Job ID = 14171474 SRX = SRX10971112 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2021-12-11T02:46:38 prefetch.2.10.7: 1) Downloading 'SRR14631236'... 2021-12-11T02:46:38 prefetch.2.10.7: Downloading via HTTPS... 2021-12-11T02:49:12 prefetch.2.10.7: HTTPS download succeed 2021-12-11T02:49:12 prefetch.2.10.7: 1) 'SRR14631236' was downloaded successfully 2021-12-11T02:49:12 prefetch.2.10.7: 'SRR14631236' has 0 unresolved dependencies Read 20506434 spots for SRR14631236/SRR14631236.sra Written 20506434 spots for SRR14631236/SRR14631236.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172283 ("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: 01:19:15 20506434 reads; of these: 20506434 (100.00%) were paired; of these: 2059957 (10.05%) aligned concordantly 0 times 15627373 (76.21%) aligned concordantly exactly 1 time 2819104 (13.75%) aligned concordantly >1 times ---- 2059957 pairs aligned concordantly 0 times; of these: 137973 (6.70%) aligned discordantly 1 time ---- 1921984 pairs aligned 0 times concordantly or discordantly; of these: 3843968 mates make up the pairs; of these: 2511114 (65.33%) aligned 0 times 574180 (14.94%) aligned exactly 1 time 758674 (19.74%) aligned >1 times 93.88% overall alignment rate Time searching: 01:19:15 Overall time: 01:19:15 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] 3410470 / 18447597 = 0.1849 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 13:22:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10971112/SRX10971112.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10971112/SRX10971112.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10971112/SRX10971112.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10971112/SRX10971112.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 13:22:54: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:22:54: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:22:59: 1000000 INFO @ Sat, 11 Dec 2021 13:23:05: 2000000 INFO @ Sat, 11 Dec 2021 13:23:11: 3000000 INFO @ Sat, 11 Dec 2021 13:23:16: 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 @ Sat, 11 Dec 2021 13:23:22: 5000000 INFO @ Sat, 11 Dec 2021 13:23:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10971112/SRX10971112.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10971112/SRX10971112.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10971112/SRX10971112.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10971112/SRX10971112.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 13:23:23: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:23:23: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:23:28: 6000000 INFO @ Sat, 11 Dec 2021 13:23:29: 1000000 INFO @ Sat, 11 Dec 2021 13:23:33: 7000000 INFO @ Sat, 11 Dec 2021 13:23:35: 2000000 INFO @ Sat, 11 Dec 2021 13:23:39: 8000000 INFO @ Sat, 11 Dec 2021 13:23:40: 3000000 INFO @ Sat, 11 Dec 2021 13:23:45: 9000000 INFO @ Sat, 11 Dec 2021 13:23:46: 4000000 INFO @ Sat, 11 Dec 2021 13:23:51: 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 13:23:52: 5000000 INFO @ Sat, 11 Dec 2021 13:23:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10971112/SRX10971112.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10971112/SRX10971112.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10971112/SRX10971112.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10971112/SRX10971112.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 13:23:53: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:23:53: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:23:57: 11000000 INFO @ Sat, 11 Dec 2021 13:23:58: 6000000 INFO @ Sat, 11 Dec 2021 13:24:01: 1000000 INFO @ Sat, 11 Dec 2021 13:24:03: 12000000 INFO @ Sat, 11 Dec 2021 13:24:04: 7000000 INFO @ Sat, 11 Dec 2021 13:24:09: 2000000 INFO @ Sat, 11 Dec 2021 13:24:09: 13000000 INFO @ Sat, 11 Dec 2021 13:24:10: 8000000 INFO @ Sat, 11 Dec 2021 13:24:15: 14000000 INFO @ Sat, 11 Dec 2021 13:24:16: 9000000 INFO @ Sat, 11 Dec 2021 13:24:16: 3000000 INFO @ Sat, 11 Dec 2021 13:24:21: 15000000 INFO @ Sat, 11 Dec 2021 13:24:22: 10000000 INFO @ Sat, 11 Dec 2021 13:24:24: 4000000 INFO @ Sat, 11 Dec 2021 13:24:27: 16000000 INFO @ Sat, 11 Dec 2021 13:24:28: 11000000 INFO @ Sat, 11 Dec 2021 13:24:31: 5000000 INFO @ Sat, 11 Dec 2021 13:24:33: 17000000 INFO @ Sat, 11 Dec 2021 13:24:34: 12000000 INFO @ Sat, 11 Dec 2021 13:24:38: 6000000 INFO @ Sat, 11 Dec 2021 13:24:39: 18000000 INFO @ Sat, 11 Dec 2021 13:24:40: 13000000 INFO @ Sat, 11 Dec 2021 13:24:45: 19000000 INFO @ Sat, 11 Dec 2021 13:24:45: 14000000 INFO @ Sat, 11 Dec 2021 13:24:45: 7000000 INFO @ Sat, 11 Dec 2021 13:24:51: 20000000 INFO @ Sat, 11 Dec 2021 13:24:51: 15000000 INFO @ Sat, 11 Dec 2021 13:24:53: 8000000 INFO @ Sat, 11 Dec 2021 13:24:57: 16000000 INFO @ Sat, 11 Dec 2021 13:24:57: 21000000 INFO @ Sat, 11 Dec 2021 13:25:00: 9000000 INFO @ Sat, 11 Dec 2021 13:25:03: 17000000 INFO @ Sat, 11 Dec 2021 13:25:04: 22000000 INFO @ Sat, 11 Dec 2021 13:25:08: 10000000 INFO @ Sat, 11 Dec 2021 13:25:09: 18000000 INFO @ Sat, 11 Dec 2021 13:25:11: 23000000 INFO @ Sat, 11 Dec 2021 13:25:15: 19000000 INFO @ Sat, 11 Dec 2021 13:25:15: 11000000 INFO @ Sat, 11 Dec 2021 13:25:18: 24000000 INFO @ Sat, 11 Dec 2021 13:25:21: 20000000 INFO @ Sat, 11 Dec 2021 13:25:23: 12000000 INFO @ Sat, 11 Dec 2021 13:25:25: 25000000 INFO @ Sat, 11 Dec 2021 13:25:27: 21000000 INFO @ Sat, 11 Dec 2021 13:25:30: 13000000 INFO @ Sat, 11 Dec 2021 13:25:32: 26000000 INFO @ Sat, 11 Dec 2021 13:25:33: 22000000 INFO @ Sat, 11 Dec 2021 13:25:38: 14000000 INFO @ Sat, 11 Dec 2021 13:25:38: 27000000 INFO @ Sat, 11 Dec 2021 13:25:39: 23000000 INFO @ Sat, 11 Dec 2021 13:25:45: 28000000 INFO @ Sat, 11 Dec 2021 13:25:45: 15000000 INFO @ Sat, 11 Dec 2021 13:25:45: 24000000 INFO @ Sat, 11 Dec 2021 13:25:51: 25000000 INFO @ Sat, 11 Dec 2021 13:25:51: 29000000 INFO @ Sat, 11 Dec 2021 13:25:52: 16000000 INFO @ Sat, 11 Dec 2021 13:25:57: 26000000 INFO @ Sat, 11 Dec 2021 13:25:58: 30000000 INFO @ Sat, 11 Dec 2021 13:25:59: 17000000 INFO @ Sat, 11 Dec 2021 13:26:03: 27000000 INFO @ Sat, 11 Dec 2021 13:26:04: 31000000 INFO @ Sat, 11 Dec 2021 13:26:07: 18000000 INFO @ Sat, 11 Dec 2021 13:26:08: 28000000 INFO @ Sat, 11 Dec 2021 13:26:09: #1 tag size is determined as 100 bps INFO @ Sat, 11 Dec 2021 13:26:09: #1 tag size = 100 INFO @ Sat, 11 Dec 2021 13:26:09: #1 total tags in treatment: 15046133 INFO @ Sat, 11 Dec 2021 13:26:09: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:26:09: #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 13:26:09: #1 tags after filtering in treatment: 14307300 INFO @ Sat, 11 Dec 2021 13:26:09: #1 Redundant rate of treatment: 0.05 INFO @ Sat, 11 Dec 2021 13:26:09: #1 finished! INFO @ Sat, 11 Dec 2021 13:26:09: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:26:09: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:26:10: #2 number of paired peaks: 230 WARNING @ Sat, 11 Dec 2021 13:26:10: Fewer paired peaks (230) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 230 pairs to build model! INFO @ Sat, 11 Dec 2021 13:26:10: start model_add_line... INFO @ Sat, 11 Dec 2021 13:26:10: start X-correlation... INFO @ Sat, 11 Dec 2021 13:26:10: end of X-cor INFO @ Sat, 11 Dec 2021 13:26:10: #2 finished! INFO @ Sat, 11 Dec 2021 13:26:10: #2 predicted fragment length is 232 bps INFO @ Sat, 11 Dec 2021 13:26:10: #2 alternative fragment length(s) may be 232 bps INFO @ Sat, 11 Dec 2021 13:26:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10971112/SRX10971112.05_model.r INFO @ Sat, 11 Dec 2021 13:26:10: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:26:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:26:13: 19000000 INFO @ Sat, 11 Dec 2021 13:26:14: 29000000 INFO @ Sat, 11 Dec 2021 13:26:20: 30000000 INFO @ Sat, 11 Dec 2021 13:26:21: 20000000 INFO @ Sat, 11 Dec 2021 13:26:25: 31000000 INFO @ Sat, 11 Dec 2021 13:26:28: 21000000 INFO @ Sat, 11 Dec 2021 13:26:29: #1 tag size is determined as 100 bps INFO @ Sat, 11 Dec 2021 13:26:29: #1 tag size = 100 INFO @ Sat, 11 Dec 2021 13:26:29: #1 total tags in treatment: 15046133 INFO @ Sat, 11 Dec 2021 13:26:29: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:26:29: #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 13:26:30: #1 tags after filtering in treatment: 14307300 INFO @ Sat, 11 Dec 2021 13:26:30: #1 Redundant rate of treatment: 0.05 INFO @ Sat, 11 Dec 2021 13:26:30: #1 finished! INFO @ Sat, 11 Dec 2021 13:26:30: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:26:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:26:31: #2 number of paired peaks: 230 WARNING @ Sat, 11 Dec 2021 13:26:31: Fewer paired peaks (230) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 230 pairs to build model! INFO @ Sat, 11 Dec 2021 13:26:31: start model_add_line... INFO @ Sat, 11 Dec 2021 13:26:31: start X-correlation... INFO @ Sat, 11 Dec 2021 13:26:31: end of X-cor INFO @ Sat, 11 Dec 2021 13:26:31: #2 finished! INFO @ Sat, 11 Dec 2021 13:26:31: #2 predicted fragment length is 232 bps INFO @ Sat, 11 Dec 2021 13:26:31: #2 alternative fragment length(s) may be 232 bps INFO @ Sat, 11 Dec 2021 13:26:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10971112/SRX10971112.10_model.r INFO @ Sat, 11 Dec 2021 13:26:31: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:26:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:26:35: 22000000 INFO @ Sat, 11 Dec 2021 13:26:41: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:26:42: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 13:26:50: 24000000 INFO @ Sat, 11 Dec 2021 13:26:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10971112/SRX10971112.05_peaks.xls INFO @ Sat, 11 Dec 2021 13:26:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10971112/SRX10971112.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:26:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10971112/SRX10971112.05_summits.bed INFO @ Sat, 11 Dec 2021 13:26:57: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1000 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:26:57: 25000000 INFO @ Sat, 11 Dec 2021 13:27:02: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:27:05: 26000000 INFO @ Sat, 11 Dec 2021 13:27:12: 27000000 INFO @ Sat, 11 Dec 2021 13:27:19: 28000000 INFO @ Sat, 11 Dec 2021 13:27:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10971112/SRX10971112.10_peaks.xls INFO @ Sat, 11 Dec 2021 13:27:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10971112/SRX10971112.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:27:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10971112/SRX10971112.10_summits.bed INFO @ Sat, 11 Dec 2021 13:27:20: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (681 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:27:26: 29000000 INFO @ Sat, 11 Dec 2021 13:27:33: 30000000 INFO @ Sat, 11 Dec 2021 13:27:40: 31000000 INFO @ Sat, 11 Dec 2021 13:27:45: #1 tag size is determined as 100 bps INFO @ Sat, 11 Dec 2021 13:27:45: #1 tag size = 100 INFO @ Sat, 11 Dec 2021 13:27:45: #1 total tags in treatment: 15046133 INFO @ Sat, 11 Dec 2021 13:27:45: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:27:45: #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 13:27:45: #1 tags after filtering in treatment: 14307300 INFO @ Sat, 11 Dec 2021 13:27:45: #1 Redundant rate of treatment: 0.05 INFO @ Sat, 11 Dec 2021 13:27:45: #1 finished! INFO @ Sat, 11 Dec 2021 13:27:45: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:27:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:27:46: #2 number of paired peaks: 230 WARNING @ Sat, 11 Dec 2021 13:27:46: Fewer paired peaks (230) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 230 pairs to build model! INFO @ Sat, 11 Dec 2021 13:27:46: start model_add_line... INFO @ Sat, 11 Dec 2021 13:27:46: start X-correlation... INFO @ Sat, 11 Dec 2021 13:27:46: end of X-cor INFO @ Sat, 11 Dec 2021 13:27:46: #2 finished! INFO @ Sat, 11 Dec 2021 13:27:46: #2 predicted fragment length is 232 bps INFO @ Sat, 11 Dec 2021 13:27:46: #2 alternative fragment length(s) may be 232 bps INFO @ Sat, 11 Dec 2021 13:27:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10971112/SRX10971112.20_model.r INFO @ Sat, 11 Dec 2021 13:27:46: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:27:46: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 13:28:19: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:28:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10971112/SRX10971112.20_peaks.xls INFO @ Sat, 11 Dec 2021 13:28:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10971112/SRX10971112.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:28:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10971112/SRX10971112.20_summits.bed INFO @ Sat, 11 Dec 2021 13:28:36: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (458 records, 4 fields): 2 millis CompletedMACS2peakCalling