Job ID = 14171468 SRX = SRX10971107 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2021-12-11T02:45:09 prefetch.2.10.7: 1) Downloading 'SRR14631231'... 2021-12-11T02:45:09 prefetch.2.10.7: Downloading via HTTPS... 2021-12-11T02:46:19 prefetch.2.10.7: HTTPS download succeed 2021-12-11T02:46:19 prefetch.2.10.7: 1) 'SRR14631231' was downloaded successfully 2021-12-11T02:46:19 prefetch.2.10.7: 'SRR14631231' has 0 unresolved dependencies Read 17095397 spots for SRR14631231/SRR14631231.sra Written 17095397 spots for SRR14631231/SRR14631231.sra fastq に変換しました。 bowtie でマッピング中... Your job 14173590 ("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: 06:55:06 17095397 reads; of these: 17095397 (100.00%) were paired; of these: 7750234 (45.34%) aligned concordantly 0 times 8020617 (46.92%) aligned concordantly exactly 1 time 1324546 (7.75%) aligned concordantly >1 times ---- 7750234 pairs aligned concordantly 0 times; of these: 125020 (1.61%) aligned discordantly 1 time ---- 7625214 pairs aligned 0 times concordantly or discordantly; of these: 15250428 mates make up the pairs; of these: 9325465 (61.15%) aligned 0 times 396317 (2.60%) aligned exactly 1 time 5528646 (36.25%) aligned >1 times 72.73% overall alignment rate Time searching: 06:55:06 Overall time: 06:55:06 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] 2846812 / 9363569 = 0.3040 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 18:54:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10971107/SRX10971107.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10971107/SRX10971107.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10971107/SRX10971107.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10971107/SRX10971107.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 18:54:34: #1 read tag files... INFO @ Sat, 11 Dec 2021 18:54:34: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 18:54:42: 1000000 INFO @ Sat, 11 Dec 2021 18:54:51: 2000000 INFO @ Sat, 11 Dec 2021 18:54:59: 3000000 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 18:55:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10971107/SRX10971107.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10971107/SRX10971107.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10971107/SRX10971107.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10971107/SRX10971107.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 18:55:04: #1 read tag files... INFO @ Sat, 11 Dec 2021 18:55:04: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 18:55:08: 4000000 INFO @ Sat, 11 Dec 2021 18:55:13: 1000000 INFO @ Sat, 11 Dec 2021 18:55:17: 5000000 INFO @ Sat, 11 Dec 2021 18:55:22: 2000000 INFO @ Sat, 11 Dec 2021 18:55:26: 6000000 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 18:55:31: 3000000 INFO @ Sat, 11 Dec 2021 18:55:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10971107/SRX10971107.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10971107/SRX10971107.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10971107/SRX10971107.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10971107/SRX10971107.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 18:55:33: #1 read tag files... INFO @ Sat, 11 Dec 2021 18:55:33: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 18:55:34: 7000000 INFO @ Sat, 11 Dec 2021 18:55:41: 4000000 INFO @ Sat, 11 Dec 2021 18:55:43: 8000000 INFO @ Sat, 11 Dec 2021 18:55:43: 1000000 INFO @ Sat, 11 Dec 2021 18:55:51: 9000000 INFO @ Sat, 11 Dec 2021 18:55:52: 5000000 INFO @ Sat, 11 Dec 2021 18:55:53: 2000000 INFO @ Sat, 11 Dec 2021 18:55:59: 10000000 INFO @ Sat, 11 Dec 2021 18:56:01: 6000000 INFO @ Sat, 11 Dec 2021 18:56:02: 3000000 INFO @ Sat, 11 Dec 2021 18:56:07: 11000000 INFO @ Sat, 11 Dec 2021 18:56:10: 7000000 INFO @ Sat, 11 Dec 2021 18:56:12: 4000000 INFO @ Sat, 11 Dec 2021 18:56:14: 12000000 INFO @ Sat, 11 Dec 2021 18:56:19: 8000000 INFO @ Sat, 11 Dec 2021 18:56:21: 5000000 INFO @ Sat, 11 Dec 2021 18:56:22: 13000000 INFO @ Sat, 11 Dec 2021 18:56:29: 14000000 INFO @ Sat, 11 Dec 2021 18:56:29: 9000000 INFO @ Sat, 11 Dec 2021 18:56:31: 6000000 INFO @ Sat, 11 Dec 2021 18:56:36: 15000000 INFO @ Sat, 11 Dec 2021 18:56:39: 10000000 INFO @ Sat, 11 Dec 2021 18:56:40: 7000000 INFO @ Sat, 11 Dec 2021 18:56:44: 16000000 INFO @ Sat, 11 Dec 2021 18:56:48: 11000000 INFO @ Sat, 11 Dec 2021 18:56:50: 8000000 INFO @ Sat, 11 Dec 2021 18:56:51: 17000000 INFO @ Sat, 11 Dec 2021 18:56:57: 12000000 INFO @ Sat, 11 Dec 2021 18:56:59: 18000000 INFO @ Sat, 11 Dec 2021 18:56:59: 9000000 INFO @ Sat, 11 Dec 2021 18:57:07: 13000000 INFO @ Sat, 11 Dec 2021 18:57:07: 19000000 INFO @ Sat, 11 Dec 2021 18:57:09: #1 tag size is determined as 100 bps INFO @ Sat, 11 Dec 2021 18:57:09: #1 tag size = 100 INFO @ Sat, 11 Dec 2021 18:57:09: #1 total tags in treatment: 6522159 INFO @ Sat, 11 Dec 2021 18:57:09: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 18:57:09: #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 18:57:09: #1 tags after filtering in treatment: 6142693 INFO @ Sat, 11 Dec 2021 18:57:09: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 11 Dec 2021 18:57:09: #1 finished! INFO @ Sat, 11 Dec 2021 18:57:09: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 18:57:09: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 18:57:09: 10000000 INFO @ Sat, 11 Dec 2021 18:57:09: #2 number of paired peaks: 553 WARNING @ Sat, 11 Dec 2021 18:57:09: Fewer paired peaks (553) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 553 pairs to build model! INFO @ Sat, 11 Dec 2021 18:57:09: start model_add_line... INFO @ Sat, 11 Dec 2021 18:57:09: start X-correlation... INFO @ Sat, 11 Dec 2021 18:57:09: end of X-cor INFO @ Sat, 11 Dec 2021 18:57:09: #2 finished! INFO @ Sat, 11 Dec 2021 18:57:09: #2 predicted fragment length is 231 bps INFO @ Sat, 11 Dec 2021 18:57:09: #2 alternative fragment length(s) may be 231 bps INFO @ Sat, 11 Dec 2021 18:57:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10971107/SRX10971107.05_model.r INFO @ Sat, 11 Dec 2021 18:57:09: #3 Call peaks... INFO @ Sat, 11 Dec 2021 18:57:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 18:57:15: 14000000 INFO @ Sat, 11 Dec 2021 18:57:18: 11000000 INFO @ Sat, 11 Dec 2021 18:57:23: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 18:57:24: 15000000 INFO @ Sat, 11 Dec 2021 18:57:27: 12000000 INFO @ Sat, 11 Dec 2021 18:57:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10971107/SRX10971107.05_peaks.xls INFO @ Sat, 11 Dec 2021 18:57:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10971107/SRX10971107.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 18:57:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10971107/SRX10971107.05_summits.bed INFO @ Sat, 11 Dec 2021 18:57:30: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (925 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 18:57:33: 16000000 INFO @ Sat, 11 Dec 2021 18:57:36: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 18:57:41: 17000000 INFO @ Sat, 11 Dec 2021 18:57:45: 14000000 INFO @ Sat, 11 Dec 2021 18:57:50: 18000000 INFO @ Sat, 11 Dec 2021 18:57:53: 15000000 INFO @ Sat, 11 Dec 2021 18:57:59: 19000000 INFO @ Sat, 11 Dec 2021 18:58:01: #1 tag size is determined as 100 bps INFO @ Sat, 11 Dec 2021 18:58:01: #1 tag size = 100 INFO @ Sat, 11 Dec 2021 18:58:01: #1 total tags in treatment: 6522159 INFO @ Sat, 11 Dec 2021 18:58:01: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 18:58:01: #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 18:58:01: #1 tags after filtering in treatment: 6142693 INFO @ Sat, 11 Dec 2021 18:58:01: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 11 Dec 2021 18:58:01: #1 finished! INFO @ Sat, 11 Dec 2021 18:58:01: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 18:58:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 18:58:02: #2 number of paired peaks: 553 WARNING @ Sat, 11 Dec 2021 18:58:02: Fewer paired peaks (553) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 553 pairs to build model! INFO @ Sat, 11 Dec 2021 18:58:02: start model_add_line... INFO @ Sat, 11 Dec 2021 18:58:02: start X-correlation... INFO @ Sat, 11 Dec 2021 18:58:02: 16000000 INFO @ Sat, 11 Dec 2021 18:58:02: end of X-cor INFO @ Sat, 11 Dec 2021 18:58:02: #2 finished! INFO @ Sat, 11 Dec 2021 18:58:02: #2 predicted fragment length is 231 bps INFO @ Sat, 11 Dec 2021 18:58:02: #2 alternative fragment length(s) may be 231 bps INFO @ Sat, 11 Dec 2021 18:58:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10971107/SRX10971107.10_model.r INFO @ Sat, 11 Dec 2021 18:58:02: #3 Call peaks... INFO @ Sat, 11 Dec 2021 18:58:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 18:58:10: 17000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 18:58:15: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 18:58:19: 18000000 INFO @ Sat, 11 Dec 2021 18:58:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10971107/SRX10971107.10_peaks.xls INFO @ Sat, 11 Dec 2021 18:58:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10971107/SRX10971107.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 18:58:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10971107/SRX10971107.10_summits.bed INFO @ Sat, 11 Dec 2021 18:58:23: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (691 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 18:58:28: 19000000 INFO @ Sat, 11 Dec 2021 18:58:29: #1 tag size is determined as 100 bps INFO @ Sat, 11 Dec 2021 18:58:29: #1 tag size = 100 INFO @ Sat, 11 Dec 2021 18:58:29: #1 total tags in treatment: 6522159 INFO @ Sat, 11 Dec 2021 18:58:29: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 18:58:29: #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 18:58:29: #1 tags after filtering in treatment: 6142693 INFO @ Sat, 11 Dec 2021 18:58:29: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 11 Dec 2021 18:58:29: #1 finished! INFO @ Sat, 11 Dec 2021 18:58:29: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 18:58:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 18:58:30: #2 number of paired peaks: 553 WARNING @ Sat, 11 Dec 2021 18:58:30: Fewer paired peaks (553) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 553 pairs to build model! INFO @ Sat, 11 Dec 2021 18:58:30: start model_add_line... INFO @ Sat, 11 Dec 2021 18:58:30: start X-correlation... INFO @ Sat, 11 Dec 2021 18:58:30: end of X-cor INFO @ Sat, 11 Dec 2021 18:58:30: #2 finished! INFO @ Sat, 11 Dec 2021 18:58:30: #2 predicted fragment length is 231 bps INFO @ Sat, 11 Dec 2021 18:58:30: #2 alternative fragment length(s) may be 231 bps INFO @ Sat, 11 Dec 2021 18:58:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10971107/SRX10971107.20_model.r INFO @ Sat, 11 Dec 2021 18:58:30: #3 Call peaks... INFO @ Sat, 11 Dec 2021 18:58:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 18:58:43: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 18:58:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10971107/SRX10971107.20_peaks.xls INFO @ Sat, 11 Dec 2021 18:58:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10971107/SRX10971107.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 18:58:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10971107/SRX10971107.20_summits.bed INFO @ Sat, 11 Dec 2021 18:58:51: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (513 records, 4 fields): 8 millis CompletedMACS2peakCalling