Job ID = 16439609 SRX = SRX9518342 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 18038597 spots for SRR13070825/SRR13070825.sra Written 18038597 spots for SRR13070825/SRR13070825.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439772 ("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: 00:25:31 18038597 reads; of these: 18038597 (100.00%) were paired; of these: 2113122 (11.71%) aligned concordantly 0 times 13681753 (75.85%) aligned concordantly exactly 1 time 2243722 (12.44%) aligned concordantly >1 times ---- 2113122 pairs aligned concordantly 0 times; of these: 275225 (13.02%) aligned discordantly 1 time ---- 1837897 pairs aligned 0 times concordantly or discordantly; of these: 3675794 mates make up the pairs; of these: 3069034 (83.49%) aligned 0 times 380016 (10.34%) aligned exactly 1 time 226744 (6.17%) aligned >1 times 91.49% overall alignment rate Time searching: 00:25:31 Overall time: 00:25:31 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 16 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] 2117433 / 16156864 = 0.1311 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 16:16:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9518342/SRX9518342.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9518342/SRX9518342.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9518342/SRX9518342.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9518342/SRX9518342.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 @ Tue, 02 Aug 2022 16:16:06: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:16:06: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:16:12: 1000000 INFO @ Tue, 02 Aug 2022 16:16:18: 2000000 INFO @ Tue, 02 Aug 2022 16:16:24: 3000000 INFO @ Tue, 02 Aug 2022 16:16:30: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 16:16:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9518342/SRX9518342.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9518342/SRX9518342.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9518342/SRX9518342.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9518342/SRX9518342.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 @ Tue, 02 Aug 2022 16:16:35: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:16:35: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:16:36: 5000000 INFO @ Tue, 02 Aug 2022 16:16:40: 1000000 INFO @ Tue, 02 Aug 2022 16:16:41: 6000000 INFO @ Tue, 02 Aug 2022 16:16:45: 2000000 INFO @ Tue, 02 Aug 2022 16:16:47: 7000000 INFO @ Tue, 02 Aug 2022 16:16:50: 3000000 INFO @ Tue, 02 Aug 2022 16:16:53: 8000000 INFO @ Tue, 02 Aug 2022 16:16:55: 4000000 INFO @ Tue, 02 Aug 2022 16:16:59: 9000000 INFO @ Tue, 02 Aug 2022 16:17:01: 5000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 16:17:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9518342/SRX9518342.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9518342/SRX9518342.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9518342/SRX9518342.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9518342/SRX9518342.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 @ Tue, 02 Aug 2022 16:17:05: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:17:05: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:17:05: 10000000 INFO @ Tue, 02 Aug 2022 16:17:06: 6000000 INFO @ Tue, 02 Aug 2022 16:17:11: 7000000 INFO @ Tue, 02 Aug 2022 16:17:11: 1000000 INFO @ Tue, 02 Aug 2022 16:17:11: 11000000 INFO @ Tue, 02 Aug 2022 16:17:16: 8000000 INFO @ Tue, 02 Aug 2022 16:17:16: 2000000 INFO @ Tue, 02 Aug 2022 16:17:17: 12000000 INFO @ Tue, 02 Aug 2022 16:17:21: 9000000 INFO @ Tue, 02 Aug 2022 16:17:22: 3000000 INFO @ Tue, 02 Aug 2022 16:17:23: 13000000 INFO @ Tue, 02 Aug 2022 16:17:26: 10000000 INFO @ Tue, 02 Aug 2022 16:17:27: 4000000 INFO @ Tue, 02 Aug 2022 16:17:29: 14000000 INFO @ Tue, 02 Aug 2022 16:17:31: 11000000 INFO @ Tue, 02 Aug 2022 16:17:33: 5000000 INFO @ Tue, 02 Aug 2022 16:17:35: 15000000 INFO @ Tue, 02 Aug 2022 16:17:36: 12000000 INFO @ Tue, 02 Aug 2022 16:17:38: 6000000 INFO @ Tue, 02 Aug 2022 16:17:40: 16000000 INFO @ Tue, 02 Aug 2022 16:17:41: 13000000 INFO @ Tue, 02 Aug 2022 16:17:44: 7000000 INFO @ Tue, 02 Aug 2022 16:17:46: 17000000 INFO @ Tue, 02 Aug 2022 16:17:46: 14000000 INFO @ Tue, 02 Aug 2022 16:17:49: 8000000 INFO @ Tue, 02 Aug 2022 16:17:51: 15000000 INFO @ Tue, 02 Aug 2022 16:17:52: 18000000 INFO @ Tue, 02 Aug 2022 16:17:54: 9000000 INFO @ Tue, 02 Aug 2022 16:17:56: 16000000 INFO @ Tue, 02 Aug 2022 16:17:58: 19000000 INFO @ Tue, 02 Aug 2022 16:18:00: 10000000 INFO @ Tue, 02 Aug 2022 16:18:01: 17000000 INFO @ Tue, 02 Aug 2022 16:18:04: 20000000 INFO @ Tue, 02 Aug 2022 16:18:05: 11000000 INFO @ Tue, 02 Aug 2022 16:18:06: 18000000 INFO @ Tue, 02 Aug 2022 16:18:10: 21000000 INFO @ Tue, 02 Aug 2022 16:18:11: 12000000 INFO @ Tue, 02 Aug 2022 16:18:12: 19000000 INFO @ Tue, 02 Aug 2022 16:18:16: 13000000 INFO @ Tue, 02 Aug 2022 16:18:16: 22000000 INFO @ Tue, 02 Aug 2022 16:18:17: 20000000 INFO @ Tue, 02 Aug 2022 16:18:21: 14000000 INFO @ Tue, 02 Aug 2022 16:18:22: 21000000 INFO @ Tue, 02 Aug 2022 16:18:22: 23000000 INFO @ Tue, 02 Aug 2022 16:18:27: 15000000 INFO @ Tue, 02 Aug 2022 16:18:27: 22000000 INFO @ Tue, 02 Aug 2022 16:18:28: 24000000 INFO @ Tue, 02 Aug 2022 16:18:32: 16000000 INFO @ Tue, 02 Aug 2022 16:18:32: 23000000 INFO @ Tue, 02 Aug 2022 16:18:34: 25000000 INFO @ Tue, 02 Aug 2022 16:18:37: 24000000 INFO @ Tue, 02 Aug 2022 16:18:37: 17000000 INFO @ Tue, 02 Aug 2022 16:18:40: 26000000 INFO @ Tue, 02 Aug 2022 16:18:42: 25000000 INFO @ Tue, 02 Aug 2022 16:18:43: 18000000 INFO @ Tue, 02 Aug 2022 16:18:46: 27000000 INFO @ Tue, 02 Aug 2022 16:18:47: 26000000 INFO @ Tue, 02 Aug 2022 16:18:48: 19000000 INFO @ Tue, 02 Aug 2022 16:18:52: 28000000 INFO @ Tue, 02 Aug 2022 16:18:53: 27000000 INFO @ Tue, 02 Aug 2022 16:18:54: 20000000 INFO @ Tue, 02 Aug 2022 16:18:57: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 16:18:57: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 16:18:57: #1 total tags in treatment: 13821118 INFO @ Tue, 02 Aug 2022 16:18:57: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:18:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 16:18:57: #1 tags after filtering in treatment: 12013175 INFO @ Tue, 02 Aug 2022 16:18:57: #1 Redundant rate of treatment: 0.13 INFO @ Tue, 02 Aug 2022 16:18:57: #1 finished! INFO @ Tue, 02 Aug 2022 16:18:57: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:18:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:18:58: 28000000 INFO @ Tue, 02 Aug 2022 16:18:58: #2 number of paired peaks: 7221 INFO @ Tue, 02 Aug 2022 16:18:58: start model_add_line... INFO @ Tue, 02 Aug 2022 16:18:58: start X-correlation... INFO @ Tue, 02 Aug 2022 16:18:59: end of X-cor INFO @ Tue, 02 Aug 2022 16:18:59: #2 finished! INFO @ Tue, 02 Aug 2022 16:18:59: #2 predicted fragment length is 195 bps INFO @ Tue, 02 Aug 2022 16:18:59: #2 alternative fragment length(s) may be 4,195 bps INFO @ Tue, 02 Aug 2022 16:18:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9518342/SRX9518342.05_model.r INFO @ Tue, 02 Aug 2022 16:18:59: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:18:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:18:59: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 16:19:02: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 16:19:02: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 16:19:02: #1 total tags in treatment: 13821118 INFO @ Tue, 02 Aug 2022 16:19:02: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:19:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 16:19:02: #1 tags after filtering in treatment: 12013175 INFO @ Tue, 02 Aug 2022 16:19:02: #1 Redundant rate of treatment: 0.13 INFO @ Tue, 02 Aug 2022 16:19:02: #1 finished! INFO @ Tue, 02 Aug 2022 16:19:02: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:19:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:19:03: #2 number of paired peaks: 7221 INFO @ Tue, 02 Aug 2022 16:19:03: start model_add_line... INFO @ Tue, 02 Aug 2022 16:19:03: start X-correlation... INFO @ Tue, 02 Aug 2022 16:19:03: end of X-cor INFO @ Tue, 02 Aug 2022 16:19:03: #2 finished! INFO @ Tue, 02 Aug 2022 16:19:03: #2 predicted fragment length is 195 bps INFO @ Tue, 02 Aug 2022 16:19:03: #2 alternative fragment length(s) may be 4,195 bps INFO @ Tue, 02 Aug 2022 16:19:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9518342/SRX9518342.10_model.r INFO @ Tue, 02 Aug 2022 16:19:03: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:19:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:19:04: 22000000 INFO @ Tue, 02 Aug 2022 16:19:10: 23000000 INFO @ Tue, 02 Aug 2022 16:19:15: 24000000 INFO @ Tue, 02 Aug 2022 16:19:20: 25000000 INFO @ Tue, 02 Aug 2022 16:19:26: 26000000 INFO @ Tue, 02 Aug 2022 16:19:31: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:19:31: 27000000 INFO @ Tue, 02 Aug 2022 16:19:34: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:19:37: 28000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 16:19:41: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 16:19:41: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 16:19:41: #1 total tags in treatment: 13821118 INFO @ Tue, 02 Aug 2022 16:19:41: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:19:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 16:19:41: #1 tags after filtering in treatment: 12013175 INFO @ Tue, 02 Aug 2022 16:19:41: #1 Redundant rate of treatment: 0.13 INFO @ Tue, 02 Aug 2022 16:19:41: #1 finished! INFO @ Tue, 02 Aug 2022 16:19:41: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:19:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:19:43: #2 number of paired peaks: 7221 INFO @ Tue, 02 Aug 2022 16:19:43: start model_add_line... INFO @ Tue, 02 Aug 2022 16:19:43: start X-correlation... INFO @ Tue, 02 Aug 2022 16:19:43: end of X-cor INFO @ Tue, 02 Aug 2022 16:19:43: #2 finished! INFO @ Tue, 02 Aug 2022 16:19:43: #2 predicted fragment length is 195 bps INFO @ Tue, 02 Aug 2022 16:19:43: #2 alternative fragment length(s) may be 4,195 bps INFO @ Tue, 02 Aug 2022 16:19:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9518342/SRX9518342.20_model.r INFO @ Tue, 02 Aug 2022 16:19:43: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:19:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:19:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9518342/SRX9518342.05_peaks.xls INFO @ Tue, 02 Aug 2022 16:19:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9518342/SRX9518342.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:19:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9518342/SRX9518342.05_summits.bed INFO @ Tue, 02 Aug 2022 16:19:45: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5510 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 16:19:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9518342/SRX9518342.10_peaks.xls INFO @ Tue, 02 Aug 2022 16:19:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9518342/SRX9518342.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:19:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9518342/SRX9518342.10_summits.bed INFO @ Tue, 02 Aug 2022 16:19:47: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4236 records, 4 fields): 40 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 16:20:15: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:20:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9518342/SRX9518342.20_peaks.xls INFO @ Tue, 02 Aug 2022 16:20:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9518342/SRX9518342.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:20:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9518342/SRX9518342.20_summits.bed INFO @ Tue, 02 Aug 2022 16:20:28: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2518 records, 4 fields): 19 millis CompletedMACS2peakCalling