Job ID = 14172216 SRX = SRX9281734 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 10647506 spots for SRR12813225/SRR12813225.sra Written 10647506 spots for SRR12813225/SRR12813225.sra Read 10607003 spots for SRR12813226/SRR12813226.sra Written 10607003 spots for SRR12813226/SRR12813226.sra Read 10795443 spots for SRR12813227/SRR12813227.sra Written 10795443 spots for SRR12813227/SRR12813227.sra Read 10728788 spots for SRR12813228/SRR12813228.sra Written 10728788 spots for SRR12813228/SRR12813228.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172713 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:06:49 42778740 reads; of these: 42778740 (100.00%) were paired; of these: 41275747 (96.49%) aligned concordantly 0 times 1156856 (2.70%) aligned concordantly exactly 1 time 346137 (0.81%) aligned concordantly >1 times ---- 41275747 pairs aligned concordantly 0 times; of these: 9168 (0.02%) aligned discordantly 1 time ---- 41266579 pairs aligned 0 times concordantly or discordantly; of these: 82533158 mates make up the pairs; of these: 82253186 (99.66%) aligned 0 times 93576 (0.11%) aligned exactly 1 time 186396 (0.23%) aligned >1 times 3.86% overall alignment rate Time searching: 00:06:50 Overall time: 00:06:50 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] 48259 / 1511105 = 0.0319 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 15:00:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281734/SRX9281734.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281734/SRX9281734.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281734/SRX9281734.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281734/SRX9281734.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, 11 Dec 2021 15:00:54: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:00:54: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:00:58: 1000000 INFO @ Sat, 11 Dec 2021 15:01:03: 2000000 INFO @ Sat, 11 Dec 2021 15:01:07: 3000000 INFO @ Sat, 11 Dec 2021 15:01:08: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 15:01:08: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 15:01:08: #1 total tags in treatment: 1454935 INFO @ Sat, 11 Dec 2021 15:01:08: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:01:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 15:01:08: #1 tags after filtering in treatment: 1405765 INFO @ Sat, 11 Dec 2021 15:01:08: #1 Redundant rate of treatment: 0.03 INFO @ Sat, 11 Dec 2021 15:01:08: #1 finished! INFO @ Sat, 11 Dec 2021 15:01:08: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:01:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:01:08: #2 number of paired peaks: 1549 INFO @ Sat, 11 Dec 2021 15:01:08: start model_add_line... INFO @ Sat, 11 Dec 2021 15:01:08: start X-correlation... INFO @ Sat, 11 Dec 2021 15:01:08: end of X-cor INFO @ Sat, 11 Dec 2021 15:01:08: #2 finished! INFO @ Sat, 11 Dec 2021 15:01:08: #2 predicted fragment length is 189 bps INFO @ Sat, 11 Dec 2021 15:01:08: #2 alternative fragment length(s) may be 120,189,205 bps INFO @ Sat, 11 Dec 2021 15:01:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281734/SRX9281734.05_model.r INFO @ Sat, 11 Dec 2021 15:01:08: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:01:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:01:11: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:01:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281734/SRX9281734.05_peaks.xls INFO @ Sat, 11 Dec 2021 15:01:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281734/SRX9281734.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:01:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281734/SRX9281734.05_summits.bed INFO @ Sat, 11 Dec 2021 15:01:13: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (255 records, 4 fields): 1 millis CompletedMACS2peakCalling WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 15:01:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281734/SRX9281734.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281734/SRX9281734.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281734/SRX9281734.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281734/SRX9281734.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, 11 Dec 2021 15:01:24: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:01:24: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:01:28: 1000000 INFO @ Sat, 11 Dec 2021 15:01:33: 2000000 INFO @ Sat, 11 Dec 2021 15:01:37: 3000000 INFO @ Sat, 11 Dec 2021 15:01:38: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 15:01:38: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 15:01:38: #1 total tags in treatment: 1454935 INFO @ Sat, 11 Dec 2021 15:01:38: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:01:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 15:01:38: #1 tags after filtering in treatment: 1405765 INFO @ Sat, 11 Dec 2021 15:01:38: #1 Redundant rate of treatment: 0.03 INFO @ Sat, 11 Dec 2021 15:01:38: #1 finished! INFO @ Sat, 11 Dec 2021 15:01:38: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:01:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:01:38: #2 number of paired peaks: 1549 INFO @ Sat, 11 Dec 2021 15:01:38: start model_add_line... INFO @ Sat, 11 Dec 2021 15:01:38: start X-correlation... INFO @ Sat, 11 Dec 2021 15:01:38: end of X-cor INFO @ Sat, 11 Dec 2021 15:01:38: #2 finished! INFO @ Sat, 11 Dec 2021 15:01:38: #2 predicted fragment length is 189 bps INFO @ Sat, 11 Dec 2021 15:01:38: #2 alternative fragment length(s) may be 120,189,205 bps INFO @ Sat, 11 Dec 2021 15:01:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281734/SRX9281734.10_model.r INFO @ Sat, 11 Dec 2021 15:01:38: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:01:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:01:41: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:01:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281734/SRX9281734.10_peaks.xls INFO @ Sat, 11 Dec 2021 15:01:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281734/SRX9281734.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:01:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281734/SRX9281734.10_summits.bed INFO @ Sat, 11 Dec 2021 15:01:43: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (142 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 15:01:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281734/SRX9281734.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281734/SRX9281734.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281734/SRX9281734.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281734/SRX9281734.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, 11 Dec 2021 15:01:54: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:01:54: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:01:59: 1000000 INFO @ Sat, 11 Dec 2021 15:02:04: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 15:02:10: 3000000 INFO @ Sat, 11 Dec 2021 15:02:11: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 15:02:11: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 15:02:11: #1 total tags in treatment: 1454935 INFO @ Sat, 11 Dec 2021 15:02:11: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:02:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 15:02:11: #1 tags after filtering in treatment: 1405765 INFO @ Sat, 11 Dec 2021 15:02:11: #1 Redundant rate of treatment: 0.03 INFO @ Sat, 11 Dec 2021 15:02:11: #1 finished! INFO @ Sat, 11 Dec 2021 15:02:11: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:02:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:02:11: #2 number of paired peaks: 1549 INFO @ Sat, 11 Dec 2021 15:02:11: start model_add_line... INFO @ Sat, 11 Dec 2021 15:02:11: start X-correlation... INFO @ Sat, 11 Dec 2021 15:02:11: end of X-cor INFO @ Sat, 11 Dec 2021 15:02:11: #2 finished! INFO @ Sat, 11 Dec 2021 15:02:11: #2 predicted fragment length is 189 bps INFO @ Sat, 11 Dec 2021 15:02:11: #2 alternative fragment length(s) may be 120,189,205 bps INFO @ Sat, 11 Dec 2021 15:02:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281734/SRX9281734.20_model.r INFO @ Sat, 11 Dec 2021 15:02:11: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:02:11: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 15:02:14: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:02:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281734/SRX9281734.20_peaks.xls INFO @ Sat, 11 Dec 2021 15:02:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281734/SRX9281734.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:02:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281734/SRX9281734.20_summits.bed INFO @ Sat, 11 Dec 2021 15:02:16: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (72 records, 4 fields): 1 millis CompletedMACS2peakCalling