Job ID = 14172256 SRX = SRX9281755 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 5245586 spots for SRR12813499/SRR12813499.sra Written 5245586 spots for SRR12813499/SRR12813499.sra Read 5224958 spots for SRR12813500/SRR12813500.sra Written 5224958 spots for SRR12813500/SRR12813500.sra Read 5354593 spots for SRR12813501/SRR12813501.sra Written 5354593 spots for SRR12813501/SRR12813501.sra Read 4891688 spots for SRR12813502/SRR12813502.sra Written 4891688 spots for SRR12813502/SRR12813502.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172746 ("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: 00:06:36 20716825 reads; of these: 20716825 (100.00%) were paired; of these: 17746801 (85.66%) aligned concordantly 0 times 2726594 (13.16%) aligned concordantly exactly 1 time 243430 (1.18%) aligned concordantly >1 times ---- 17746801 pairs aligned concordantly 0 times; of these: 11787 (0.07%) aligned discordantly 1 time ---- 17735014 pairs aligned 0 times concordantly or discordantly; of these: 35470028 mates make up the pairs; of these: 35078651 (98.90%) aligned 0 times 213058 (0.60%) aligned exactly 1 time 178319 (0.50%) aligned >1 times 15.34% overall alignment rate Time searching: 00:06:37 Overall time: 00:06:37 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] 541626 / 2973870 = 0.1821 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 15:06:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281755/SRX9281755.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281755/SRX9281755.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281755/SRX9281755.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281755/SRX9281755.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 15:06:30: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:06:30: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:06:37: 1000000 INFO @ Sat, 11 Dec 2021 15:06:44: 2000000 INFO @ Sat, 11 Dec 2021 15:06:51: 3000000 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 15:06:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281755/SRX9281755.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281755/SRX9281755.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281755/SRX9281755.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281755/SRX9281755.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 15:06:58: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:06:58: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:06:58: 4000000 INFO @ Sat, 11 Dec 2021 15:07:07: 1000000 INFO @ Sat, 11 Dec 2021 15:07:07: 5000000 INFO @ Sat, 11 Dec 2021 15:07:09: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 15:07:09: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 15:07:09: #1 total tags in treatment: 2428502 INFO @ Sat, 11 Dec 2021 15:07:09: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:07:09: #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 15:07:09: #1 tags after filtering in treatment: 1500643 INFO @ Sat, 11 Dec 2021 15:07:09: #1 Redundant rate of treatment: 0.38 INFO @ Sat, 11 Dec 2021 15:07:09: #1 finished! INFO @ Sat, 11 Dec 2021 15:07:09: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:07:09: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:07:09: #2 number of paired peaks: 10708 INFO @ Sat, 11 Dec 2021 15:07:09: start model_add_line... INFO @ Sat, 11 Dec 2021 15:07:09: start X-correlation... INFO @ Sat, 11 Dec 2021 15:07:10: end of X-cor INFO @ Sat, 11 Dec 2021 15:07:10: #2 finished! INFO @ Sat, 11 Dec 2021 15:07:10: #2 predicted fragment length is 149 bps INFO @ Sat, 11 Dec 2021 15:07:10: #2 alternative fragment length(s) may be 149,308 bps INFO @ Sat, 11 Dec 2021 15:07:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281755/SRX9281755.05_model.r INFO @ Sat, 11 Dec 2021 15:07:10: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:07:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:07:14: 2000000 INFO @ Sat, 11 Dec 2021 15:07:15: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:07:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281755/SRX9281755.05_peaks.xls INFO @ Sat, 11 Dec 2021 15:07:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281755/SRX9281755.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:07:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281755/SRX9281755.05_summits.bed INFO @ Sat, 11 Dec 2021 15:07:18: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (7857 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 15:07:21: 3000000 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 15:07:28: 4000000 INFO @ Sat, 11 Dec 2021 15:07:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281755/SRX9281755.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281755/SRX9281755.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281755/SRX9281755.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281755/SRX9281755.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 15:07:28: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:07:28: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:07:36: 5000000 INFO @ Sat, 11 Dec 2021 15:07:36: 1000000 INFO @ Sat, 11 Dec 2021 15:07:38: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 15:07:38: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 15:07:38: #1 total tags in treatment: 2428502 INFO @ Sat, 11 Dec 2021 15:07:38: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:07:38: #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 15:07:38: #1 tags after filtering in treatment: 1500643 INFO @ Sat, 11 Dec 2021 15:07:38: #1 Redundant rate of treatment: 0.38 INFO @ Sat, 11 Dec 2021 15:07:38: #1 finished! INFO @ Sat, 11 Dec 2021 15:07:38: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:07:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:07:39: #2 number of paired peaks: 10708 INFO @ Sat, 11 Dec 2021 15:07:39: start model_add_line... INFO @ Sat, 11 Dec 2021 15:07:39: start X-correlation... INFO @ Sat, 11 Dec 2021 15:07:39: end of X-cor INFO @ Sat, 11 Dec 2021 15:07:39: #2 finished! INFO @ Sat, 11 Dec 2021 15:07:39: #2 predicted fragment length is 149 bps INFO @ Sat, 11 Dec 2021 15:07:39: #2 alternative fragment length(s) may be 149,308 bps INFO @ Sat, 11 Dec 2021 15:07:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281755/SRX9281755.10_model.r INFO @ Sat, 11 Dec 2021 15:07:39: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:07:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:07:44: 2000000 INFO @ Sat, 11 Dec 2021 15:07:44: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:07:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281755/SRX9281755.10_peaks.xls INFO @ Sat, 11 Dec 2021 15:07:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281755/SRX9281755.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:07:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281755/SRX9281755.10_summits.bed INFO @ Sat, 11 Dec 2021 15:07:47: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (6081 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 15:07:51: 3000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 15:07:58: 4000000 INFO @ Sat, 11 Dec 2021 15:08:05: 5000000 INFO @ Sat, 11 Dec 2021 15:08:07: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 15:08:07: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 15:08:07: #1 total tags in treatment: 2428502 INFO @ Sat, 11 Dec 2021 15:08:07: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:08:07: #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 15:08:07: #1 tags after filtering in treatment: 1500643 INFO @ Sat, 11 Dec 2021 15:08:07: #1 Redundant rate of treatment: 0.38 INFO @ Sat, 11 Dec 2021 15:08:07: #1 finished! INFO @ Sat, 11 Dec 2021 15:08:07: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:08:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:08:08: #2 number of paired peaks: 10708 INFO @ Sat, 11 Dec 2021 15:08:08: start model_add_line... INFO @ Sat, 11 Dec 2021 15:08:08: start X-correlation... INFO @ Sat, 11 Dec 2021 15:08:08: end of X-cor INFO @ Sat, 11 Dec 2021 15:08:08: #2 finished! INFO @ Sat, 11 Dec 2021 15:08:08: #2 predicted fragment length is 149 bps INFO @ Sat, 11 Dec 2021 15:08:08: #2 alternative fragment length(s) may be 149,308 bps INFO @ Sat, 11 Dec 2021 15:08:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281755/SRX9281755.20_model.r INFO @ Sat, 11 Dec 2021 15:08:08: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:08:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:08:13: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:08:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281755/SRX9281755.20_peaks.xls INFO @ Sat, 11 Dec 2021 15:08:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281755/SRX9281755.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:08:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281755/SRX9281755.20_summits.bed INFO @ Sat, 11 Dec 2021 15:08:15: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (2782 records, 4 fields): 13 millis CompletedMACS2peakCalling