Job ID = 14172096 SRX = SRX7628906 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 20457424 spots for SRR10963268/SRR10963268.sra Written 20457424 spots for SRR10963268/SRR10963268.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172616 ("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: 00:26:18 20457424 reads; of these: 20457424 (100.00%) were paired; of these: 11219057 (54.84%) aligned concordantly 0 times 6735004 (32.92%) aligned concordantly exactly 1 time 2503363 (12.24%) aligned concordantly >1 times ---- 11219057 pairs aligned concordantly 0 times; of these: 28268 (0.25%) aligned discordantly 1 time ---- 11190789 pairs aligned 0 times concordantly or discordantly; of these: 22381578 mates make up the pairs; of these: 21919134 (97.93%) aligned 0 times 236188 (1.06%) aligned exactly 1 time 226256 (1.01%) aligned >1 times 46.43% overall alignment rate Time searching: 00:26:19 Overall time: 00:26:19 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] 807051 / 9263075 = 0.0871 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 @ Sat, 11 Dec 2021 14:44:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7628906/SRX7628906.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7628906/SRX7628906.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7628906/SRX7628906.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7628906/SRX7628906.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 @ Sat, 11 Dec 2021 14:44:04: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:44:04: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:44:11: 1000000 INFO @ Sat, 11 Dec 2021 14:44:18: 2000000 INFO @ Sat, 11 Dec 2021 14:44:25: 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 @ Sat, 11 Dec 2021 14:44:32: 4000000 INFO @ Sat, 11 Dec 2021 14:44:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7628906/SRX7628906.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7628906/SRX7628906.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7628906/SRX7628906.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7628906/SRX7628906.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 @ Sat, 11 Dec 2021 14:44:33: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:44:33: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:44:39: 5000000 INFO @ Sat, 11 Dec 2021 14:44:41: 1000000 INFO @ Sat, 11 Dec 2021 14:44:46: 6000000 INFO @ Sat, 11 Dec 2021 14:44:50: 2000000 INFO @ Sat, 11 Dec 2021 14:44:53: 7000000 INFO @ Sat, 11 Dec 2021 14:44:59: 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 @ Sat, 11 Dec 2021 14:45:01: 8000000 INFO @ Sat, 11 Dec 2021 14:45:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7628906/SRX7628906.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7628906/SRX7628906.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7628906/SRX7628906.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7628906/SRX7628906.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 @ Sat, 11 Dec 2021 14:45:03: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:45:03: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:45:07: 4000000 INFO @ Sat, 11 Dec 2021 14:45:08: 9000000 INFO @ Sat, 11 Dec 2021 14:45:14: 1000000 INFO @ Sat, 11 Dec 2021 14:45:15: 10000000 INFO @ Sat, 11 Dec 2021 14:45:16: 5000000 INFO @ Sat, 11 Dec 2021 14:45:23: 11000000 INFO @ Sat, 11 Dec 2021 14:45:25: 2000000 INFO @ Sat, 11 Dec 2021 14:45:25: 6000000 INFO @ Sat, 11 Dec 2021 14:45:31: 12000000 INFO @ Sat, 11 Dec 2021 14:45:34: 7000000 INFO @ Sat, 11 Dec 2021 14:45:36: 3000000 INFO @ Sat, 11 Dec 2021 14:45:38: 13000000 INFO @ Sat, 11 Dec 2021 14:45:43: 8000000 INFO @ Sat, 11 Dec 2021 14:45:46: 14000000 INFO @ Sat, 11 Dec 2021 14:45:47: 4000000 INFO @ Sat, 11 Dec 2021 14:45:52: 9000000 INFO @ Sat, 11 Dec 2021 14:45:54: 15000000 INFO @ Sat, 11 Dec 2021 14:45:58: 5000000 INFO @ Sat, 11 Dec 2021 14:46:01: 10000000 INFO @ Sat, 11 Dec 2021 14:46:02: 16000000 INFO @ Sat, 11 Dec 2021 14:46:09: 17000000 INFO @ Sat, 11 Dec 2021 14:46:09: 6000000 INFO @ Sat, 11 Dec 2021 14:46:10: 11000000 INFO @ Sat, 11 Dec 2021 14:46:12: #1 tag size is determined as 42 bps INFO @ Sat, 11 Dec 2021 14:46:12: #1 tag size = 42 INFO @ Sat, 11 Dec 2021 14:46:12: #1 total tags in treatment: 8432572 INFO @ Sat, 11 Dec 2021 14:46:12: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:46:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 14:46:12: #1 tags after filtering in treatment: 7626539 INFO @ Sat, 11 Dec 2021 14:46:12: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 11 Dec 2021 14:46:12: #1 finished! INFO @ Sat, 11 Dec 2021 14:46:12: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:46:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:46:13: #2 number of paired peaks: 4109 INFO @ Sat, 11 Dec 2021 14:46:13: start model_add_line... INFO @ Sat, 11 Dec 2021 14:46:13: start X-correlation... INFO @ Sat, 11 Dec 2021 14:46:13: end of X-cor INFO @ Sat, 11 Dec 2021 14:46:13: #2 finished! INFO @ Sat, 11 Dec 2021 14:46:13: #2 predicted fragment length is 166 bps INFO @ Sat, 11 Dec 2021 14:46:13: #2 alternative fragment length(s) may be 166 bps INFO @ Sat, 11 Dec 2021 14:46:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7628906/SRX7628906.05_model.r INFO @ Sat, 11 Dec 2021 14:46:13: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:46:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:46:18: 12000000 INFO @ Sat, 11 Dec 2021 14:46:20: 7000000 INFO @ Sat, 11 Dec 2021 14:46:27: 13000000 INFO @ Sat, 11 Dec 2021 14:46:32: 8000000 INFO @ Sat, 11 Dec 2021 14:46:37: 14000000 INFO @ Sat, 11 Dec 2021 14:46:41: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 14:46:43: 9000000 INFO @ Sat, 11 Dec 2021 14:46:46: 15000000 INFO @ Sat, 11 Dec 2021 14:46:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7628906/SRX7628906.05_peaks.xls INFO @ Sat, 11 Dec 2021 14:46:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7628906/SRX7628906.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:46:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7628906/SRX7628906.05_summits.bed INFO @ Sat, 11 Dec 2021 14:46:53: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7392 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 14:46:54: 10000000 INFO @ Sat, 11 Dec 2021 14:46:55: 16000000 INFO @ Sat, 11 Dec 2021 14:47:02: 17000000 INFO @ Sat, 11 Dec 2021 14:47:05: #1 tag size is determined as 42 bps INFO @ Sat, 11 Dec 2021 14:47:05: #1 tag size = 42 INFO @ Sat, 11 Dec 2021 14:47:05: #1 total tags in treatment: 8432572 INFO @ Sat, 11 Dec 2021 14:47:05: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:47:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 14:47:06: #1 tags after filtering in treatment: 7626539 INFO @ Sat, 11 Dec 2021 14:47:06: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 11 Dec 2021 14:47:06: #1 finished! INFO @ Sat, 11 Dec 2021 14:47:06: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:47:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:47:06: 11000000 INFO @ Sat, 11 Dec 2021 14:47:07: #2 number of paired peaks: 4109 INFO @ Sat, 11 Dec 2021 14:47:07: start model_add_line... INFO @ Sat, 11 Dec 2021 14:47:07: start X-correlation... INFO @ Sat, 11 Dec 2021 14:47:07: end of X-cor INFO @ Sat, 11 Dec 2021 14:47:07: #2 finished! INFO @ Sat, 11 Dec 2021 14:47:07: #2 predicted fragment length is 166 bps INFO @ Sat, 11 Dec 2021 14:47:07: #2 alternative fragment length(s) may be 166 bps INFO @ Sat, 11 Dec 2021 14:47:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7628906/SRX7628906.10_model.r INFO @ Sat, 11 Dec 2021 14:47:07: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:47:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:47:17: 12000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 14:47:27: 13000000 INFO @ Sat, 11 Dec 2021 14:47:34: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:47:38: 14000000 INFO @ Sat, 11 Dec 2021 14:47:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7628906/SRX7628906.10_peaks.xls INFO @ Sat, 11 Dec 2021 14:47:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7628906/SRX7628906.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:47:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7628906/SRX7628906.10_summits.bed INFO @ Sat, 11 Dec 2021 14:47:46: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4717 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 14:47:49: 15000000 INFO @ Sat, 11 Dec 2021 14:47:59: 16000000 INFO @ Sat, 11 Dec 2021 14:48:10: 17000000 INFO @ Sat, 11 Dec 2021 14:48:14: #1 tag size is determined as 42 bps INFO @ Sat, 11 Dec 2021 14:48:14: #1 tag size = 42 INFO @ Sat, 11 Dec 2021 14:48:14: #1 total tags in treatment: 8432572 INFO @ Sat, 11 Dec 2021 14:48:14: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:48:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 14:48:14: #1 tags after filtering in treatment: 7626539 INFO @ Sat, 11 Dec 2021 14:48:14: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 11 Dec 2021 14:48:14: #1 finished! INFO @ Sat, 11 Dec 2021 14:48:14: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:48:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:48:15: #2 number of paired peaks: 4109 INFO @ Sat, 11 Dec 2021 14:48:15: start model_add_line... INFO @ Sat, 11 Dec 2021 14:48:15: start X-correlation... INFO @ Sat, 11 Dec 2021 14:48:15: end of X-cor INFO @ Sat, 11 Dec 2021 14:48:15: #2 finished! INFO @ Sat, 11 Dec 2021 14:48:15: #2 predicted fragment length is 166 bps INFO @ Sat, 11 Dec 2021 14:48:15: #2 alternative fragment length(s) may be 166 bps INFO @ Sat, 11 Dec 2021 14:48:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7628906/SRX7628906.20_model.r INFO @ Sat, 11 Dec 2021 14:48:15: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:48:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:48:42: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:48:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7628906/SRX7628906.20_peaks.xls INFO @ Sat, 11 Dec 2021 14:48:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7628906/SRX7628906.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:48:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7628906/SRX7628906.20_summits.bed INFO @ Sat, 11 Dec 2021 14:48:55: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2358 records, 4 fields): 8 millis CompletedMACS2peakCalling