Job ID = 14167966 SRX = ERX3978920 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 11880047 spots for ERR3975989/ERR3975989.sra Written 11880047 spots for ERR3975989/ERR3975989.sra fastq に変換しました。 bowtie でマッピング中... Your job 14168808 ("srTdm6") has been submitted Time loading reference: 00:00:01 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 01:09:36 11880047 reads; of these: 11880047 (100.00%) were paired; of these: 1420402 (11.96%) aligned concordantly 0 times 7972220 (67.11%) aligned concordantly exactly 1 time 2487425 (20.94%) aligned concordantly >1 times ---- 1420402 pairs aligned concordantly 0 times; of these: 420152 (29.58%) aligned discordantly 1 time ---- 1000250 pairs aligned 0 times concordantly or discordantly; of these: 2000500 mates make up the pairs; of these: 881733 (44.08%) aligned 0 times 519892 (25.99%) aligned exactly 1 time 598875 (29.94%) aligned >1 times 96.29% overall alignment rate Time searching: 01:09:39 Overall time: 01:09:39 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] 7777053 / 10848801 = 0.7169 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 15:15:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978920/ERX3978920.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978920/ERX3978920.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978920/ERX3978920.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978920/ERX3978920.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 15:15:50: #1 read tag files... INFO @ Fri, 10 Dec 2021 15:15:50: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 15:16:00: 1000000 INFO @ Fri, 10 Dec 2021 15:16:09: 2000000 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 15:16:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978920/ERX3978920.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978920/ERX3978920.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978920/ERX3978920.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978920/ERX3978920.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 15:16:18: #1 read tag files... INFO @ Fri, 10 Dec 2021 15:16:18: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 15:16:18: 3000000 INFO @ Fri, 10 Dec 2021 15:16:28: 1000000 INFO @ Fri, 10 Dec 2021 15:16:28: 4000000 INFO @ Fri, 10 Dec 2021 15:16:38: 2000000 INFO @ Fri, 10 Dec 2021 15:16:38: 5000000 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 15:16:47: 3000000 INFO @ Fri, 10 Dec 2021 15:16:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978920/ERX3978920.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978920/ERX3978920.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978920/ERX3978920.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978920/ERX3978920.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 15:16:48: #1 read tag files... INFO @ Fri, 10 Dec 2021 15:16:48: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 15:16:48: 6000000 INFO @ Fri, 10 Dec 2021 15:16:56: 4000000 INFO @ Fri, 10 Dec 2021 15:16:59: 7000000 INFO @ Fri, 10 Dec 2021 15:17:01: 1000000 INFO @ Fri, 10 Dec 2021 15:17:02: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 15:17:02: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 15:17:02: #1 total tags in treatment: 2920849 INFO @ Fri, 10 Dec 2021 15:17:02: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 15:17:02: #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 15:17:02: #1 tags after filtering in treatment: 2682666 INFO @ Fri, 10 Dec 2021 15:17:02: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 10 Dec 2021 15:17:02: #1 finished! INFO @ Fri, 10 Dec 2021 15:17:02: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 15:17:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 15:17:02: #2 number of paired peaks: 2023 INFO @ Fri, 10 Dec 2021 15:17:02: start model_add_line... INFO @ Fri, 10 Dec 2021 15:17:02: start X-correlation... INFO @ Fri, 10 Dec 2021 15:17:02: end of X-cor INFO @ Fri, 10 Dec 2021 15:17:02: #2 finished! INFO @ Fri, 10 Dec 2021 15:17:02: #2 predicted fragment length is 166 bps INFO @ Fri, 10 Dec 2021 15:17:02: #2 alternative fragment length(s) may be 166 bps INFO @ Fri, 10 Dec 2021 15:17:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978920/ERX3978920.05_model.r INFO @ Fri, 10 Dec 2021 15:17:02: #3 Call peaks... INFO @ Fri, 10 Dec 2021 15:17:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 15:17:05: 5000000 INFO @ Fri, 10 Dec 2021 15:17:12: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 15:17:13: 2000000 INFO @ Fri, 10 Dec 2021 15:17:14: 6000000 INFO @ Fri, 10 Dec 2021 15:17:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978920/ERX3978920.05_peaks.xls INFO @ Fri, 10 Dec 2021 15:17:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978920/ERX3978920.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 15:17:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978920/ERX3978920.05_summits.bed INFO @ Fri, 10 Dec 2021 15:17:16: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (3357 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 15:17:24: 3000000 INFO @ Fri, 10 Dec 2021 15:17:24: 7000000 INFO @ Fri, 10 Dec 2021 15:17:27: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 15:17:27: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 15:17:27: #1 total tags in treatment: 2920849 INFO @ Fri, 10 Dec 2021 15:17:27: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 15:17:27: #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 15:17:27: #1 tags after filtering in treatment: 2682666 INFO @ Fri, 10 Dec 2021 15:17:27: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 10 Dec 2021 15:17:27: #1 finished! INFO @ Fri, 10 Dec 2021 15:17:27: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 15:17:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 15:17:27: #2 number of paired peaks: 2023 INFO @ Fri, 10 Dec 2021 15:17:27: start model_add_line... INFO @ Fri, 10 Dec 2021 15:17:27: start X-correlation... INFO @ Fri, 10 Dec 2021 15:17:27: end of X-cor INFO @ Fri, 10 Dec 2021 15:17:27: #2 finished! INFO @ Fri, 10 Dec 2021 15:17:27: #2 predicted fragment length is 166 bps INFO @ Fri, 10 Dec 2021 15:17:27: #2 alternative fragment length(s) may be 166 bps INFO @ Fri, 10 Dec 2021 15:17:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978920/ERX3978920.10_model.r INFO @ Fri, 10 Dec 2021 15:17:27: #3 Call peaks... INFO @ Fri, 10 Dec 2021 15:17:27: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 15:17:34: 4000000 INFO @ Fri, 10 Dec 2021 15:17:36: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 15:17:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978920/ERX3978920.10_peaks.xls INFO @ Fri, 10 Dec 2021 15:17:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978920/ERX3978920.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 15:17:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978920/ERX3978920.10_summits.bed INFO @ Fri, 10 Dec 2021 15:17:41: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (1422 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 15:17:45: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 15:17:55: 6000000 INFO @ Fri, 10 Dec 2021 15:18:06: 7000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 15:18:09: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 15:18:09: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 15:18:09: #1 total tags in treatment: 2920849 INFO @ Fri, 10 Dec 2021 15:18:09: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 15:18:09: #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 15:18:09: #1 tags after filtering in treatment: 2682666 INFO @ Fri, 10 Dec 2021 15:18:09: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 10 Dec 2021 15:18:09: #1 finished! INFO @ Fri, 10 Dec 2021 15:18:09: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 15:18:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 15:18:09: #2 number of paired peaks: 2023 INFO @ Fri, 10 Dec 2021 15:18:09: start model_add_line... INFO @ Fri, 10 Dec 2021 15:18:09: start X-correlation... INFO @ Fri, 10 Dec 2021 15:18:09: end of X-cor INFO @ Fri, 10 Dec 2021 15:18:09: #2 finished! INFO @ Fri, 10 Dec 2021 15:18:09: #2 predicted fragment length is 166 bps INFO @ Fri, 10 Dec 2021 15:18:09: #2 alternative fragment length(s) may be 166 bps INFO @ Fri, 10 Dec 2021 15:18:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978920/ERX3978920.20_model.r INFO @ Fri, 10 Dec 2021 15:18:09: #3 Call peaks... INFO @ Fri, 10 Dec 2021 15:18:09: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 15:18:19: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 15:18:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978920/ERX3978920.20_peaks.xls INFO @ Fri, 10 Dec 2021 15:18:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978920/ERX3978920.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 15:18:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978920/ERX3978920.20_summits.bed INFO @ Fri, 10 Dec 2021 15:18:24: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (750 records, 4 fields): 6 millis CompletedMACS2peakCalling