Job ID = 16439598 SRX = SRX11548835 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 15741423 spots for SRR15243006/SRR15243006.sra Written 15741423 spots for SRR15243006/SRR15243006.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439844 ("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: 00:35:09 15741423 reads; of these: 15741423 (100.00%) were paired; of these: 7880529 (50.06%) aligned concordantly 0 times 6361757 (40.41%) aligned concordantly exactly 1 time 1499137 (9.52%) aligned concordantly >1 times ---- 7880529 pairs aligned concordantly 0 times; of these: 117805 (1.49%) aligned discordantly 1 time ---- 7762724 pairs aligned 0 times concordantly or discordantly; of these: 15525448 mates make up the pairs; of these: 15031938 (96.82%) aligned 0 times 239860 (1.54%) aligned exactly 1 time 253650 (1.63%) aligned >1 times 52.25% overall alignment rate Time searching: 00:35:09 Overall time: 00:35:09 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_sort_core] merging from 8 files... [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] 3708238 / 7971381 = 0.4652 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 16:22:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11548835/SRX11548835.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11548835/SRX11548835.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11548835/SRX11548835.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11548835/SRX11548835.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, 02 Aug 2022 16:22:50: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:22:50: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:23:06: 1000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 16:23:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11548835/SRX11548835.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11548835/SRX11548835.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11548835/SRX11548835.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11548835/SRX11548835.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, 02 Aug 2022 16:23:20: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:23:20: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:23:21: 2000000 INFO @ Tue, 02 Aug 2022 16:23:32: 1000000 INFO @ Tue, 02 Aug 2022 16:23:37: 3000000 INFO @ Tue, 02 Aug 2022 16:23:44: 2000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 16:23:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11548835/SRX11548835.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11548835/SRX11548835.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11548835/SRX11548835.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11548835/SRX11548835.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, 02 Aug 2022 16:23:50: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:23:50: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:23:52: 4000000 INFO @ Tue, 02 Aug 2022 16:23:56: 3000000 INFO @ Tue, 02 Aug 2022 16:24:03: 1000000 INFO @ Tue, 02 Aug 2022 16:24:08: 5000000 INFO @ Tue, 02 Aug 2022 16:24:09: 4000000 INFO @ Tue, 02 Aug 2022 16:24:16: 2000000 INFO @ Tue, 02 Aug 2022 16:24:21: 5000000 INFO @ Tue, 02 Aug 2022 16:24:23: 6000000 INFO @ Tue, 02 Aug 2022 16:24:29: 3000000 INFO @ Tue, 02 Aug 2022 16:24:32: 6000000 INFO @ Tue, 02 Aug 2022 16:24:38: 7000000 INFO @ Tue, 02 Aug 2022 16:24:42: 4000000 INFO @ Tue, 02 Aug 2022 16:24:44: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 16:24:52: 8000000 INFO @ Tue, 02 Aug 2022 16:24:54: 5000000 INFO @ Tue, 02 Aug 2022 16:24:56: 8000000 INFO @ Tue, 02 Aug 2022 16:25:06: 9000000 INFO @ Tue, 02 Aug 2022 16:25:07: 6000000 INFO @ Tue, 02 Aug 2022 16:25:07: 9000000 INFO @ Tue, 02 Aug 2022 16:25:07: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 16:25:07: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 16:25:07: #1 total tags in treatment: 4174716 INFO @ Tue, 02 Aug 2022 16:25:07: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:25:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 16:25:07: #1 tags after filtering in treatment: 3315268 INFO @ Tue, 02 Aug 2022 16:25:07: #1 Redundant rate of treatment: 0.21 INFO @ Tue, 02 Aug 2022 16:25:07: #1 finished! INFO @ Tue, 02 Aug 2022 16:25:07: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:25:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:25:07: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 16:25:07: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 16:25:07: #1 total tags in treatment: 4174716 INFO @ Tue, 02 Aug 2022 16:25:07: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:25:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 16:25:07: #1 tags after filtering in treatment: 3315268 INFO @ Tue, 02 Aug 2022 16:25:07: #1 Redundant rate of treatment: 0.21 INFO @ Tue, 02 Aug 2022 16:25:07: #1 finished! INFO @ Tue, 02 Aug 2022 16:25:07: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:25:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:25:07: #2 number of paired peaks: 5370 INFO @ Tue, 02 Aug 2022 16:25:07: start model_add_line... INFO @ Tue, 02 Aug 2022 16:25:08: start X-correlation... INFO @ Tue, 02 Aug 2022 16:25:08: end of X-cor INFO @ Tue, 02 Aug 2022 16:25:08: #2 finished! INFO @ Tue, 02 Aug 2022 16:25:08: #2 predicted fragment length is 200 bps INFO @ Tue, 02 Aug 2022 16:25:08: #2 alternative fragment length(s) may be 200 bps INFO @ Tue, 02 Aug 2022 16:25:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11548835/SRX11548835.05_model.r INFO @ Tue, 02 Aug 2022 16:25:08: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:25:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:25:08: #2 number of paired peaks: 5370 INFO @ Tue, 02 Aug 2022 16:25:08: start model_add_line... INFO @ Tue, 02 Aug 2022 16:25:08: start X-correlation... INFO @ Tue, 02 Aug 2022 16:25:08: end of X-cor INFO @ Tue, 02 Aug 2022 16:25:08: #2 finished! INFO @ Tue, 02 Aug 2022 16:25:08: #2 predicted fragment length is 200 bps INFO @ Tue, 02 Aug 2022 16:25:08: #2 alternative fragment length(s) may be 200 bps INFO @ Tue, 02 Aug 2022 16:25:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11548835/SRX11548835.10_model.r INFO @ Tue, 02 Aug 2022 16:25:08: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:25:08: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 16:25:19: 7000000 INFO @ Tue, 02 Aug 2022 16:25:22: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:25:23: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:25:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11548835/SRX11548835.10_peaks.xls INFO @ Tue, 02 Aug 2022 16:25:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11548835/SRX11548835.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:25:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11548835/SRX11548835.10_summits.bed INFO @ Tue, 02 Aug 2022 16:25:29: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (5346 records, 4 fields): 37 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 16:25:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11548835/SRX11548835.05_peaks.xls INFO @ Tue, 02 Aug 2022 16:25:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11548835/SRX11548835.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:25:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11548835/SRX11548835.05_summits.bed INFO @ Tue, 02 Aug 2022 16:25:30: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6510 records, 4 fields): 109 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 16:25:31: 8000000 INFO @ Tue, 02 Aug 2022 16:25:42: 9000000 INFO @ Tue, 02 Aug 2022 16:25:43: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 16:25:43: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 16:25:43: #1 total tags in treatment: 4174716 INFO @ Tue, 02 Aug 2022 16:25:43: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:25:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 16:25:43: #1 tags after filtering in treatment: 3315268 INFO @ Tue, 02 Aug 2022 16:25:43: #1 Redundant rate of treatment: 0.21 INFO @ Tue, 02 Aug 2022 16:25:43: #1 finished! INFO @ Tue, 02 Aug 2022 16:25:43: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:25:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:25:43: #2 number of paired peaks: 5370 INFO @ Tue, 02 Aug 2022 16:25:43: start model_add_line... INFO @ Tue, 02 Aug 2022 16:25:43: start X-correlation... INFO @ Tue, 02 Aug 2022 16:25:44: end of X-cor INFO @ Tue, 02 Aug 2022 16:25:44: #2 finished! INFO @ Tue, 02 Aug 2022 16:25:44: #2 predicted fragment length is 200 bps INFO @ Tue, 02 Aug 2022 16:25:44: #2 alternative fragment length(s) may be 200 bps INFO @ Tue, 02 Aug 2022 16:25:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11548835/SRX11548835.20_model.r INFO @ Tue, 02 Aug 2022 16:25:44: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:25:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:25:58: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:26:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11548835/SRX11548835.20_peaks.xls INFO @ Tue, 02 Aug 2022 16:26:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11548835/SRX11548835.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:26:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11548835/SRX11548835.20_summits.bed INFO @ Tue, 02 Aug 2022 16:26:05: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (4038 records, 4 fields): 60 millis CompletedMACS2peakCalling