Job ID = 16438413 SRX = SRX12622680 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 3695230 spots for SRR16345096/SRR16345096.sra Written 3695230 spots for SRR16345096/SRR16345096.sra fastq に変換しました。 bowtie でマッピング中... Your job 16438515 ("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: 00:00:45 3695230 reads; of these: 3695230 (100.00%) were paired; of these: 3599910 (97.42%) aligned concordantly 0 times 66382 (1.80%) aligned concordantly exactly 1 time 28938 (0.78%) aligned concordantly >1 times ---- 3599910 pairs aligned concordantly 0 times; of these: 176 (0.00%) aligned discordantly 1 time ---- 3599734 pairs aligned 0 times concordantly or discordantly; of these: 7199468 mates make up the pairs; of these: 7181441 (99.75%) aligned 0 times 5433 (0.08%) aligned exactly 1 time 12594 (0.17%) aligned >1 times 2.83% overall alignment rate Time searching: 00:00:46 Overall time: 00:00:46 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] 1472 / 95443 = 0.0154 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 13:52:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12622680/SRX12622680.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12622680/SRX12622680.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12622680/SRX12622680.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12622680/SRX12622680.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 13:52:22: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:52:22: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:52:24: #1 tag size is determined as 39 bps INFO @ Tue, 02 Aug 2022 13:52:24: #1 tag size = 39 INFO @ Tue, 02 Aug 2022 13:52:24: #1 total tags in treatment: 93851 INFO @ Tue, 02 Aug 2022 13:52:24: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:52:24: #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 13:52:24: #1 tags after filtering in treatment: 92609 INFO @ Tue, 02 Aug 2022 13:52:24: #1 Redundant rate of treatment: 0.01 INFO @ Tue, 02 Aug 2022 13:52:24: #1 finished! INFO @ Tue, 02 Aug 2022 13:52:24: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:52:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:52:24: #2 number of paired peaks: 4352 INFO @ Tue, 02 Aug 2022 13:52:24: start model_add_line... INFO @ Tue, 02 Aug 2022 13:52:24: start X-correlation... INFO @ Tue, 02 Aug 2022 13:52:24: end of X-cor INFO @ Tue, 02 Aug 2022 13:52:24: #2 finished! INFO @ Tue, 02 Aug 2022 13:52:24: #2 predicted fragment length is 300 bps INFO @ Tue, 02 Aug 2022 13:52:24: #2 alternative fragment length(s) may be 300 bps INFO @ Tue, 02 Aug 2022 13:52:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12622680/SRX12622680.05_model.r INFO @ Tue, 02 Aug 2022 13:52:24: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:52:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:52:24: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:52:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12622680/SRX12622680.05_peaks.xls INFO @ Tue, 02 Aug 2022 13:52:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12622680/SRX12622680.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:52:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12622680/SRX12622680.05_summits.bed INFO @ Tue, 02 Aug 2022 13:52:25: Done! pass1 - making usageList (3 chroms): 2 millis pass2 - checking and writing primary data (38 records, 4 fields): 34 millis CompletedMACS2peakCalling 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 13:52:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12622680/SRX12622680.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12622680/SRX12622680.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12622680/SRX12622680.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12622680/SRX12622680.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 13:52:51: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:52:51: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:52:52: #1 tag size is determined as 39 bps INFO @ Tue, 02 Aug 2022 13:52:52: #1 tag size = 39 INFO @ Tue, 02 Aug 2022 13:52:52: #1 total tags in treatment: 93851 INFO @ Tue, 02 Aug 2022 13:52:52: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:52:52: #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 13:52:52: #1 tags after filtering in treatment: 92609 INFO @ Tue, 02 Aug 2022 13:52:52: #1 Redundant rate of treatment: 0.01 INFO @ Tue, 02 Aug 2022 13:52:52: #1 finished! INFO @ Tue, 02 Aug 2022 13:52:52: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:52:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:52:52: #2 number of paired peaks: 4352 INFO @ Tue, 02 Aug 2022 13:52:52: start model_add_line... INFO @ Tue, 02 Aug 2022 13:52:52: start X-correlation... INFO @ Tue, 02 Aug 2022 13:52:52: end of X-cor INFO @ Tue, 02 Aug 2022 13:52:52: #2 finished! INFO @ Tue, 02 Aug 2022 13:52:52: #2 predicted fragment length is 300 bps INFO @ Tue, 02 Aug 2022 13:52:52: #2 alternative fragment length(s) may be 300 bps INFO @ Tue, 02 Aug 2022 13:52:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12622680/SRX12622680.10_model.r INFO @ Tue, 02 Aug 2022 13:52:52: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:52:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:52:53: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:52:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12622680/SRX12622680.10_peaks.xls INFO @ Tue, 02 Aug 2022 13:52:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12622680/SRX12622680.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:52:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12622680/SRX12622680.10_summits.bed INFO @ Tue, 02 Aug 2022 13:52:53: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (26 records, 4 fields): 18 millis CompletedMACS2peakCalling 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 13:53:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12622680/SRX12622680.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12622680/SRX12622680.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12622680/SRX12622680.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12622680/SRX12622680.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 13:53:21: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:53:21: #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, 02 Aug 2022 13:53:22: #1 tag size is determined as 39 bps INFO @ Tue, 02 Aug 2022 13:53:22: #1 tag size = 39 INFO @ Tue, 02 Aug 2022 13:53:22: #1 total tags in treatment: 93851 INFO @ Tue, 02 Aug 2022 13:53:22: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:53:22: #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 13:53:22: #1 tags after filtering in treatment: 92609 INFO @ Tue, 02 Aug 2022 13:53:22: #1 Redundant rate of treatment: 0.01 INFO @ Tue, 02 Aug 2022 13:53:22: #1 finished! INFO @ Tue, 02 Aug 2022 13:53:22: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:53:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:53:22: #2 number of paired peaks: 4352 INFO @ Tue, 02 Aug 2022 13:53:22: start model_add_line... INFO @ Tue, 02 Aug 2022 13:53:22: start X-correlation... INFO @ Tue, 02 Aug 2022 13:53:22: end of X-cor INFO @ Tue, 02 Aug 2022 13:53:22: #2 finished! INFO @ Tue, 02 Aug 2022 13:53:22: #2 predicted fragment length is 300 bps INFO @ Tue, 02 Aug 2022 13:53:22: #2 alternative fragment length(s) may be 300 bps INFO @ Tue, 02 Aug 2022 13:53:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12622680/SRX12622680.20_model.r INFO @ Tue, 02 Aug 2022 13:53:23: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:53:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:53:23: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:53:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12622680/SRX12622680.20_peaks.xls INFO @ Tue, 02 Aug 2022 13:53:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12622680/SRX12622680.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:53:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12622680/SRX12622680.20_summits.bed INFO @ Tue, 02 Aug 2022 13:53:23: Done! pass1 - making usageList (2 chroms): 1 millis pass2 - checking and writing primary data (9 records, 4 fields): 84 millis CompletedMACS2peakCalling