Job ID = 14168117 SRX = ERX3978945 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 35117438 spots for ERR3976015/ERR3976015.sra Written 35117438 spots for ERR3976015/ERR3976015.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169476 ("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: 02:16:40 35117438 reads; of these: 35117438 (100.00%) were paired; of these: 4192011 (11.94%) aligned concordantly 0 times 23947951 (68.19%) aligned concordantly exactly 1 time 6977476 (19.87%) aligned concordantly >1 times ---- 4192011 pairs aligned concordantly 0 times; of these: 867509 (20.69%) aligned discordantly 1 time ---- 3324502 pairs aligned 0 times concordantly or discordantly; of these: 6649004 mates make up the pairs; of these: 3382695 (50.88%) aligned 0 times 1473297 (22.16%) aligned exactly 1 time 1793012 (26.97%) aligned >1 times 95.18% overall alignment rate Time searching: 02:16:40 Overall time: 02:16:40 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 28 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] 21831338 / 31676721 = 0.6892 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 18:10:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978945/ERX3978945.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978945/ERX3978945.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978945/ERX3978945.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978945/ERX3978945.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 18:10:51: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:10:51: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:10:59: 1000000 INFO @ Fri, 10 Dec 2021 18:11:07: 2000000 INFO @ Fri, 10 Dec 2021 18:11:14: 3000000 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 18:11:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978945/ERX3978945.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978945/ERX3978945.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978945/ERX3978945.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978945/ERX3978945.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 18:11:20: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:11:20: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:11:22: 4000000 INFO @ Fri, 10 Dec 2021 18:11:30: 5000000 INFO @ Fri, 10 Dec 2021 18:11:31: 1000000 INFO @ Fri, 10 Dec 2021 18:11:38: 6000000 INFO @ Fri, 10 Dec 2021 18:11:42: 2000000 INFO @ Fri, 10 Dec 2021 18:11:45: 7000000 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 18:11:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978945/ERX3978945.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978945/ERX3978945.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978945/ERX3978945.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978945/ERX3978945.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 18:11:50: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:11:50: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:11:53: 3000000 INFO @ Fri, 10 Dec 2021 18:11:53: 8000000 INFO @ Fri, 10 Dec 2021 18:12:01: 9000000 INFO @ Fri, 10 Dec 2021 18:12:02: 1000000 INFO @ Fri, 10 Dec 2021 18:12:04: 4000000 INFO @ Fri, 10 Dec 2021 18:12:09: 10000000 INFO @ Fri, 10 Dec 2021 18:12:15: 2000000 INFO @ Fri, 10 Dec 2021 18:12:15: 5000000 INFO @ Fri, 10 Dec 2021 18:12:17: 11000000 INFO @ Fri, 10 Dec 2021 18:12:25: 12000000 INFO @ Fri, 10 Dec 2021 18:12:25: 6000000 INFO @ Fri, 10 Dec 2021 18:12:27: 3000000 INFO @ Fri, 10 Dec 2021 18:12:33: 13000000 INFO @ Fri, 10 Dec 2021 18:12:36: 7000000 INFO @ Fri, 10 Dec 2021 18:12:38: 4000000 INFO @ Fri, 10 Dec 2021 18:12:41: 14000000 INFO @ Fri, 10 Dec 2021 18:12:47: 8000000 INFO @ Fri, 10 Dec 2021 18:12:48: 15000000 INFO @ Fri, 10 Dec 2021 18:12:50: 5000000 INFO @ Fri, 10 Dec 2021 18:12:57: 16000000 INFO @ Fri, 10 Dec 2021 18:12:58: 9000000 INFO @ Fri, 10 Dec 2021 18:13:01: 6000000 INFO @ Fri, 10 Dec 2021 18:13:04: 17000000 INFO @ Fri, 10 Dec 2021 18:13:09: 10000000 INFO @ Fri, 10 Dec 2021 18:13:12: 7000000 INFO @ Fri, 10 Dec 2021 18:13:13: 18000000 INFO @ Fri, 10 Dec 2021 18:13:19: 11000000 INFO @ Fri, 10 Dec 2021 18:13:21: 19000000 INFO @ Fri, 10 Dec 2021 18:13:24: 8000000 INFO @ Fri, 10 Dec 2021 18:13:29: 20000000 INFO @ Fri, 10 Dec 2021 18:13:30: 12000000 INFO @ Fri, 10 Dec 2021 18:13:35: 9000000 INFO @ Fri, 10 Dec 2021 18:13:37: 21000000 INFO @ Fri, 10 Dec 2021 18:13:40: 13000000 INFO @ Fri, 10 Dec 2021 18:13:44: 22000000 INFO @ Fri, 10 Dec 2021 18:13:47: 10000000 INFO @ Fri, 10 Dec 2021 18:13:51: 14000000 INFO @ Fri, 10 Dec 2021 18:13:52: 23000000 INFO @ Fri, 10 Dec 2021 18:13:53: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 18:13:53: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 18:13:53: #1 total tags in treatment: 9554986 INFO @ Fri, 10 Dec 2021 18:13:53: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:13:53: #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 18:13:54: #1 tags after filtering in treatment: 8366818 INFO @ Fri, 10 Dec 2021 18:13:54: #1 Redundant rate of treatment: 0.12 INFO @ Fri, 10 Dec 2021 18:13:54: #1 finished! INFO @ Fri, 10 Dec 2021 18:13:54: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:13:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:13:55: #2 number of paired peaks: 4974 INFO @ Fri, 10 Dec 2021 18:13:55: start model_add_line... INFO @ Fri, 10 Dec 2021 18:13:55: start X-correlation... INFO @ Fri, 10 Dec 2021 18:13:55: end of X-cor INFO @ Fri, 10 Dec 2021 18:13:55: #2 finished! INFO @ Fri, 10 Dec 2021 18:13:55: #2 predicted fragment length is 212 bps INFO @ Fri, 10 Dec 2021 18:13:55: #2 alternative fragment length(s) may be 212 bps INFO @ Fri, 10 Dec 2021 18:13:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978945/ERX3978945.05_model.r INFO @ Fri, 10 Dec 2021 18:13:55: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:13:55: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 18:13:58: 11000000 INFO @ Fri, 10 Dec 2021 18:14:01: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 18:14:09: 12000000 INFO @ Fri, 10 Dec 2021 18:14:12: 16000000 INFO @ Fri, 10 Dec 2021 18:14:20: 13000000 INFO @ Fri, 10 Dec 2021 18:14:22: 17000000 INFO @ Fri, 10 Dec 2021 18:14:23: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:14:31: 14000000 INFO @ Fri, 10 Dec 2021 18:14:33: 18000000 INFO @ Fri, 10 Dec 2021 18:14:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978945/ERX3978945.05_peaks.xls INFO @ Fri, 10 Dec 2021 18:14:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978945/ERX3978945.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:14:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978945/ERX3978945.05_summits.bed INFO @ Fri, 10 Dec 2021 18:14:37: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (11248 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 18:14:41: 15000000 INFO @ Fri, 10 Dec 2021 18:14:43: 19000000 INFO @ Fri, 10 Dec 2021 18:14:52: 16000000 INFO @ Fri, 10 Dec 2021 18:14:54: 20000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 18:15:03: 17000000 INFO @ Fri, 10 Dec 2021 18:15:04: 21000000 INFO @ Fri, 10 Dec 2021 18:15:13: 18000000 INFO @ Fri, 10 Dec 2021 18:15:15: 22000000 INFO @ Fri, 10 Dec 2021 18:15:24: 19000000 INFO @ Fri, 10 Dec 2021 18:15:25: 23000000 INFO @ Fri, 10 Dec 2021 18:15:27: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 18:15:27: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 18:15:27: #1 total tags in treatment: 9554986 INFO @ Fri, 10 Dec 2021 18:15:27: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:15:27: #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 18:15:27: #1 tags after filtering in treatment: 8366818 INFO @ Fri, 10 Dec 2021 18:15:27: #1 Redundant rate of treatment: 0.12 INFO @ Fri, 10 Dec 2021 18:15:27: #1 finished! INFO @ Fri, 10 Dec 2021 18:15:27: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:15:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:15:29: #2 number of paired peaks: 4974 INFO @ Fri, 10 Dec 2021 18:15:29: start model_add_line... INFO @ Fri, 10 Dec 2021 18:15:29: start X-correlation... INFO @ Fri, 10 Dec 2021 18:15:29: end of X-cor INFO @ Fri, 10 Dec 2021 18:15:29: #2 finished! INFO @ Fri, 10 Dec 2021 18:15:29: #2 predicted fragment length is 212 bps INFO @ Fri, 10 Dec 2021 18:15:29: #2 alternative fragment length(s) may be 212 bps INFO @ Fri, 10 Dec 2021 18:15:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978945/ERX3978945.10_model.r INFO @ Fri, 10 Dec 2021 18:15:29: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:15:29: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 18:15:35: 20000000 INFO @ Fri, 10 Dec 2021 18:15:45: 21000000 INFO @ Fri, 10 Dec 2021 18:15:55: 22000000 INFO @ Fri, 10 Dec 2021 18:15:57: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:16:06: 23000000 INFO @ Fri, 10 Dec 2021 18:16:08: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 18:16:08: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 18:16:08: #1 total tags in treatment: 9554986 INFO @ Fri, 10 Dec 2021 18:16:08: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:16:08: #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 18:16:08: #1 tags after filtering in treatment: 8366818 INFO @ Fri, 10 Dec 2021 18:16:08: #1 Redundant rate of treatment: 0.12 INFO @ Fri, 10 Dec 2021 18:16:08: #1 finished! INFO @ Fri, 10 Dec 2021 18:16:08: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:16:08: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:16:09: #2 number of paired peaks: 4974 INFO @ Fri, 10 Dec 2021 18:16:09: start model_add_line... INFO @ Fri, 10 Dec 2021 18:16:10: start X-correlation... INFO @ Fri, 10 Dec 2021 18:16:10: end of X-cor INFO @ Fri, 10 Dec 2021 18:16:10: #2 finished! INFO @ Fri, 10 Dec 2021 18:16:10: #2 predicted fragment length is 212 bps INFO @ Fri, 10 Dec 2021 18:16:10: #2 alternative fragment length(s) may be 212 bps INFO @ Fri, 10 Dec 2021 18:16:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978945/ERX3978945.20_model.r INFO @ Fri, 10 Dec 2021 18:16:10: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:16:10: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 18:16:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978945/ERX3978945.10_peaks.xls INFO @ Fri, 10 Dec 2021 18:16:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978945/ERX3978945.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:16:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978945/ERX3978945.10_summits.bed INFO @ Fri, 10 Dec 2021 18:16:11: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (8275 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 18:16:37: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:16:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978945/ERX3978945.20_peaks.xls INFO @ Fri, 10 Dec 2021 18:16:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978945/ERX3978945.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:16:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978945/ERX3978945.20_summits.bed INFO @ Fri, 10 Dec 2021 18:16:51: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5690 records, 4 fields): 10 millis CompletedMACS2peakCalling