Job ID = 14168123 SRX = ERX3978947 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 10287110 spots for ERR3976017/ERR3976017.sra Written 10287110 spots for ERR3976017/ERR3976017.sra fastq に変換しました。 bowtie でマッピング中... Your job 14168983 ("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: 00:25:38 10287110 reads; of these: 10287110 (100.00%) were paired; of these: 1206465 (11.73%) aligned concordantly 0 times 7220046 (70.19%) aligned concordantly exactly 1 time 1860599 (18.09%) aligned concordantly >1 times ---- 1206465 pairs aligned concordantly 0 times; of these: 303085 (25.12%) aligned discordantly 1 time ---- 903380 pairs aligned 0 times concordantly or discordantly; of these: 1806760 mates make up the pairs; of these: 949509 (52.55%) aligned 0 times 369105 (20.43%) aligned exactly 1 time 488146 (27.02%) aligned >1 times 95.38% overall alignment rate Time searching: 00:25:38 Overall time: 00:25:38 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] 6413859 / 9355220 = 0.6856 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 16:00:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978947/ERX3978947.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978947/ERX3978947.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978947/ERX3978947.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978947/ERX3978947.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 16:00:09: #1 read tag files... INFO @ Fri, 10 Dec 2021 16:00:09: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 16:00:15: 1000000 INFO @ Fri, 10 Dec 2021 16:00:22: 2000000 INFO @ Fri, 10 Dec 2021 16:00:28: 3000000 INFO @ Fri, 10 Dec 2021 16:00:34: 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 16:00:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978947/ERX3978947.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978947/ERX3978947.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978947/ERX3978947.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978947/ERX3978947.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 16:00:39: #1 read tag files... INFO @ Fri, 10 Dec 2021 16:00:39: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 16:00:41: 5000000 INFO @ Fri, 10 Dec 2021 16:00:45: 1000000 INFO @ Fri, 10 Dec 2021 16:00:48: 6000000 INFO @ Fri, 10 Dec 2021 16:00:51: 2000000 INFO @ Fri, 10 Dec 2021 16:00:53: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 16:00:53: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 16:00:53: #1 total tags in treatment: 2821201 INFO @ Fri, 10 Dec 2021 16:00:53: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 16:00:53: #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 16:00:53: #1 tags after filtering in treatment: 2623751 INFO @ Fri, 10 Dec 2021 16:00:53: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 10 Dec 2021 16:00:53: #1 finished! INFO @ Fri, 10 Dec 2021 16:00:53: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 16:00:53: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 16:00:54: #2 number of paired peaks: 5653 INFO @ Fri, 10 Dec 2021 16:00:54: start model_add_line... INFO @ Fri, 10 Dec 2021 16:00:54: start X-correlation... INFO @ Fri, 10 Dec 2021 16:00:54: end of X-cor INFO @ Fri, 10 Dec 2021 16:00:54: #2 finished! INFO @ Fri, 10 Dec 2021 16:00:54: #2 predicted fragment length is 213 bps INFO @ Fri, 10 Dec 2021 16:00:54: #2 alternative fragment length(s) may be 213 bps INFO @ Fri, 10 Dec 2021 16:00:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978947/ERX3978947.05_model.r INFO @ Fri, 10 Dec 2021 16:00:54: #3 Call peaks... INFO @ Fri, 10 Dec 2021 16:00:54: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 16:00:56: 3000000 INFO @ Fri, 10 Dec 2021 16:01:00: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 16:01:02: 4000000 INFO @ Fri, 10 Dec 2021 16:01:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978947/ERX3978947.05_peaks.xls INFO @ Fri, 10 Dec 2021 16:01:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978947/ERX3978947.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 16:01:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978947/ERX3978947.05_summits.bed INFO @ Fri, 10 Dec 2021 16:01:03: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6352 records, 4 fields): 16 millis CompletedMACS2peakCalling 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 16:01:07: 5000000 INFO @ Fri, 10 Dec 2021 16:01:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978947/ERX3978947.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978947/ERX3978947.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978947/ERX3978947.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978947/ERX3978947.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 16:01:09: #1 read tag files... INFO @ Fri, 10 Dec 2021 16:01:09: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 16:01:13: 6000000 INFO @ Fri, 10 Dec 2021 16:01:15: 1000000 INFO @ Fri, 10 Dec 2021 16:01:18: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 16:01:18: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 16:01:18: #1 total tags in treatment: 2821201 INFO @ Fri, 10 Dec 2021 16:01:18: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 16:01:18: #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 16:01:18: #1 tags after filtering in treatment: 2623751 INFO @ Fri, 10 Dec 2021 16:01:18: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 10 Dec 2021 16:01:18: #1 finished! INFO @ Fri, 10 Dec 2021 16:01:18: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 16:01:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 16:01:18: #2 number of paired peaks: 5653 INFO @ Fri, 10 Dec 2021 16:01:18: start model_add_line... INFO @ Fri, 10 Dec 2021 16:01:18: start X-correlation... INFO @ Fri, 10 Dec 2021 16:01:18: end of X-cor INFO @ Fri, 10 Dec 2021 16:01:18: #2 finished! INFO @ Fri, 10 Dec 2021 16:01:18: #2 predicted fragment length is 213 bps INFO @ Fri, 10 Dec 2021 16:01:18: #2 alternative fragment length(s) may be 213 bps INFO @ Fri, 10 Dec 2021 16:01:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978947/ERX3978947.10_model.r INFO @ Fri, 10 Dec 2021 16:01:18: #3 Call peaks... INFO @ Fri, 10 Dec 2021 16:01:18: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 16:01:20: 2000000 INFO @ Fri, 10 Dec 2021 16:01:24: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 16:01:26: 3000000 INFO @ Fri, 10 Dec 2021 16:01:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978947/ERX3978947.10_peaks.xls INFO @ Fri, 10 Dec 2021 16:01:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978947/ERX3978947.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 16:01:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978947/ERX3978947.10_summits.bed INFO @ Fri, 10 Dec 2021 16:01:27: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4521 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 16:01:31: 4000000 INFO @ Fri, 10 Dec 2021 16:01:37: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 16:01:42: 6000000 INFO @ Fri, 10 Dec 2021 16:01:47: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 16:01:47: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 16:01:47: #1 total tags in treatment: 2821201 INFO @ Fri, 10 Dec 2021 16:01:47: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 16:01:47: #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 16:01:47: #1 tags after filtering in treatment: 2623751 INFO @ Fri, 10 Dec 2021 16:01:47: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 10 Dec 2021 16:01:47: #1 finished! INFO @ Fri, 10 Dec 2021 16:01:47: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 16:01:47: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 16:01:47: #2 number of paired peaks: 5653 INFO @ Fri, 10 Dec 2021 16:01:47: start model_add_line... INFO @ Fri, 10 Dec 2021 16:01:47: start X-correlation... INFO @ Fri, 10 Dec 2021 16:01:47: end of X-cor INFO @ Fri, 10 Dec 2021 16:01:47: #2 finished! INFO @ Fri, 10 Dec 2021 16:01:47: #2 predicted fragment length is 213 bps INFO @ Fri, 10 Dec 2021 16:01:47: #2 alternative fragment length(s) may be 213 bps INFO @ Fri, 10 Dec 2021 16:01:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978947/ERX3978947.20_model.r INFO @ Fri, 10 Dec 2021 16:01:47: #3 Call peaks... INFO @ Fri, 10 Dec 2021 16:01:47: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 16:01:53: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 16:01:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978947/ERX3978947.20_peaks.xls INFO @ Fri, 10 Dec 2021 16:01:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978947/ERX3978947.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 16:01:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978947/ERX3978947.20_summits.bed INFO @ Fri, 10 Dec 2021 16:01:56: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2254 records, 4 fields): 3 millis CompletedMACS2peakCalling