Job ID = 14170995 SRX = SRX9005701 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 10653331 spots for SRR12515102/SRR12515102.sra Written 10653331 spots for SRR12515102/SRR12515102.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171536 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:26:19 10653331 reads; of these: 10653331 (100.00%) were paired; of these: 548898 (5.15%) aligned concordantly 0 times 6871471 (64.50%) aligned concordantly exactly 1 time 3232962 (30.35%) aligned concordantly >1 times ---- 548898 pairs aligned concordantly 0 times; of these: 20759 (3.78%) aligned discordantly 1 time ---- 528139 pairs aligned 0 times concordantly or discordantly; of these: 1056278 mates make up the pairs; of these: 685650 (64.91%) aligned 0 times 216945 (20.54%) aligned exactly 1 time 153683 (14.55%) aligned >1 times 96.78% overall alignment rate Time searching: 00:26:20 Overall time: 00:26:20 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 12 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] 1562110 / 10095949 = 0.1547 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 09:42:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9005701/SRX9005701.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9005701/SRX9005701.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9005701/SRX9005701.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9005701/SRX9005701.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 09:42:04: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:42:04: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:42:09: 1000000 INFO @ Sat, 11 Dec 2021 09:42:15: 2000000 INFO @ Sat, 11 Dec 2021 09:42:20: 3000000 INFO @ Sat, 11 Dec 2021 09:42:25: 4000000 INFO @ Sat, 11 Dec 2021 09:42:30: 5000000 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 09:42:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9005701/SRX9005701.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9005701/SRX9005701.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9005701/SRX9005701.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9005701/SRX9005701.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 09:42:34: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:42:34: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:42:35: 6000000 INFO @ Sat, 11 Dec 2021 09:42:40: 1000000 INFO @ Sat, 11 Dec 2021 09:42:41: 7000000 INFO @ Sat, 11 Dec 2021 09:42:46: 2000000 INFO @ Sat, 11 Dec 2021 09:42:47: 8000000 INFO @ Sat, 11 Dec 2021 09:42:51: 3000000 INFO @ Sat, 11 Dec 2021 09:42:53: 9000000 INFO @ Sat, 11 Dec 2021 09:42:57: 4000000 INFO @ Sat, 11 Dec 2021 09:42:58: 10000000 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 09:43:03: 5000000 INFO @ Sat, 11 Dec 2021 09:43:04: 11000000 INFO @ Sat, 11 Dec 2021 09:43:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9005701/SRX9005701.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9005701/SRX9005701.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9005701/SRX9005701.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9005701/SRX9005701.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 09:43:04: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:43:04: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:43:08: 6000000 INFO @ Sat, 11 Dec 2021 09:43:10: 12000000 INFO @ Sat, 11 Dec 2021 09:43:10: 1000000 INFO @ Sat, 11 Dec 2021 09:43:14: 7000000 INFO @ Sat, 11 Dec 2021 09:43:16: 13000000 INFO @ Sat, 11 Dec 2021 09:43:16: 2000000 INFO @ Sat, 11 Dec 2021 09:43:20: 8000000 INFO @ Sat, 11 Dec 2021 09:43:22: 14000000 INFO @ Sat, 11 Dec 2021 09:43:22: 3000000 INFO @ Sat, 11 Dec 2021 09:43:25: 9000000 INFO @ Sat, 11 Dec 2021 09:43:28: 15000000 INFO @ Sat, 11 Dec 2021 09:43:28: 4000000 INFO @ Sat, 11 Dec 2021 09:43:31: 10000000 INFO @ Sat, 11 Dec 2021 09:43:33: 16000000 INFO @ Sat, 11 Dec 2021 09:43:34: 5000000 INFO @ Sat, 11 Dec 2021 09:43:37: 11000000 INFO @ Sat, 11 Dec 2021 09:43:39: 17000000 INFO @ Sat, 11 Dec 2021 09:43:40: 6000000 INFO @ Sat, 11 Dec 2021 09:43:42: #1 tag size is determined as 72 bps INFO @ Sat, 11 Dec 2021 09:43:42: #1 tag size = 72 INFO @ Sat, 11 Dec 2021 09:43:42: #1 total tags in treatment: 8544036 INFO @ Sat, 11 Dec 2021 09:43:42: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:43:42: #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 09:43:42: #1 tags after filtering in treatment: 7470317 INFO @ Sat, 11 Dec 2021 09:43:42: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 11 Dec 2021 09:43:42: #1 finished! INFO @ Sat, 11 Dec 2021 09:43:42: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:43:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:43:43: 12000000 INFO @ Sat, 11 Dec 2021 09:43:43: #2 number of paired peaks: 2988 INFO @ Sat, 11 Dec 2021 09:43:43: start model_add_line... INFO @ Sat, 11 Dec 2021 09:43:43: start X-correlation... INFO @ Sat, 11 Dec 2021 09:43:43: end of X-cor INFO @ Sat, 11 Dec 2021 09:43:43: #2 finished! INFO @ Sat, 11 Dec 2021 09:43:43: #2 predicted fragment length is 179 bps INFO @ Sat, 11 Dec 2021 09:43:43: #2 alternative fragment length(s) may be 179 bps INFO @ Sat, 11 Dec 2021 09:43:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9005701/SRX9005701.05_model.r INFO @ Sat, 11 Dec 2021 09:43:43: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:43:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:43:45: 7000000 INFO @ Sat, 11 Dec 2021 09:43:48: 13000000 INFO @ Sat, 11 Dec 2021 09:43:51: 8000000 INFO @ Sat, 11 Dec 2021 09:43:54: 14000000 INFO @ Sat, 11 Dec 2021 09:43:57: 9000000 INFO @ Sat, 11 Dec 2021 09:44:00: 15000000 INFO @ Sat, 11 Dec 2021 09:44:01: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:44:02: 10000000 INFO @ Sat, 11 Dec 2021 09:44:05: 16000000 INFO @ Sat, 11 Dec 2021 09:44:08: 11000000 INFO @ Sat, 11 Dec 2021 09:44:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9005701/SRX9005701.05_peaks.xls INFO @ Sat, 11 Dec 2021 09:44:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9005701/SRX9005701.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:44:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9005701/SRX9005701.05_summits.bed INFO @ Sat, 11 Dec 2021 09:44:10: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7447 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 09:44:11: 17000000 INFO @ Sat, 11 Dec 2021 09:44:14: #1 tag size is determined as 72 bps INFO @ Sat, 11 Dec 2021 09:44:14: #1 tag size = 72 INFO @ Sat, 11 Dec 2021 09:44:14: #1 total tags in treatment: 8544036 INFO @ Sat, 11 Dec 2021 09:44:14: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:44:14: #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 09:44:14: 12000000 INFO @ Sat, 11 Dec 2021 09:44:14: #1 tags after filtering in treatment: 7470317 INFO @ Sat, 11 Dec 2021 09:44:14: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 11 Dec 2021 09:44:14: #1 finished! INFO @ Sat, 11 Dec 2021 09:44:14: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:44:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:44:15: #2 number of paired peaks: 2988 INFO @ Sat, 11 Dec 2021 09:44:15: start model_add_line... INFO @ Sat, 11 Dec 2021 09:44:15: start X-correlation... INFO @ Sat, 11 Dec 2021 09:44:15: end of X-cor INFO @ Sat, 11 Dec 2021 09:44:15: #2 finished! INFO @ Sat, 11 Dec 2021 09:44:15: #2 predicted fragment length is 179 bps INFO @ Sat, 11 Dec 2021 09:44:15: #2 alternative fragment length(s) may be 179 bps INFO @ Sat, 11 Dec 2021 09:44:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9005701/SRX9005701.10_model.r INFO @ Sat, 11 Dec 2021 09:44:15: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:44:15: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 09:44:19: 13000000 INFO @ Sat, 11 Dec 2021 09:44:25: 14000000 INFO @ Sat, 11 Dec 2021 09:44:30: 15000000 INFO @ Sat, 11 Dec 2021 09:44:33: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:44:35: 16000000 INFO @ Sat, 11 Dec 2021 09:44:40: 17000000 INFO @ Sat, 11 Dec 2021 09:44:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9005701/SRX9005701.10_peaks.xls INFO @ Sat, 11 Dec 2021 09:44:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9005701/SRX9005701.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:44:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9005701/SRX9005701.10_summits.bed INFO @ Sat, 11 Dec 2021 09:44:41: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5084 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 09:44:43: #1 tag size is determined as 72 bps INFO @ Sat, 11 Dec 2021 09:44:43: #1 tag size = 72 INFO @ Sat, 11 Dec 2021 09:44:43: #1 total tags in treatment: 8544036 INFO @ Sat, 11 Dec 2021 09:44:43: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:44:43: #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 09:44:43: #1 tags after filtering in treatment: 7470317 INFO @ Sat, 11 Dec 2021 09:44:43: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 11 Dec 2021 09:44:43: #1 finished! INFO @ Sat, 11 Dec 2021 09:44:43: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:44:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:44:44: #2 number of paired peaks: 2988 INFO @ Sat, 11 Dec 2021 09:44:44: start model_add_line... INFO @ Sat, 11 Dec 2021 09:44:44: start X-correlation... INFO @ Sat, 11 Dec 2021 09:44:44: end of X-cor INFO @ Sat, 11 Dec 2021 09:44:44: #2 finished! INFO @ Sat, 11 Dec 2021 09:44:44: #2 predicted fragment length is 179 bps INFO @ Sat, 11 Dec 2021 09:44:44: #2 alternative fragment length(s) may be 179 bps INFO @ Sat, 11 Dec 2021 09:44:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9005701/SRX9005701.20_model.r INFO @ Sat, 11 Dec 2021 09:44:44: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:44:44: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 09:45:02: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:45:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9005701/SRX9005701.20_peaks.xls INFO @ Sat, 11 Dec 2021 09:45:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9005701/SRX9005701.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:45:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9005701/SRX9005701.20_summits.bed INFO @ Sat, 11 Dec 2021 09:45:10: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3279 records, 4 fields): 4 millis CompletedMACS2peakCalling