Job ID = 14168345 SRX = ERX3978859 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 26465726 spots for ERR3975928/ERR3975928.sra Written 26465726 spots for ERR3975928/ERR3975928.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169675 ("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: 01:16:13 26465726 reads; of these: 26465726 (100.00%) were paired; of these: 3172711 (11.99%) aligned concordantly 0 times 18032552 (68.14%) aligned concordantly exactly 1 time 5260463 (19.88%) aligned concordantly >1 times ---- 3172711 pairs aligned concordantly 0 times; of these: 530444 (16.72%) aligned discordantly 1 time ---- 2642267 pairs aligned 0 times concordantly or discordantly; of these: 5284534 mates make up the pairs; of these: 2874857 (54.40%) aligned 0 times 1012693 (19.16%) aligned exactly 1 time 1396984 (26.44%) aligned >1 times 94.57% overall alignment rate Time searching: 01:16:13 Overall time: 01:16:13 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 24 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] 15898530 / 23680953 = 0.6714 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 19:21:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978859/ERX3978859.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978859/ERX3978859.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978859/ERX3978859.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978859/ERX3978859.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 19:21:22: #1 read tag files... INFO @ Fri, 10 Dec 2021 19:21:22: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 19:21:27: 1000000 INFO @ Fri, 10 Dec 2021 19:21:33: 2000000 INFO @ Fri, 10 Dec 2021 19:21:38: 3000000 INFO @ Fri, 10 Dec 2021 19:21:43: 4000000 INFO @ Fri, 10 Dec 2021 19:21:48: 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 @ Fri, 10 Dec 2021 19:21:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978859/ERX3978859.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978859/ERX3978859.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978859/ERX3978859.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978859/ERX3978859.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 19:21:51: #1 read tag files... INFO @ Fri, 10 Dec 2021 19:21:51: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 19:21:54: 6000000 INFO @ Fri, 10 Dec 2021 19:21:58: 1000000 INFO @ Fri, 10 Dec 2021 19:22:00: 7000000 INFO @ Fri, 10 Dec 2021 19:22:06: 2000000 INFO @ Fri, 10 Dec 2021 19:22:06: 8000000 INFO @ Fri, 10 Dec 2021 19:22:12: 9000000 INFO @ Fri, 10 Dec 2021 19:22:13: 3000000 INFO @ Fri, 10 Dec 2021 19:22:18: 10000000 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 19:22:20: 4000000 INFO @ Fri, 10 Dec 2021 19:22:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978859/ERX3978859.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978859/ERX3978859.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978859/ERX3978859.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978859/ERX3978859.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 19:22:21: #1 read tag files... INFO @ Fri, 10 Dec 2021 19:22:21: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 19:22:24: 11000000 INFO @ Fri, 10 Dec 2021 19:22:27: 5000000 INFO @ Fri, 10 Dec 2021 19:22:28: 1000000 INFO @ Fri, 10 Dec 2021 19:22:31: 12000000 INFO @ Fri, 10 Dec 2021 19:22:34: 2000000 INFO @ Fri, 10 Dec 2021 19:22:34: 6000000 INFO @ Fri, 10 Dec 2021 19:22:37: 13000000 INFO @ Fri, 10 Dec 2021 19:22:40: 3000000 INFO @ Fri, 10 Dec 2021 19:22:42: 7000000 INFO @ Fri, 10 Dec 2021 19:22:43: 14000000 INFO @ Fri, 10 Dec 2021 19:22:47: 4000000 INFO @ Fri, 10 Dec 2021 19:22:49: 8000000 INFO @ Fri, 10 Dec 2021 19:22:49: 15000000 INFO @ Fri, 10 Dec 2021 19:22:53: 5000000 INFO @ Fri, 10 Dec 2021 19:22:56: 16000000 INFO @ Fri, 10 Dec 2021 19:22:56: 9000000 INFO @ Fri, 10 Dec 2021 19:22:59: 6000000 INFO @ Fri, 10 Dec 2021 19:23:02: 17000000 INFO @ Fri, 10 Dec 2021 19:23:03: 10000000 INFO @ Fri, 10 Dec 2021 19:23:05: 7000000 INFO @ Fri, 10 Dec 2021 19:23:08: 18000000 INFO @ Fri, 10 Dec 2021 19:23:10: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 19:23:10: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 19:23:10: #1 total tags in treatment: 7711822 INFO @ Fri, 10 Dec 2021 19:23:10: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 19:23:10: #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 19:23:10: #1 tags after filtering in treatment: 7074639 INFO @ Fri, 10 Dec 2021 19:23:10: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 10 Dec 2021 19:23:10: #1 finished! INFO @ Fri, 10 Dec 2021 19:23:10: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 19:23:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 19:23:11: 11000000 INFO @ Fri, 10 Dec 2021 19:23:11: #2 number of paired peaks: 2470 INFO @ Fri, 10 Dec 2021 19:23:11: start model_add_line... INFO @ Fri, 10 Dec 2021 19:23:11: start X-correlation... INFO @ Fri, 10 Dec 2021 19:23:11: end of X-cor INFO @ Fri, 10 Dec 2021 19:23:11: #2 finished! INFO @ Fri, 10 Dec 2021 19:23:11: #2 predicted fragment length is 161 bps INFO @ Fri, 10 Dec 2021 19:23:11: #2 alternative fragment length(s) may be 161 bps INFO @ Fri, 10 Dec 2021 19:23:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978859/ERX3978859.05_model.r INFO @ Fri, 10 Dec 2021 19:23:11: #3 Call peaks... INFO @ Fri, 10 Dec 2021 19:23:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 19:23:12: 8000000 INFO @ Fri, 10 Dec 2021 19:23:18: 9000000 INFO @ Fri, 10 Dec 2021 19:23:18: 12000000 INFO @ Fri, 10 Dec 2021 19:23:24: 10000000 INFO @ Fri, 10 Dec 2021 19:23:25: 13000000 INFO @ Fri, 10 Dec 2021 19:23:26: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 19:23:30: 11000000 INFO @ Fri, 10 Dec 2021 19:23:32: 14000000 INFO @ Fri, 10 Dec 2021 19:23:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978859/ERX3978859.05_peaks.xls INFO @ Fri, 10 Dec 2021 19:23:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978859/ERX3978859.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 19:23:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978859/ERX3978859.05_summits.bed INFO @ Fri, 10 Dec 2021 19:23:35: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (10308 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 19:23:37: 12000000 INFO @ Fri, 10 Dec 2021 19:23:40: 15000000 INFO @ Fri, 10 Dec 2021 19:23:43: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 19:23:47: 16000000 INFO @ Fri, 10 Dec 2021 19:23:49: 14000000 INFO @ Fri, 10 Dec 2021 19:23:54: 17000000 INFO @ Fri, 10 Dec 2021 19:23:55: 15000000 INFO @ Fri, 10 Dec 2021 19:24:01: 18000000 INFO @ Fri, 10 Dec 2021 19:24:02: 16000000 INFO @ Fri, 10 Dec 2021 19:24:03: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 19:24:03: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 19:24:03: #1 total tags in treatment: 7711822 INFO @ Fri, 10 Dec 2021 19:24:03: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 19:24:03: #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 19:24:03: #1 tags after filtering in treatment: 7074639 INFO @ Fri, 10 Dec 2021 19:24:03: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 10 Dec 2021 19:24:03: #1 finished! INFO @ Fri, 10 Dec 2021 19:24:03: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 19:24:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 19:24:04: #2 number of paired peaks: 2470 INFO @ Fri, 10 Dec 2021 19:24:04: start model_add_line... INFO @ Fri, 10 Dec 2021 19:24:04: start X-correlation... INFO @ Fri, 10 Dec 2021 19:24:04: end of X-cor INFO @ Fri, 10 Dec 2021 19:24:04: #2 finished! INFO @ Fri, 10 Dec 2021 19:24:04: #2 predicted fragment length is 161 bps INFO @ Fri, 10 Dec 2021 19:24:04: #2 alternative fragment length(s) may be 161 bps INFO @ Fri, 10 Dec 2021 19:24:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978859/ERX3978859.10_model.r INFO @ Fri, 10 Dec 2021 19:24:04: #3 Call peaks... INFO @ Fri, 10 Dec 2021 19:24:04: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 19:24:08: 17000000 INFO @ Fri, 10 Dec 2021 19:24:13: 18000000 INFO @ Fri, 10 Dec 2021 19:24:15: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 19:24:15: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 19:24:15: #1 total tags in treatment: 7711822 INFO @ Fri, 10 Dec 2021 19:24:15: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 19:24:15: #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 19:24:15: #1 tags after filtering in treatment: 7074639 INFO @ Fri, 10 Dec 2021 19:24:15: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 10 Dec 2021 19:24:15: #1 finished! INFO @ Fri, 10 Dec 2021 19:24:15: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 19:24:15: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 19:24:16: #2 number of paired peaks: 2470 INFO @ Fri, 10 Dec 2021 19:24:16: start model_add_line... INFO @ Fri, 10 Dec 2021 19:24:16: start X-correlation... INFO @ Fri, 10 Dec 2021 19:24:16: end of X-cor INFO @ Fri, 10 Dec 2021 19:24:16: #2 finished! INFO @ Fri, 10 Dec 2021 19:24:16: #2 predicted fragment length is 161 bps INFO @ Fri, 10 Dec 2021 19:24:16: #2 alternative fragment length(s) may be 161 bps INFO @ Fri, 10 Dec 2021 19:24:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978859/ERX3978859.20_model.r INFO @ Fri, 10 Dec 2021 19:24:16: #3 Call peaks... INFO @ Fri, 10 Dec 2021 19:24:16: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 19:24:20: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 19:24:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978859/ERX3978859.10_peaks.xls INFO @ Fri, 10 Dec 2021 19:24:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978859/ERX3978859.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 19:24:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978859/ERX3978859.10_summits.bed INFO @ Fri, 10 Dec 2021 19:24:28: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6760 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 19:24:32: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 19:24:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978859/ERX3978859.20_peaks.xls INFO @ Fri, 10 Dec 2021 19:24:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978859/ERX3978859.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 19:24:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978859/ERX3978859.20_summits.bed INFO @ Fri, 10 Dec 2021 19:24:40: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3734 records, 4 fields): 5 millis CompletedMACS2peakCalling