Job ID = 14172245 SRX = SRX9281747 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 12600332 spots for SRR12813467/SRR12813467.sra Written 12600332 spots for SRR12813467/SRR12813467.sra Read 12582613 spots for SRR12813468/SRR12813468.sra Written 12582613 spots for SRR12813468/SRR12813468.sra Read 12787079 spots for SRR12813469/SRR12813469.sra Written 12787079 spots for SRR12813469/SRR12813469.sra Read 12518256 spots for SRR12813470/SRR12813470.sra Written 12518256 spots for SRR12813470/SRR12813470.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172789 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:12:17 50488280 reads; of these: 50488280 (100.00%) were paired; of these: 47904631 (94.88%) aligned concordantly 0 times 1905555 (3.77%) aligned concordantly exactly 1 time 678094 (1.34%) aligned concordantly >1 times ---- 47904631 pairs aligned concordantly 0 times; of these: 11209 (0.02%) aligned discordantly 1 time ---- 47893422 pairs aligned 0 times concordantly or discordantly; of these: 95786844 mates make up the pairs; of these: 95031556 (99.21%) aligned 0 times 279277 (0.29%) aligned exactly 1 time 476011 (0.50%) aligned >1 times 5.89% overall alignment rate Time searching: 00:12:18 Overall time: 00:12:18 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] 119378 / 2591228 = 0.0461 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 15:12:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281747/SRX9281747.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281747/SRX9281747.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281747/SRX9281747.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281747/SRX9281747.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 15:12:15: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:12:15: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:12:20: 1000000 INFO @ Sat, 11 Dec 2021 15:12:26: 2000000 INFO @ Sat, 11 Dec 2021 15:12:31: 3000000 INFO @ Sat, 11 Dec 2021 15:12:36: 4000000 INFO @ Sat, 11 Dec 2021 15:12:41: 5000000 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 15:12:45: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 15:12:45: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 15:12:45: #1 total tags in treatment: 2464454 INFO @ Sat, 11 Dec 2021 15:12:45: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:12:45: #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 15:12:45: #1 tags after filtering in treatment: 2356304 INFO @ Sat, 11 Dec 2021 15:12:45: #1 Redundant rate of treatment: 0.04 INFO @ Sat, 11 Dec 2021 15:12:45: #1 finished! INFO @ Sat, 11 Dec 2021 15:12:45: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:12:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:12:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281747/SRX9281747.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281747/SRX9281747.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281747/SRX9281747.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281747/SRX9281747.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 15:12:45: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:12:45: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:12:45: #2 number of paired peaks: 1014 INFO @ Sat, 11 Dec 2021 15:12:45: start model_add_line... INFO @ Sat, 11 Dec 2021 15:12:45: start X-correlation... INFO @ Sat, 11 Dec 2021 15:12:45: end of X-cor INFO @ Sat, 11 Dec 2021 15:12:45: #2 finished! INFO @ Sat, 11 Dec 2021 15:12:45: #2 predicted fragment length is 118 bps INFO @ Sat, 11 Dec 2021 15:12:45: #2 alternative fragment length(s) may be 118 bps INFO @ Sat, 11 Dec 2021 15:12:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281747/SRX9281747.05_model.r INFO @ Sat, 11 Dec 2021 15:12:45: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:12:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:12:50: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:12:51: 1000000 INFO @ Sat, 11 Dec 2021 15:12:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281747/SRX9281747.05_peaks.xls INFO @ Sat, 11 Dec 2021 15:12:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281747/SRX9281747.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:12:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281747/SRX9281747.05_summits.bed INFO @ Sat, 11 Dec 2021 15:12:53: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (398 records, 4 fields): 59 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 15:12:56: 2000000 INFO @ Sat, 11 Dec 2021 15:13:02: 3000000 INFO @ Sat, 11 Dec 2021 15:13:08: 4000000 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 15:13:13: 5000000 INFO @ Sat, 11 Dec 2021 15:13:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281747/SRX9281747.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281747/SRX9281747.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281747/SRX9281747.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281747/SRX9281747.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 15:13:15: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:13:15: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:13:17: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 15:13:17: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 15:13:17: #1 total tags in treatment: 2464454 INFO @ Sat, 11 Dec 2021 15:13:17: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:13:17: #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 15:13:17: #1 tags after filtering in treatment: 2356304 INFO @ Sat, 11 Dec 2021 15:13:17: #1 Redundant rate of treatment: 0.04 INFO @ Sat, 11 Dec 2021 15:13:17: #1 finished! INFO @ Sat, 11 Dec 2021 15:13:17: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:13:17: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:13:17: #2 number of paired peaks: 1014 INFO @ Sat, 11 Dec 2021 15:13:17: start model_add_line... INFO @ Sat, 11 Dec 2021 15:13:17: start X-correlation... INFO @ Sat, 11 Dec 2021 15:13:17: end of X-cor INFO @ Sat, 11 Dec 2021 15:13:17: #2 finished! INFO @ Sat, 11 Dec 2021 15:13:17: #2 predicted fragment length is 118 bps INFO @ Sat, 11 Dec 2021 15:13:17: #2 alternative fragment length(s) may be 118 bps INFO @ Sat, 11 Dec 2021 15:13:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281747/SRX9281747.10_model.r INFO @ Sat, 11 Dec 2021 15:13:17: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:13:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:13:20: 1000000 INFO @ Sat, 11 Dec 2021 15:13:22: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:13:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281747/SRX9281747.10_peaks.xls INFO @ Sat, 11 Dec 2021 15:13:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281747/SRX9281747.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:13:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281747/SRX9281747.10_summits.bed INFO @ Sat, 11 Dec 2021 15:13:25: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (192 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 15:13:25: 2000000 INFO @ Sat, 11 Dec 2021 15:13:30: 3000000 INFO @ Sat, 11 Dec 2021 15:13:35: 4000000 INFO @ Sat, 11 Dec 2021 15:13:40: 5000000 INFO @ Sat, 11 Dec 2021 15:13:44: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 15:13:44: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 15:13:44: #1 total tags in treatment: 2464454 INFO @ Sat, 11 Dec 2021 15:13:44: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:13:44: #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 15:13:44: #1 tags after filtering in treatment: 2356304 INFO @ Sat, 11 Dec 2021 15:13:44: #1 Redundant rate of treatment: 0.04 INFO @ Sat, 11 Dec 2021 15:13:44: #1 finished! INFO @ Sat, 11 Dec 2021 15:13:44: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:13:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:13:44: #2 number of paired peaks: 1014 INFO @ Sat, 11 Dec 2021 15:13:44: start model_add_line... INFO @ Sat, 11 Dec 2021 15:13:44: start X-correlation... INFO @ Sat, 11 Dec 2021 15:13:44: end of X-cor INFO @ Sat, 11 Dec 2021 15:13:44: #2 finished! INFO @ Sat, 11 Dec 2021 15:13:44: #2 predicted fragment length is 118 bps INFO @ Sat, 11 Dec 2021 15:13:44: #2 alternative fragment length(s) may be 118 bps INFO @ Sat, 11 Dec 2021 15:13:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281747/SRX9281747.20_model.r INFO @ Sat, 11 Dec 2021 15:13:44: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:13:44: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 15:13:49: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:13:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281747/SRX9281747.20_peaks.xls INFO @ Sat, 11 Dec 2021 15:13:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281747/SRX9281747.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:13:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281747/SRX9281747.20_summits.bed INFO @ Sat, 11 Dec 2021 15:13:52: Done! pass1 - making usageList (4 chroms): 0 millis pass2 - checking and writing primary data (94 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。