Job ID = 14168046 SRX = ERX3978939 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 39004487 spots for ERR3976009/ERR3976009.sra Written 39004487 spots for ERR3976009/ERR3976009.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169046 ("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: 01:33:49 39004487 reads; of these: 39004487 (100.00%) were paired; of these: 5328984 (13.66%) aligned concordantly 0 times 26178742 (67.12%) aligned concordantly exactly 1 time 7496761 (19.22%) aligned concordantly >1 times ---- 5328984 pairs aligned concordantly 0 times; of these: 679227 (12.75%) aligned discordantly 1 time ---- 4649757 pairs aligned 0 times concordantly or discordantly; of these: 9299514 mates make up the pairs; of these: 5813708 (62.52%) aligned 0 times 1711125 (18.40%) aligned exactly 1 time 1774681 (19.08%) aligned >1 times 92.55% overall alignment rate Time searching: 01:33:49 Overall time: 01:33:49 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 32 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] 22755549 / 34218944 = 0.6650 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 16:37:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978939/ERX3978939.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978939/ERX3978939.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978939/ERX3978939.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978939/ERX3978939.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 16:37:41: #1 read tag files... INFO @ Fri, 10 Dec 2021 16:37:41: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 16:37:46: 1000000 INFO @ Fri, 10 Dec 2021 16:37:52: 2000000 INFO @ Fri, 10 Dec 2021 16:37:58: 3000000 INFO @ Fri, 10 Dec 2021 16:38:03: 4000000 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 16:38:09: 5000000 INFO @ Fri, 10 Dec 2021 16:38:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978939/ERX3978939.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978939/ERX3978939.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978939/ERX3978939.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978939/ERX3978939.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 16:38:10: #1 read tag files... INFO @ Fri, 10 Dec 2021 16:38:10: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 16:38:15: 6000000 INFO @ Fri, 10 Dec 2021 16:38:17: 1000000 INFO @ Fri, 10 Dec 2021 16:38:22: 7000000 INFO @ Fri, 10 Dec 2021 16:38:23: 2000000 INFO @ Fri, 10 Dec 2021 16:38:28: 8000000 INFO @ Fri, 10 Dec 2021 16:38:30: 3000000 INFO @ Fri, 10 Dec 2021 16:38:35: 9000000 INFO @ Fri, 10 Dec 2021 16:38:37: 4000000 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 16:38:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978939/ERX3978939.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978939/ERX3978939.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978939/ERX3978939.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978939/ERX3978939.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 16:38:40: #1 read tag files... INFO @ Fri, 10 Dec 2021 16:38:40: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 16:38:41: 10000000 INFO @ Fri, 10 Dec 2021 16:38:43: 5000000 INFO @ Fri, 10 Dec 2021 16:38:48: 1000000 INFO @ Fri, 10 Dec 2021 16:38:49: 11000000 INFO @ Fri, 10 Dec 2021 16:38:51: 6000000 INFO @ Fri, 10 Dec 2021 16:38:56: 12000000 INFO @ Fri, 10 Dec 2021 16:38:57: 2000000 INFO @ Fri, 10 Dec 2021 16:38:58: 7000000 INFO @ Fri, 10 Dec 2021 16:39:03: 13000000 INFO @ Fri, 10 Dec 2021 16:39:05: 3000000 INFO @ Fri, 10 Dec 2021 16:39:05: 8000000 INFO @ Fri, 10 Dec 2021 16:39:11: 14000000 INFO @ Fri, 10 Dec 2021 16:39:13: 4000000 INFO @ Fri, 10 Dec 2021 16:39:13: 9000000 INFO @ Fri, 10 Dec 2021 16:39:18: 15000000 INFO @ Fri, 10 Dec 2021 16:39:20: 10000000 INFO @ Fri, 10 Dec 2021 16:39:21: 5000000 INFO @ Fri, 10 Dec 2021 16:39:25: 16000000 INFO @ Fri, 10 Dec 2021 16:39:27: 11000000 INFO @ Fri, 10 Dec 2021 16:39:29: 6000000 INFO @ Fri, 10 Dec 2021 16:39:32: 17000000 INFO @ Fri, 10 Dec 2021 16:39:35: 12000000 INFO @ Fri, 10 Dec 2021 16:39:37: 7000000 INFO @ Fri, 10 Dec 2021 16:39:40: 18000000 INFO @ Fri, 10 Dec 2021 16:39:42: 13000000 INFO @ Fri, 10 Dec 2021 16:39:45: 8000000 INFO @ Fri, 10 Dec 2021 16:39:47: 19000000 INFO @ Fri, 10 Dec 2021 16:39:49: 14000000 INFO @ Fri, 10 Dec 2021 16:39:53: 9000000 INFO @ Fri, 10 Dec 2021 16:39:55: 20000000 INFO @ Fri, 10 Dec 2021 16:39:57: 15000000 INFO @ Fri, 10 Dec 2021 16:40:01: 10000000 INFO @ Fri, 10 Dec 2021 16:40:02: 21000000 INFO @ Fri, 10 Dec 2021 16:40:04: 16000000 INFO @ Fri, 10 Dec 2021 16:40:09: 11000000 INFO @ Fri, 10 Dec 2021 16:40:10: 22000000 INFO @ Fri, 10 Dec 2021 16:40:12: 17000000 INFO @ Fri, 10 Dec 2021 16:40:17: 12000000 INFO @ Fri, 10 Dec 2021 16:40:17: 23000000 INFO @ Fri, 10 Dec 2021 16:40:19: 18000000 INFO @ Fri, 10 Dec 2021 16:40:25: 24000000 INFO @ Fri, 10 Dec 2021 16:40:25: 13000000 INFO @ Fri, 10 Dec 2021 16:40:26: 19000000 INFO @ Fri, 10 Dec 2021 16:40:32: 25000000 INFO @ Fri, 10 Dec 2021 16:40:33: 14000000 INFO @ Fri, 10 Dec 2021 16:40:34: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 16:40:39: 26000000 INFO @ Fri, 10 Dec 2021 16:40:41: 21000000 INFO @ Fri, 10 Dec 2021 16:40:41: 15000000 INFO @ Fri, 10 Dec 2021 16:40:44: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 16:40:44: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 16:40:44: #1 total tags in treatment: 11377121 INFO @ Fri, 10 Dec 2021 16:40:44: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 16:40:44: #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 16:40:44: #1 tags after filtering in treatment: 10296581 INFO @ Fri, 10 Dec 2021 16:40:44: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 10 Dec 2021 16:40:44: #1 finished! INFO @ Fri, 10 Dec 2021 16:40:44: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 16:40:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 16:40:45: #2 number of paired peaks: 1210 INFO @ Fri, 10 Dec 2021 16:40:45: start model_add_line... INFO @ Fri, 10 Dec 2021 16:40:45: start X-correlation... INFO @ Fri, 10 Dec 2021 16:40:45: end of X-cor INFO @ Fri, 10 Dec 2021 16:40:45: #2 finished! INFO @ Fri, 10 Dec 2021 16:40:45: #2 predicted fragment length is 179 bps INFO @ Fri, 10 Dec 2021 16:40:45: #2 alternative fragment length(s) may be 179 bps INFO @ Fri, 10 Dec 2021 16:40:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978939/ERX3978939.05_model.r INFO @ Fri, 10 Dec 2021 16:40:45: #3 Call peaks... INFO @ Fri, 10 Dec 2021 16:40:45: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 16:40:48: 22000000 INFO @ Fri, 10 Dec 2021 16:40:49: 16000000 INFO @ Fri, 10 Dec 2021 16:40:55: 23000000 INFO @ Fri, 10 Dec 2021 16:40:57: 17000000 INFO @ Fri, 10 Dec 2021 16:41:02: 24000000 INFO @ Fri, 10 Dec 2021 16:41:05: 18000000 INFO @ Fri, 10 Dec 2021 16:41:07: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 16:41:09: 25000000 INFO @ Fri, 10 Dec 2021 16:41:14: 19000000 INFO @ Fri, 10 Dec 2021 16:41:16: 26000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 16:41:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978939/ERX3978939.05_peaks.xls INFO @ Fri, 10 Dec 2021 16:41:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978939/ERX3978939.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 16:41:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978939/ERX3978939.05_summits.bed INFO @ Fri, 10 Dec 2021 16:41:19: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (10046 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 16:41:21: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 16:41:21: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 16:41:21: #1 total tags in treatment: 11377121 INFO @ Fri, 10 Dec 2021 16:41:21: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 16:41:21: #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 16:41:21: #1 tags after filtering in treatment: 10296581 INFO @ Fri, 10 Dec 2021 16:41:21: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 10 Dec 2021 16:41:21: #1 finished! INFO @ Fri, 10 Dec 2021 16:41:21: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 16:41:21: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 16:41:22: 20000000 INFO @ Fri, 10 Dec 2021 16:41:22: #2 number of paired peaks: 1210 INFO @ Fri, 10 Dec 2021 16:41:22: start model_add_line... INFO @ Fri, 10 Dec 2021 16:41:22: start X-correlation... INFO @ Fri, 10 Dec 2021 16:41:22: end of X-cor INFO @ Fri, 10 Dec 2021 16:41:22: #2 finished! INFO @ Fri, 10 Dec 2021 16:41:22: #2 predicted fragment length is 179 bps INFO @ Fri, 10 Dec 2021 16:41:22: #2 alternative fragment length(s) may be 179 bps INFO @ Fri, 10 Dec 2021 16:41:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978939/ERX3978939.10_model.r INFO @ Fri, 10 Dec 2021 16:41:22: #3 Call peaks... INFO @ Fri, 10 Dec 2021 16:41:22: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 16:41:29: 21000000 INFO @ Fri, 10 Dec 2021 16:41:37: 22000000 INFO @ Fri, 10 Dec 2021 16:41:43: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 16:41:45: 23000000 INFO @ Fri, 10 Dec 2021 16:41:53: 24000000 INFO @ Fri, 10 Dec 2021 16:41:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978939/ERX3978939.10_peaks.xls INFO @ Fri, 10 Dec 2021 16:41:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978939/ERX3978939.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 16:41:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978939/ERX3978939.10_summits.bed INFO @ Fri, 10 Dec 2021 16:41:54: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5714 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 16:42:00: 25000000 INFO @ Fri, 10 Dec 2021 16:42:08: 26000000 INFO @ Fri, 10 Dec 2021 16:42:13: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 16:42:13: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 16:42:13: #1 total tags in treatment: 11377121 INFO @ Fri, 10 Dec 2021 16:42:13: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 16:42:13: #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 16:42:13: #1 tags after filtering in treatment: 10296581 INFO @ Fri, 10 Dec 2021 16:42:13: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 10 Dec 2021 16:42:13: #1 finished! INFO @ Fri, 10 Dec 2021 16:42:13: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 16:42:13: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 16:42:14: #2 number of paired peaks: 1210 INFO @ Fri, 10 Dec 2021 16:42:14: start model_add_line... INFO @ Fri, 10 Dec 2021 16:42:14: start X-correlation... INFO @ Fri, 10 Dec 2021 16:42:14: end of X-cor INFO @ Fri, 10 Dec 2021 16:42:14: #2 finished! INFO @ Fri, 10 Dec 2021 16:42:14: #2 predicted fragment length is 179 bps INFO @ Fri, 10 Dec 2021 16:42:14: #2 alternative fragment length(s) may be 179 bps INFO @ Fri, 10 Dec 2021 16:42:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978939/ERX3978939.20_model.r INFO @ Fri, 10 Dec 2021 16:42:14: #3 Call peaks... INFO @ Fri, 10 Dec 2021 16:42:14: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 16:42:36: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 16:42:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978939/ERX3978939.20_peaks.xls INFO @ Fri, 10 Dec 2021 16:42:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978939/ERX3978939.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 16:42:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978939/ERX3978939.20_summits.bed INFO @ Fri, 10 Dec 2021 16:42:46: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2587 records, 4 fields): 4 millis CompletedMACS2peakCalling