Job ID = 14168822 SRX = ERX3978890 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 10893522 spots for ERR3975959/ERR3975959.sra Written 10893522 spots for ERR3975959/ERR3975959.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169897 ("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: 00:29:19 10893522 reads; of these: 10893522 (100.00%) were paired; of these: 1423377 (13.07%) aligned concordantly 0 times 7697548 (70.66%) aligned concordantly exactly 1 time 1772597 (16.27%) aligned concordantly >1 times ---- 1423377 pairs aligned concordantly 0 times; of these: 537237 (37.74%) aligned discordantly 1 time ---- 886140 pairs aligned 0 times concordantly or discordantly; of these: 1772280 mates make up the pairs; of these: 860686 (48.56%) aligned 0 times 471965 (26.63%) aligned exactly 1 time 439629 (24.81%) aligned >1 times 96.05% overall alignment rate Time searching: 00:29:19 Overall time: 00:29:19 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 12 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] 6845583 / 9979570 = 0.6860 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 @ Fri, 10 Dec 2021 21:18:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978890/ERX3978890.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978890/ERX3978890.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978890/ERX3978890.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978890/ERX3978890.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 @ Fri, 10 Dec 2021 21:18:31: #1 read tag files... INFO @ Fri, 10 Dec 2021 21:18:31: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 21:18:36: 1000000 INFO @ Fri, 10 Dec 2021 21:18:42: 2000000 INFO @ Fri, 10 Dec 2021 21:18:47: 3000000 INFO @ Fri, 10 Dec 2021 21:18:53: 4000000 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 @ Fri, 10 Dec 2021 21:18:59: 5000000 INFO @ Fri, 10 Dec 2021 21:19:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978890/ERX3978890.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978890/ERX3978890.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978890/ERX3978890.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978890/ERX3978890.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 @ Fri, 10 Dec 2021 21:19:01: #1 read tag files... INFO @ Fri, 10 Dec 2021 21:19:01: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 21:19:05: 6000000 INFO @ Fri, 10 Dec 2021 21:19:08: 1000000 INFO @ Fri, 10 Dec 2021 21:19:11: 7000000 INFO @ Fri, 10 Dec 2021 21:19:13: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 21:19:13: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 21:19:13: #1 total tags in treatment: 2930825 INFO @ Fri, 10 Dec 2021 21:19:13: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 21:19:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 21:19:13: #1 tags after filtering in treatment: 2667597 INFO @ Fri, 10 Dec 2021 21:19:13: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 10 Dec 2021 21:19:13: #1 finished! INFO @ Fri, 10 Dec 2021 21:19:13: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 21:19:13: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 21:19:13: #2 number of paired peaks: 6891 INFO @ Fri, 10 Dec 2021 21:19:13: start model_add_line... INFO @ Fri, 10 Dec 2021 21:19:13: start X-correlation... INFO @ Fri, 10 Dec 2021 21:19:13: end of X-cor INFO @ Fri, 10 Dec 2021 21:19:13: #2 finished! INFO @ Fri, 10 Dec 2021 21:19:13: #2 predicted fragment length is 227 bps INFO @ Fri, 10 Dec 2021 21:19:13: #2 alternative fragment length(s) may be 227 bps INFO @ Fri, 10 Dec 2021 21:19:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978890/ERX3978890.05_model.r INFO @ Fri, 10 Dec 2021 21:19:13: #3 Call peaks... INFO @ Fri, 10 Dec 2021 21:19:13: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 21:19:14: 2000000 INFO @ Fri, 10 Dec 2021 21:19:20: 3000000 INFO @ Fri, 10 Dec 2021 21:19:21: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 21:19:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978890/ERX3978890.05_peaks.xls INFO @ Fri, 10 Dec 2021 21:19:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978890/ERX3978890.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 21:19:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978890/ERX3978890.05_summits.bed INFO @ Fri, 10 Dec 2021 21:19:25: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (6354 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 21:19:26: 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 @ Fri, 10 Dec 2021 21:19:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978890/ERX3978890.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978890/ERX3978890.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978890/ERX3978890.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978890/ERX3978890.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 @ Fri, 10 Dec 2021 21:19:31: #1 read tag files... INFO @ Fri, 10 Dec 2021 21:19:31: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 21:19:32: 5000000 INFO @ Fri, 10 Dec 2021 21:19:37: 1000000 INFO @ Fri, 10 Dec 2021 21:19:39: 6000000 INFO @ Fri, 10 Dec 2021 21:19:43: 2000000 INFO @ Fri, 10 Dec 2021 21:19:45: 7000000 INFO @ Fri, 10 Dec 2021 21:19:47: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 21:19:47: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 21:19:47: #1 total tags in treatment: 2930825 INFO @ Fri, 10 Dec 2021 21:19:47: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 21:19:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 21:19:47: #1 tags after filtering in treatment: 2667597 INFO @ Fri, 10 Dec 2021 21:19:47: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 10 Dec 2021 21:19:47: #1 finished! INFO @ Fri, 10 Dec 2021 21:19:47: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 21:19:47: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 21:19:47: #2 number of paired peaks: 6891 INFO @ Fri, 10 Dec 2021 21:19:47: start model_add_line... INFO @ Fri, 10 Dec 2021 21:19:47: start X-correlation... INFO @ Fri, 10 Dec 2021 21:19:47: end of X-cor INFO @ Fri, 10 Dec 2021 21:19:47: #2 finished! INFO @ Fri, 10 Dec 2021 21:19:47: #2 predicted fragment length is 227 bps INFO @ Fri, 10 Dec 2021 21:19:47: #2 alternative fragment length(s) may be 227 bps INFO @ Fri, 10 Dec 2021 21:19:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978890/ERX3978890.10_model.r INFO @ Fri, 10 Dec 2021 21:19:47: #3 Call peaks... INFO @ Fri, 10 Dec 2021 21:19:47: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 21:19:49: 3000000 INFO @ Fri, 10 Dec 2021 21:19:55: 4000000 INFO @ Fri, 10 Dec 2021 21:19:55: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 21:19:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978890/ERX3978890.10_peaks.xls INFO @ Fri, 10 Dec 2021 21:19:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978890/ERX3978890.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 21:19:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978890/ERX3978890.10_summits.bed INFO @ Fri, 10 Dec 2021 21:19:59: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5238 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 21:20:01: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 21:20:07: 6000000 INFO @ Fri, 10 Dec 2021 21:20:13: 7000000 INFO @ Fri, 10 Dec 2021 21:20:14: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 21:20:14: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 21:20:14: #1 total tags in treatment: 2930825 INFO @ Fri, 10 Dec 2021 21:20:14: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 21:20:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 21:20:14: #1 tags after filtering in treatment: 2667597 INFO @ Fri, 10 Dec 2021 21:20:14: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 10 Dec 2021 21:20:14: #1 finished! INFO @ Fri, 10 Dec 2021 21:20:14: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 21:20:14: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 21:20:14: #2 number of paired peaks: 6891 INFO @ Fri, 10 Dec 2021 21:20:14: start model_add_line... INFO @ Fri, 10 Dec 2021 21:20:15: start X-correlation... INFO @ Fri, 10 Dec 2021 21:20:15: end of X-cor INFO @ Fri, 10 Dec 2021 21:20:15: #2 finished! INFO @ Fri, 10 Dec 2021 21:20:15: #2 predicted fragment length is 227 bps INFO @ Fri, 10 Dec 2021 21:20:15: #2 alternative fragment length(s) may be 227 bps INFO @ Fri, 10 Dec 2021 21:20:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978890/ERX3978890.20_model.r INFO @ Fri, 10 Dec 2021 21:20:15: #3 Call peaks... INFO @ Fri, 10 Dec 2021 21:20:15: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 21:20:22: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 21:20:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978890/ERX3978890.20_peaks.xls INFO @ Fri, 10 Dec 2021 21:20:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978890/ERX3978890.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 21:20:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978890/ERX3978890.20_summits.bed INFO @ Fri, 10 Dec 2021 21:20:26: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3536 records, 4 fields): 5 millis CompletedMACS2peakCalling