Job ID = 14172484 SRX = SRX7628891 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 17661667 spots for SRR10963253/SRR10963253.sra Written 17661667 spots for SRR10963253/SRR10963253.sra fastq に変換しました。 bowtie でマッピング中... Your job 14173014 ("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: 00:25:21 17661667 reads; of these: 17661667 (100.00%) were paired; of these: 4256150 (24.10%) aligned concordantly 0 times 10243061 (58.00%) aligned concordantly exactly 1 time 3162456 (17.91%) aligned concordantly >1 times ---- 4256150 pairs aligned concordantly 0 times; of these: 416726 (9.79%) aligned discordantly 1 time ---- 3839424 pairs aligned 0 times concordantly or discordantly; of these: 7678848 mates make up the pairs; of these: 6285860 (81.86%) aligned 0 times 568922 (7.41%) aligned exactly 1 time 824066 (10.73%) aligned >1 times 82.20% overall alignment rate Time searching: 00:25:21 Overall time: 00:25:21 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] 904410 / 13814603 = 0.0655 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 16:08:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7628891/SRX7628891.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7628891/SRX7628891.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7628891/SRX7628891.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7628891/SRX7628891.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 16:08:30: #1 read tag files... INFO @ Sat, 11 Dec 2021 16:08:30: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 16:08:34: 1000000 INFO @ Sat, 11 Dec 2021 16:08:39: 2000000 INFO @ Sat, 11 Dec 2021 16:08:43: 3000000 INFO @ Sat, 11 Dec 2021 16:08:47: 4000000 INFO @ Sat, 11 Dec 2021 16:08:52: 5000000 INFO @ Sat, 11 Dec 2021 16:08:56: 6000000 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 16:09:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7628891/SRX7628891.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7628891/SRX7628891.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7628891/SRX7628891.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7628891/SRX7628891.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 16:09:00: #1 read tag files... INFO @ Sat, 11 Dec 2021 16:09:00: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 16:09:01: 7000000 INFO @ Sat, 11 Dec 2021 16:09:05: 1000000 INFO @ Sat, 11 Dec 2021 16:09:06: 8000000 INFO @ Sat, 11 Dec 2021 16:09:10: 2000000 INFO @ Sat, 11 Dec 2021 16:09:11: 9000000 INFO @ Sat, 11 Dec 2021 16:09:15: 3000000 INFO @ Sat, 11 Dec 2021 16:09:17: 10000000 INFO @ Sat, 11 Dec 2021 16:09:21: 4000000 INFO @ Sat, 11 Dec 2021 16:09:22: 11000000 INFO @ Sat, 11 Dec 2021 16:09:26: 5000000 INFO @ Sat, 11 Dec 2021 16:09:27: 12000000 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 16:09:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7628891/SRX7628891.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7628891/SRX7628891.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7628891/SRX7628891.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7628891/SRX7628891.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 16:09:30: #1 read tag files... INFO @ Sat, 11 Dec 2021 16:09:30: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 16:09:31: 6000000 INFO @ Sat, 11 Dec 2021 16:09:32: 13000000 INFO @ Sat, 11 Dec 2021 16:09:35: 1000000 INFO @ Sat, 11 Dec 2021 16:09:36: 7000000 INFO @ Sat, 11 Dec 2021 16:09:37: 14000000 INFO @ Sat, 11 Dec 2021 16:09:40: 2000000 INFO @ Sat, 11 Dec 2021 16:09:41: 8000000 INFO @ Sat, 11 Dec 2021 16:09:42: 15000000 INFO @ Sat, 11 Dec 2021 16:09:45: 3000000 INFO @ Sat, 11 Dec 2021 16:09:46: 9000000 INFO @ Sat, 11 Dec 2021 16:09:47: 16000000 INFO @ Sat, 11 Dec 2021 16:09:50: 4000000 INFO @ Sat, 11 Dec 2021 16:09:51: 10000000 INFO @ Sat, 11 Dec 2021 16:09:52: 17000000 INFO @ Sat, 11 Dec 2021 16:09:55: 5000000 INFO @ Sat, 11 Dec 2021 16:09:56: 11000000 INFO @ Sat, 11 Dec 2021 16:09:57: 18000000 INFO @ Sat, 11 Dec 2021 16:10:00: 6000000 INFO @ Sat, 11 Dec 2021 16:10:01: 12000000 INFO @ Sat, 11 Dec 2021 16:10:02: 19000000 INFO @ Sat, 11 Dec 2021 16:10:05: 7000000 INFO @ Sat, 11 Dec 2021 16:10:06: 13000000 INFO @ Sat, 11 Dec 2021 16:10:07: 20000000 INFO @ Sat, 11 Dec 2021 16:10:11: 8000000 INFO @ Sat, 11 Dec 2021 16:10:12: 14000000 INFO @ Sat, 11 Dec 2021 16:10:12: 21000000 INFO @ Sat, 11 Dec 2021 16:10:16: 9000000 INFO @ Sat, 11 Dec 2021 16:10:17: 15000000 INFO @ Sat, 11 Dec 2021 16:10:17: 22000000 INFO @ Sat, 11 Dec 2021 16:10:21: 10000000 INFO @ Sat, 11 Dec 2021 16:10:22: 16000000 INFO @ Sat, 11 Dec 2021 16:10:22: 23000000 INFO @ Sat, 11 Dec 2021 16:10:26: 11000000 INFO @ Sat, 11 Dec 2021 16:10:27: 17000000 INFO @ Sat, 11 Dec 2021 16:10:28: 24000000 INFO @ Sat, 11 Dec 2021 16:10:31: 12000000 INFO @ Sat, 11 Dec 2021 16:10:32: 18000000 INFO @ Sat, 11 Dec 2021 16:10:33: 25000000 INFO @ Sat, 11 Dec 2021 16:10:36: 13000000 INFO @ Sat, 11 Dec 2021 16:10:37: 19000000 INFO @ Sat, 11 Dec 2021 16:10:38: 26000000 INFO @ Sat, 11 Dec 2021 16:10:41: 14000000 INFO @ Sat, 11 Dec 2021 16:10:42: 20000000 INFO @ Sat, 11 Dec 2021 16:10:43: 27000000 INFO @ Sat, 11 Dec 2021 16:10:44: #1 tag size is determined as 42 bps INFO @ Sat, 11 Dec 2021 16:10:44: #1 tag size = 42 INFO @ Sat, 11 Dec 2021 16:10:44: #1 total tags in treatment: 12512070 INFO @ Sat, 11 Dec 2021 16:10:44: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 16:10:44: #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 16:10:44: #1 tags after filtering in treatment: 6921457 INFO @ Sat, 11 Dec 2021 16:10:44: #1 Redundant rate of treatment: 0.45 INFO @ Sat, 11 Dec 2021 16:10:44: #1 finished! INFO @ Sat, 11 Dec 2021 16:10:44: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 16:10:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 16:10:45: #2 number of paired peaks: 10126 INFO @ Sat, 11 Dec 2021 16:10:45: start model_add_line... INFO @ Sat, 11 Dec 2021 16:10:45: start X-correlation... INFO @ Sat, 11 Dec 2021 16:10:45: end of X-cor INFO @ Sat, 11 Dec 2021 16:10:45: #2 finished! INFO @ Sat, 11 Dec 2021 16:10:45: #2 predicted fragment length is 224 bps INFO @ Sat, 11 Dec 2021 16:10:45: #2 alternative fragment length(s) may be 224 bps INFO @ Sat, 11 Dec 2021 16:10:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7628891/SRX7628891.05_model.r INFO @ Sat, 11 Dec 2021 16:10:45: #3 Call peaks... INFO @ Sat, 11 Dec 2021 16:10:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 16:10:46: 15000000 INFO @ Sat, 11 Dec 2021 16:10:47: 21000000 INFO @ Sat, 11 Dec 2021 16:10:51: 16000000 INFO @ Sat, 11 Dec 2021 16:10:52: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 16:10:56: 17000000 INFO @ Sat, 11 Dec 2021 16:10:57: 23000000 INFO @ Sat, 11 Dec 2021 16:11:01: 18000000 INFO @ Sat, 11 Dec 2021 16:11:02: 24000000 INFO @ Sat, 11 Dec 2021 16:11:06: 19000000 INFO @ Sat, 11 Dec 2021 16:11:07: 25000000 INFO @ Sat, 11 Dec 2021 16:11:09: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 16:11:11: 20000000 INFO @ Sat, 11 Dec 2021 16:11:12: 26000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 16:11:16: 21000000 INFO @ Sat, 11 Dec 2021 16:11:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7628891/SRX7628891.05_peaks.xls INFO @ Sat, 11 Dec 2021 16:11:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7628891/SRX7628891.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 16:11:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7628891/SRX7628891.05_summits.bed INFO @ Sat, 11 Dec 2021 16:11:17: Done! INFO @ Sat, 11 Dec 2021 16:11:17: 27000000 pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (8517 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 16:11:18: #1 tag size is determined as 42 bps INFO @ Sat, 11 Dec 2021 16:11:18: #1 tag size = 42 INFO @ Sat, 11 Dec 2021 16:11:18: #1 total tags in treatment: 12512070 INFO @ Sat, 11 Dec 2021 16:11:18: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 16:11:18: #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 16:11:19: #1 tags after filtering in treatment: 6921457 INFO @ Sat, 11 Dec 2021 16:11:19: #1 Redundant rate of treatment: 0.45 INFO @ Sat, 11 Dec 2021 16:11:19: #1 finished! INFO @ Sat, 11 Dec 2021 16:11:19: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 16:11:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 16:11:20: #2 number of paired peaks: 10126 INFO @ Sat, 11 Dec 2021 16:11:20: start model_add_line... INFO @ Sat, 11 Dec 2021 16:11:20: start X-correlation... INFO @ Sat, 11 Dec 2021 16:11:20: end of X-cor INFO @ Sat, 11 Dec 2021 16:11:20: #2 finished! INFO @ Sat, 11 Dec 2021 16:11:20: #2 predicted fragment length is 224 bps INFO @ Sat, 11 Dec 2021 16:11:20: #2 alternative fragment length(s) may be 224 bps INFO @ Sat, 11 Dec 2021 16:11:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7628891/SRX7628891.10_model.r INFO @ Sat, 11 Dec 2021 16:11:20: #3 Call peaks... INFO @ Sat, 11 Dec 2021 16:11:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 16:11:21: 22000000 INFO @ Sat, 11 Dec 2021 16:11:26: 23000000 INFO @ Sat, 11 Dec 2021 16:11:31: 24000000 INFO @ Sat, 11 Dec 2021 16:11:36: 25000000 INFO @ Sat, 11 Dec 2021 16:11:41: 26000000 INFO @ Sat, 11 Dec 2021 16:11:43: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 16:11:46: 27000000 INFO @ Sat, 11 Dec 2021 16:11:47: #1 tag size is determined as 42 bps INFO @ Sat, 11 Dec 2021 16:11:47: #1 tag size = 42 INFO @ Sat, 11 Dec 2021 16:11:47: #1 total tags in treatment: 12512070 INFO @ Sat, 11 Dec 2021 16:11:47: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 16:11:47: #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 16:11:47: #1 tags after filtering in treatment: 6921457 INFO @ Sat, 11 Dec 2021 16:11:47: #1 Redundant rate of treatment: 0.45 INFO @ Sat, 11 Dec 2021 16:11:47: #1 finished! INFO @ Sat, 11 Dec 2021 16:11:47: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 16:11:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 16:11:48: #2 number of paired peaks: 10126 INFO @ Sat, 11 Dec 2021 16:11:48: start model_add_line... INFO @ Sat, 11 Dec 2021 16:11:48: start X-correlation... INFO @ Sat, 11 Dec 2021 16:11:48: end of X-cor INFO @ Sat, 11 Dec 2021 16:11:48: #2 finished! INFO @ Sat, 11 Dec 2021 16:11:48: #2 predicted fragment length is 224 bps INFO @ Sat, 11 Dec 2021 16:11:48: #2 alternative fragment length(s) may be 224 bps INFO @ Sat, 11 Dec 2021 16:11:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7628891/SRX7628891.20_model.r INFO @ Sat, 11 Dec 2021 16:11:48: #3 Call peaks... INFO @ Sat, 11 Dec 2021 16:11:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 16:11:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7628891/SRX7628891.10_peaks.xls INFO @ Sat, 11 Dec 2021 16:11:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7628891/SRX7628891.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 16:11:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7628891/SRX7628891.10_summits.bed INFO @ Sat, 11 Dec 2021 16:11:51: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7588 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 16:12:11: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 16:12:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7628891/SRX7628891.20_peaks.xls INFO @ Sat, 11 Dec 2021 16:12:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7628891/SRX7628891.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 16:12:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7628891/SRX7628891.20_summits.bed INFO @ Sat, 11 Dec 2021 16:12:20: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6562 records, 4 fields): 7 millis CompletedMACS2peakCalling