Job ID = 14168198 SRX = ERX3978950 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 9312749 spots for ERR3976021/ERR3976021.sra Written 9312749 spots for ERR3976021/ERR3976021.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169058 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:17:49 9312749 reads; of these: 9312749 (100.00%) were paired; of these: 866420 (9.30%) aligned concordantly 0 times 7515442 (80.70%) aligned concordantly exactly 1 time 930887 (10.00%) aligned concordantly >1 times ---- 866420 pairs aligned concordantly 0 times; of these: 283145 (32.68%) aligned discordantly 1 time ---- 583275 pairs aligned 0 times concordantly or discordantly; of these: 1166550 mates make up the pairs; of these: 619417 (53.10%) aligned 0 times 261331 (22.40%) aligned exactly 1 time 285802 (24.50%) aligned >1 times 96.67% overall alignment rate Time searching: 00:17:50 Overall time: 00:17:50 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] 7164731 / 8713704 = 0.8222 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 16:26:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978950/ERX3978950.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978950/ERX3978950.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978950/ERX3978950.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978950/ERX3978950.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 16:26:02: #1 read tag files... INFO @ Fri, 10 Dec 2021 16:26:02: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 16:26:07: 1000000 INFO @ Fri, 10 Dec 2021 16:26:11: 2000000 INFO @ Fri, 10 Dec 2021 16:26:16: 3000000 INFO @ Fri, 10 Dec 2021 16:26:19: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 16:26:19: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 16:26:19: #1 total tags in treatment: 1473667 INFO @ Fri, 10 Dec 2021 16:26:19: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 16:26:19: #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 16:26:19: #1 tags after filtering in treatment: 1373651 INFO @ Fri, 10 Dec 2021 16:26:19: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 10 Dec 2021 16:26:19: #1 finished! INFO @ Fri, 10 Dec 2021 16:26:19: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 16:26:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 16:26:20: #2 number of paired peaks: 7739 INFO @ Fri, 10 Dec 2021 16:26:20: start model_add_line... INFO @ Fri, 10 Dec 2021 16:26:20: start X-correlation... INFO @ Fri, 10 Dec 2021 16:26:20: end of X-cor INFO @ Fri, 10 Dec 2021 16:26:20: #2 finished! INFO @ Fri, 10 Dec 2021 16:26:20: #2 predicted fragment length is 230 bps INFO @ Fri, 10 Dec 2021 16:26:20: #2 alternative fragment length(s) may be 230 bps INFO @ Fri, 10 Dec 2021 16:26:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978950/ERX3978950.05_model.r INFO @ Fri, 10 Dec 2021 16:26:20: #3 Call peaks... INFO @ Fri, 10 Dec 2021 16:26:20: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 16:26:23: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 16:26:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978950/ERX3978950.05_peaks.xls INFO @ Fri, 10 Dec 2021 16:26:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978950/ERX3978950.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 16:26:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978950/ERX3978950.05_summits.bed INFO @ Fri, 10 Dec 2021 16:26:25: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5533 records, 4 fields): 6 millis CompletedMACS2peakCalling 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 16:26:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978950/ERX3978950.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978950/ERX3978950.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978950/ERX3978950.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978950/ERX3978950.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 16:26:32: #1 read tag files... INFO @ Fri, 10 Dec 2021 16:26:32: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 16:26:37: 1000000 INFO @ Fri, 10 Dec 2021 16:26:41: 2000000 INFO @ Fri, 10 Dec 2021 16:26:46: 3000000 INFO @ Fri, 10 Dec 2021 16:26:49: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 16:26:49: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 16:26:49: #1 total tags in treatment: 1473667 INFO @ Fri, 10 Dec 2021 16:26:49: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 16:26:49: #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 16:26:49: #1 tags after filtering in treatment: 1373651 INFO @ Fri, 10 Dec 2021 16:26:49: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 10 Dec 2021 16:26:49: #1 finished! INFO @ Fri, 10 Dec 2021 16:26:49: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 16:26:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 16:26:50: #2 number of paired peaks: 7739 INFO @ Fri, 10 Dec 2021 16:26:50: start model_add_line... INFO @ Fri, 10 Dec 2021 16:26:50: start X-correlation... INFO @ Fri, 10 Dec 2021 16:26:50: end of X-cor INFO @ Fri, 10 Dec 2021 16:26:50: #2 finished! INFO @ Fri, 10 Dec 2021 16:26:50: #2 predicted fragment length is 230 bps INFO @ Fri, 10 Dec 2021 16:26:50: #2 alternative fragment length(s) may be 230 bps INFO @ Fri, 10 Dec 2021 16:26:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978950/ERX3978950.10_model.r INFO @ Fri, 10 Dec 2021 16:26:50: #3 Call peaks... INFO @ Fri, 10 Dec 2021 16:26:50: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 16:26:53: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 16:26:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978950/ERX3978950.10_peaks.xls INFO @ Fri, 10 Dec 2021 16:26:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978950/ERX3978950.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 16:26:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978950/ERX3978950.10_summits.bed INFO @ Fri, 10 Dec 2021 16:26:55: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4253 records, 4 fields): 6 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 16:27:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978950/ERX3978950.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978950/ERX3978950.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978950/ERX3978950.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978950/ERX3978950.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 16:27:02: #1 read tag files... INFO @ Fri, 10 Dec 2021 16:27:02: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 16:27:07: 1000000 INFO @ Fri, 10 Dec 2021 16:27:11: 2000000 INFO @ Fri, 10 Dec 2021 16:27:16: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 16:27:19: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 16:27:19: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 16:27:19: #1 total tags in treatment: 1473667 INFO @ Fri, 10 Dec 2021 16:27:19: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 16:27:19: #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 16:27:19: #1 tags after filtering in treatment: 1373651 INFO @ Fri, 10 Dec 2021 16:27:19: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 10 Dec 2021 16:27:19: #1 finished! INFO @ Fri, 10 Dec 2021 16:27:19: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 16:27:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 16:27:20: #2 number of paired peaks: 7739 INFO @ Fri, 10 Dec 2021 16:27:20: start model_add_line... INFO @ Fri, 10 Dec 2021 16:27:20: start X-correlation... INFO @ Fri, 10 Dec 2021 16:27:20: end of X-cor INFO @ Fri, 10 Dec 2021 16:27:20: #2 finished! INFO @ Fri, 10 Dec 2021 16:27:20: #2 predicted fragment length is 230 bps INFO @ Fri, 10 Dec 2021 16:27:20: #2 alternative fragment length(s) may be 230 bps INFO @ Fri, 10 Dec 2021 16:27:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978950/ERX3978950.20_model.r INFO @ Fri, 10 Dec 2021 16:27:20: #3 Call peaks... INFO @ Fri, 10 Dec 2021 16:27:20: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 16:27:23: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 16:27:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978950/ERX3978950.20_peaks.xls INFO @ Fri, 10 Dec 2021 16:27:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978950/ERX3978950.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 16:27:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978950/ERX3978950.20_summits.bed INFO @ Fri, 10 Dec 2021 16:27:24: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2376 records, 4 fields): 4 millis CompletedMACS2peakCalling