Job ID = 14167988 SRX = ERX3978929 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 27137556 spots for ERR3975999/ERR3975999.sra Written 27137556 spots for ERR3975999/ERR3975999.sra fastq に変換しました。 bowtie でマッピング中... Your job 14168993 ("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: 01:45:35 27137556 reads; of these: 27137556 (100.00%) were paired; of these: 3263883 (12.03%) aligned concordantly 0 times 19320533 (71.19%) aligned concordantly exactly 1 time 4553140 (16.78%) aligned concordantly >1 times ---- 3263883 pairs aligned concordantly 0 times; of these: 689716 (21.13%) aligned discordantly 1 time ---- 2574167 pairs aligned 0 times concordantly or discordantly; of these: 5148334 mates make up the pairs; of these: 2668342 (51.83%) aligned 0 times 1254527 (24.37%) aligned exactly 1 time 1225465 (23.80%) aligned >1 times 95.08% overall alignment rate Time searching: 01:45:36 Overall time: 01:45:36 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] 19719607 / 24426482 = 0.8073 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 16:16:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978929/ERX3978929.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978929/ERX3978929.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978929/ERX3978929.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978929/ERX3978929.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 16:16:00: #1 read tag files... INFO @ Fri, 10 Dec 2021 16:16:00: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 16:16:11: 1000000 INFO @ Fri, 10 Dec 2021 16:16:22: 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 16:16:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978929/ERX3978929.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978929/ERX3978929.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978929/ERX3978929.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978929/ERX3978929.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 16:16:29: #1 read tag files... INFO @ Fri, 10 Dec 2021 16:16:29: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 16:16:34: 3000000 INFO @ Fri, 10 Dec 2021 16:16:37: 1000000 INFO @ Fri, 10 Dec 2021 16:16:45: 4000000 INFO @ Fri, 10 Dec 2021 16:16:46: 2000000 INFO @ Fri, 10 Dec 2021 16:16:54: 3000000 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 16:16:57: 5000000 INFO @ Fri, 10 Dec 2021 16:16:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978929/ERX3978929.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978929/ERX3978929.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978929/ERX3978929.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978929/ERX3978929.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 16:16:59: #1 read tag files... INFO @ Fri, 10 Dec 2021 16:16:59: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 16:17:03: 4000000 INFO @ Fri, 10 Dec 2021 16:17:08: 1000000 INFO @ Fri, 10 Dec 2021 16:17:10: 6000000 INFO @ Fri, 10 Dec 2021 16:17:11: 5000000 INFO @ Fri, 10 Dec 2021 16:17:16: 2000000 INFO @ Fri, 10 Dec 2021 16:17:20: 6000000 INFO @ Fri, 10 Dec 2021 16:17:22: 7000000 INFO @ Fri, 10 Dec 2021 16:17:25: 3000000 INFO @ Fri, 10 Dec 2021 16:17:29: 7000000 INFO @ Fri, 10 Dec 2021 16:17:34: 4000000 INFO @ Fri, 10 Dec 2021 16:17:35: 8000000 INFO @ Fri, 10 Dec 2021 16:17:38: 8000000 INFO @ Fri, 10 Dec 2021 16:17:43: 5000000 INFO @ Fri, 10 Dec 2021 16:17:47: 9000000 INFO @ Fri, 10 Dec 2021 16:17:47: 9000000 INFO @ Fri, 10 Dec 2021 16:17:52: 6000000 INFO @ Fri, 10 Dec 2021 16:17:57: 10000000 INFO @ Fri, 10 Dec 2021 16:18:00: 10000000 INFO @ Fri, 10 Dec 2021 16:18:01: 7000000 INFO @ Fri, 10 Dec 2021 16:18:06: 11000000 INFO @ Fri, 10 Dec 2021 16:18:10: 8000000 INFO @ Fri, 10 Dec 2021 16:18:12: 11000000 INFO @ Fri, 10 Dec 2021 16:18:15: 12000000 INFO @ Fri, 10 Dec 2021 16:18:16: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 16:18:16: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 16:18:16: #1 total tags in treatment: 4669269 INFO @ Fri, 10 Dec 2021 16:18:16: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 16:18:16: #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 16:18:17: #1 tags after filtering in treatment: 4116218 INFO @ Fri, 10 Dec 2021 16:18:17: #1 Redundant rate of treatment: 0.12 INFO @ Fri, 10 Dec 2021 16:18:17: #1 finished! INFO @ Fri, 10 Dec 2021 16:18:17: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 16:18:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 16:18:17: #2 number of paired peaks: 5773 INFO @ Fri, 10 Dec 2021 16:18:17: start model_add_line... INFO @ Fri, 10 Dec 2021 16:18:17: start X-correlation... INFO @ Fri, 10 Dec 2021 16:18:17: end of X-cor INFO @ Fri, 10 Dec 2021 16:18:17: #2 finished! INFO @ Fri, 10 Dec 2021 16:18:17: #2 predicted fragment length is 169 bps INFO @ Fri, 10 Dec 2021 16:18:17: #2 alternative fragment length(s) may be 169 bps INFO @ Fri, 10 Dec 2021 16:18:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978929/ERX3978929.10_model.r INFO @ Fri, 10 Dec 2021 16:18:18: #3 Call peaks... INFO @ Fri, 10 Dec 2021 16:18:18: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 16:18:19: 9000000 INFO @ Fri, 10 Dec 2021 16:18:24: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 16:18:26: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 16:18:26: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 16:18:26: #1 total tags in treatment: 4669269 INFO @ Fri, 10 Dec 2021 16:18:26: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 16:18:26: #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 16:18:26: #1 tags after filtering in treatment: 4116218 INFO @ Fri, 10 Dec 2021 16:18:26: #1 Redundant rate of treatment: 0.12 INFO @ Fri, 10 Dec 2021 16:18:26: #1 finished! INFO @ Fri, 10 Dec 2021 16:18:26: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 16:18:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 16:18:27: #2 number of paired peaks: 5773 INFO @ Fri, 10 Dec 2021 16:18:27: start model_add_line... INFO @ Fri, 10 Dec 2021 16:18:27: start X-correlation... INFO @ Fri, 10 Dec 2021 16:18:27: end of X-cor INFO @ Fri, 10 Dec 2021 16:18:27: #2 finished! INFO @ Fri, 10 Dec 2021 16:18:27: #2 predicted fragment length is 169 bps INFO @ Fri, 10 Dec 2021 16:18:27: #2 alternative fragment length(s) may be 169 bps INFO @ Fri, 10 Dec 2021 16:18:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978929/ERX3978929.05_model.r INFO @ Fri, 10 Dec 2021 16:18:27: #3 Call peaks... INFO @ Fri, 10 Dec 2021 16:18:27: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 16:18:28: 10000000 INFO @ Fri, 10 Dec 2021 16:18:33: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 16:18:36: 11000000 INFO @ Fri, 10 Dec 2021 16:18:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978929/ERX3978929.10_peaks.xls INFO @ Fri, 10 Dec 2021 16:18:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978929/ERX3978929.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 16:18:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978929/ERX3978929.10_summits.bed INFO @ Fri, 10 Dec 2021 16:18:41: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6707 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 16:18:42: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 16:18:45: 12000000 INFO @ Fri, 10 Dec 2021 16:18:46: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 16:18:46: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 16:18:46: #1 total tags in treatment: 4669269 INFO @ Fri, 10 Dec 2021 16:18:46: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 16:18:46: #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 16:18:46: #1 tags after filtering in treatment: 4116218 INFO @ Fri, 10 Dec 2021 16:18:46: #1 Redundant rate of treatment: 0.12 INFO @ Fri, 10 Dec 2021 16:18:46: #1 finished! INFO @ Fri, 10 Dec 2021 16:18:46: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 16:18:46: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 16:18:47: #2 number of paired peaks: 5773 INFO @ Fri, 10 Dec 2021 16:18:47: start model_add_line... INFO @ Fri, 10 Dec 2021 16:18:47: start X-correlation... INFO @ Fri, 10 Dec 2021 16:18:47: end of X-cor INFO @ Fri, 10 Dec 2021 16:18:47: #2 finished! INFO @ Fri, 10 Dec 2021 16:18:47: #2 predicted fragment length is 169 bps INFO @ Fri, 10 Dec 2021 16:18:47: #2 alternative fragment length(s) may be 169 bps INFO @ Fri, 10 Dec 2021 16:18:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978929/ERX3978929.20_model.r INFO @ Fri, 10 Dec 2021 16:18:47: #3 Call peaks... INFO @ Fri, 10 Dec 2021 16:18:47: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 16:18:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978929/ERX3978929.05_peaks.xls INFO @ Fri, 10 Dec 2021 16:18:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978929/ERX3978929.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 16:18:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978929/ERX3978929.05_summits.bed INFO @ Fri, 10 Dec 2021 16:18:51: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (9730 records, 4 fields): 17 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 16:19:03: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 16:19:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978929/ERX3978929.20_peaks.xls INFO @ Fri, 10 Dec 2021 16:19:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978929/ERX3978929.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 16:19:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978929/ERX3978929.20_summits.bed INFO @ Fri, 10 Dec 2021 16:19:10: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (3890 records, 4 fields): 15 millis CompletedMACS2peakCalling