Job ID = 14167471 SRX = ERX3978917 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 28143367 spots for ERR3975986/ERR3975986.sra Written 28143367 spots for ERR3975986/ERR3975986.sra fastq に変換しました。 bowtie でマッピング中... Your job 14168841 ("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: 02:51:22 28143367 reads; of these: 28143367 (100.00%) were paired; of these: 10050487 (35.71%) aligned concordantly 0 times 13412215 (47.66%) aligned concordantly exactly 1 time 4680665 (16.63%) aligned concordantly >1 times ---- 10050487 pairs aligned concordantly 0 times; of these: 606712 (6.04%) aligned discordantly 1 time ---- 9443775 pairs aligned 0 times concordantly or discordantly; of these: 18887550 mates make up the pairs; of these: 8814968 (46.67%) aligned 0 times 5698628 (30.17%) aligned exactly 1 time 4373954 (23.16%) aligned >1 times 84.34% overall alignment rate Time searching: 02:51:22 Overall time: 02:51:22 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 20 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] 14890208 / 18491814 = 0.8052 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 15:28:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978917/ERX3978917.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978917/ERX3978917.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978917/ERX3978917.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978917/ERX3978917.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 15:28:52: #1 read tag files... INFO @ Fri, 10 Dec 2021 15:28:52: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 15:28:57: 1000000 INFO @ Fri, 10 Dec 2021 15:29:03: 2000000 INFO @ Fri, 10 Dec 2021 15:29:09: 3000000 INFO @ Fri, 10 Dec 2021 15:29:15: 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 15:29:21: 5000000 INFO @ Fri, 10 Dec 2021 15:29:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978917/ERX3978917.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978917/ERX3978917.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978917/ERX3978917.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978917/ERX3978917.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 15:29:22: #1 read tag files... INFO @ Fri, 10 Dec 2021 15:29:22: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 15:29:28: 6000000 INFO @ Fri, 10 Dec 2021 15:29:32: 1000000 INFO @ Fri, 10 Dec 2021 15:29:36: 7000000 INFO @ Fri, 10 Dec 2021 15:29:42: 2000000 INFO @ Fri, 10 Dec 2021 15:29:44: 8000000 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 15:29:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978917/ERX3978917.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978917/ERX3978917.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978917/ERX3978917.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978917/ERX3978917.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 15:29:51: #1 read tag files... INFO @ Fri, 10 Dec 2021 15:29:51: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 15:29:52: 9000000 INFO @ Fri, 10 Dec 2021 15:29:52: 3000000 INFO @ Fri, 10 Dec 2021 15:29:59: 1000000 INFO @ Fri, 10 Dec 2021 15:30:00: 10000000 INFO @ Fri, 10 Dec 2021 15:30:02: 4000000 INFO @ Fri, 10 Dec 2021 15:30:07: 2000000 INFO @ Fri, 10 Dec 2021 15:30:08: 11000000 INFO @ Fri, 10 Dec 2021 15:30:12: 5000000 INFO @ Fri, 10 Dec 2021 15:30:15: 3000000 INFO @ Fri, 10 Dec 2021 15:30:16: 12000000 INFO @ Fri, 10 Dec 2021 15:30:23: 6000000 INFO @ Fri, 10 Dec 2021 15:30:23: 4000000 INFO @ Fri, 10 Dec 2021 15:30:24: 13000000 INFO @ Fri, 10 Dec 2021 15:30:31: 5000000 INFO @ Fri, 10 Dec 2021 15:30:32: 14000000 INFO @ Fri, 10 Dec 2021 15:30:33: 7000000 INFO @ Fri, 10 Dec 2021 15:30:38: 6000000 INFO @ Fri, 10 Dec 2021 15:30:40: 15000000 INFO @ Fri, 10 Dec 2021 15:30:43: 8000000 INFO @ Fri, 10 Dec 2021 15:30:46: 7000000 INFO @ Fri, 10 Dec 2021 15:30:48: 16000000 INFO @ Fri, 10 Dec 2021 15:30:53: 9000000 INFO @ Fri, 10 Dec 2021 15:30:54: 8000000 INFO @ Fri, 10 Dec 2021 15:30:56: 17000000 INFO @ Fri, 10 Dec 2021 15:31:02: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 15:31:02: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 15:31:02: #1 total tags in treatment: 3592644 INFO @ Fri, 10 Dec 2021 15:31:02: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 15:31:02: #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 15:31:02: #1 tags after filtering in treatment: 3043521 INFO @ Fri, 10 Dec 2021 15:31:02: #1 Redundant rate of treatment: 0.15 INFO @ Fri, 10 Dec 2021 15:31:02: #1 finished! INFO @ Fri, 10 Dec 2021 15:31:02: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 15:31:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 15:31:02: 9000000 INFO @ Fri, 10 Dec 2021 15:31:02: #2 number of paired peaks: 4256 INFO @ Fri, 10 Dec 2021 15:31:02: start model_add_line... INFO @ Fri, 10 Dec 2021 15:31:02: start X-correlation... INFO @ Fri, 10 Dec 2021 15:31:02: end of X-cor INFO @ Fri, 10 Dec 2021 15:31:02: #2 finished! INFO @ Fri, 10 Dec 2021 15:31:02: #2 predicted fragment length is 167 bps INFO @ Fri, 10 Dec 2021 15:31:02: #2 alternative fragment length(s) may be 167 bps INFO @ Fri, 10 Dec 2021 15:31:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978917/ERX3978917.05_model.r INFO @ Fri, 10 Dec 2021 15:31:02: #3 Call peaks... INFO @ Fri, 10 Dec 2021 15:31:02: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 15:31:03: 10000000 INFO @ Fri, 10 Dec 2021 15:31:10: 10000000 INFO @ Fri, 10 Dec 2021 15:31:10: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 15:31:13: 11000000 INFO @ Fri, 10 Dec 2021 15:31:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978917/ERX3978917.05_peaks.xls INFO @ Fri, 10 Dec 2021 15:31:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978917/ERX3978917.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 15:31:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978917/ERX3978917.05_summits.bed INFO @ Fri, 10 Dec 2021 15:31:14: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8724 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 15:31:17: 11000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 15:31:24: 12000000 INFO @ Fri, 10 Dec 2021 15:31:26: 12000000 INFO @ Fri, 10 Dec 2021 15:31:34: 13000000 INFO @ Fri, 10 Dec 2021 15:31:35: 13000000 INFO @ Fri, 10 Dec 2021 15:31:45: 14000000 INFO @ Fri, 10 Dec 2021 15:31:45: 14000000 INFO @ Fri, 10 Dec 2021 15:31:53: 15000000 INFO @ Fri, 10 Dec 2021 15:31:56: 15000000 INFO @ Fri, 10 Dec 2021 15:32:01: 16000000 INFO @ Fri, 10 Dec 2021 15:32:06: 16000000 INFO @ Fri, 10 Dec 2021 15:32:09: 17000000 INFO @ Fri, 10 Dec 2021 15:32:15: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 15:32:15: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 15:32:15: #1 total tags in treatment: 3592644 INFO @ Fri, 10 Dec 2021 15:32:15: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 15:32:15: #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 15:32:15: #1 tags after filtering in treatment: 3043521 INFO @ Fri, 10 Dec 2021 15:32:15: #1 Redundant rate of treatment: 0.15 INFO @ Fri, 10 Dec 2021 15:32:15: #1 finished! INFO @ Fri, 10 Dec 2021 15:32:15: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 15:32:15: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 15:32:15: #2 number of paired peaks: 4256 INFO @ Fri, 10 Dec 2021 15:32:15: start model_add_line... INFO @ Fri, 10 Dec 2021 15:32:15: start X-correlation... INFO @ Fri, 10 Dec 2021 15:32:15: end of X-cor INFO @ Fri, 10 Dec 2021 15:32:15: #2 finished! INFO @ Fri, 10 Dec 2021 15:32:15: #2 predicted fragment length is 167 bps INFO @ Fri, 10 Dec 2021 15:32:15: #2 alternative fragment length(s) may be 167 bps INFO @ Fri, 10 Dec 2021 15:32:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978917/ERX3978917.20_model.r INFO @ Fri, 10 Dec 2021 15:32:15: #3 Call peaks... INFO @ Fri, 10 Dec 2021 15:32:15: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 15:32:16: 17000000 INFO @ Fri, 10 Dec 2021 15:32:22: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 15:32:22: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 15:32:22: #1 total tags in treatment: 3592644 INFO @ Fri, 10 Dec 2021 15:32:22: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 15:32:22: #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 15:32:22: #1 tags after filtering in treatment: 3043521 INFO @ Fri, 10 Dec 2021 15:32:22: #1 Redundant rate of treatment: 0.15 INFO @ Fri, 10 Dec 2021 15:32:22: #1 finished! INFO @ Fri, 10 Dec 2021 15:32:22: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 15:32:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 15:32:22: #2 number of paired peaks: 4256 INFO @ Fri, 10 Dec 2021 15:32:22: start model_add_line... INFO @ Fri, 10 Dec 2021 15:32:22: start X-correlation... INFO @ Fri, 10 Dec 2021 15:32:22: end of X-cor INFO @ Fri, 10 Dec 2021 15:32:22: #2 finished! INFO @ Fri, 10 Dec 2021 15:32:22: #2 predicted fragment length is 167 bps INFO @ Fri, 10 Dec 2021 15:32:22: #2 alternative fragment length(s) may be 167 bps INFO @ Fri, 10 Dec 2021 15:32:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978917/ERX3978917.10_model.r INFO @ Fri, 10 Dec 2021 15:32:22: #3 Call peaks... INFO @ Fri, 10 Dec 2021 15:32:22: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 15:32:23: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 15:32:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978917/ERX3978917.20_peaks.xls INFO @ Fri, 10 Dec 2021 15:32:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978917/ERX3978917.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 15:32:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978917/ERX3978917.20_summits.bed INFO @ Fri, 10 Dec 2021 15:32:26: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1422 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 15:32:32: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 15:32:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978917/ERX3978917.10_peaks.xls INFO @ Fri, 10 Dec 2021 15:32:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978917/ERX3978917.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 15:32:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978917/ERX3978917.10_summits.bed INFO @ Fri, 10 Dec 2021 15:32:37: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4770 records, 4 fields): 7 millis CompletedMACS2peakCalling