragment length is 290 bps INFO @ Tue, 30 Jun 2020 00:26:45: #2 alternative fragment length(s) may be 4,111,290 bps INFO @ Tue, 30 Jun 2020 00:26:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6441109/SRX6441109.20_model.r INFO @ Tue, 30 Jun 2020 00:26:45: #3 Call peaks... INFO @ Tue, 30 Jun 2020 00:26:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 00:26:45: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 00:26:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6441109/SRX6441109.20_peaks.xls INFO @ Tue, 30 Jun 2020 00:26:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6441109/SRX6441109.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:26:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6441109/SRX6441109.20_summits.bed INFO @ Tue, 30 Jun 2020 00:26:45: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling