Job ID = 14171485 SRX = SRX10971118 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2021-12-11T02:48:08 prefetch.2.10.7: 1) Downloading 'SRR14631242'... 2021-12-11T02:48:08 prefetch.2.10.7: Downloading via HTTPS... 2021-12-11T02:49:52 prefetch.2.10.7: HTTPS download succeed 2021-12-11T02:49:52 prefetch.2.10.7: 1) 'SRR14631242' was downloaded successfully 2021-12-11T02:49:52 prefetch.2.10.7: 'SRR14631242' has 0 unresolved dependencies Read 26248643 spots for SRR14631242/SRR14631242.sra Written 26248643 spots for SRR14631242/SRR14631242.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172517 ("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: 02:08:51 26248643 reads; of these: 26248643 (100.00%) were paired; of these: 4385049 (16.71%) aligned concordantly 0 times 18556090 (70.69%) aligned concordantly exactly 1 time 3307504 (12.60%) aligned concordantly >1 times ---- 4385049 pairs aligned concordantly 0 times; of these: 846671 (19.31%) aligned discordantly 1 time ---- 3538378 pairs aligned 0 times concordantly or discordantly; of these: 7076756 mates make up the pairs; of these: 4447097 (62.84%) aligned 0 times 952014 (13.45%) aligned exactly 1 time 1677645 (23.71%) aligned >1 times 91.53% overall alignment rate Time searching: 02:08:51 Overall time: 02:08:51 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 20 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] 3168633 / 22354963 = 0.1417 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 14:15:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10971118/SRX10971118.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10971118/SRX10971118.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10971118/SRX10971118.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10971118/SRX10971118.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 14:15:26: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:15:26: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:15:33: 1000000 INFO @ Sat, 11 Dec 2021 14:15:41: 2000000 INFO @ Sat, 11 Dec 2021 14:15:49: 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 14:15:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10971118/SRX10971118.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10971118/SRX10971118.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10971118/SRX10971118.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10971118/SRX10971118.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 14:15:55: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:15:55: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:15:57: 4000000 INFO @ Sat, 11 Dec 2021 14:16:02: 1000000 INFO @ Sat, 11 Dec 2021 14:16:05: 5000000 INFO @ Sat, 11 Dec 2021 14:16:09: 2000000 INFO @ Sat, 11 Dec 2021 14:16:13: 6000000 INFO @ Sat, 11 Dec 2021 14:16:16: 3000000 INFO @ Sat, 11 Dec 2021 14:16:21: 7000000 INFO @ Sat, 11 Dec 2021 14:16:23: 4000000 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 14:16:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10971118/SRX10971118.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10971118/SRX10971118.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10971118/SRX10971118.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10971118/SRX10971118.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 14:16:25: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:16:25: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:16:29: 8000000 INFO @ Sat, 11 Dec 2021 14:16:30: 5000000 INFO @ Sat, 11 Dec 2021 14:16:32: 1000000 INFO @ Sat, 11 Dec 2021 14:16:37: 6000000 INFO @ Sat, 11 Dec 2021 14:16:38: 9000000 INFO @ Sat, 11 Dec 2021 14:16:39: 2000000 INFO @ Sat, 11 Dec 2021 14:16:44: 7000000 INFO @ Sat, 11 Dec 2021 14:16:46: 10000000 INFO @ Sat, 11 Dec 2021 14:16:46: 3000000 INFO @ Sat, 11 Dec 2021 14:16:51: 8000000 INFO @ Sat, 11 Dec 2021 14:16:53: 4000000 INFO @ Sat, 11 Dec 2021 14:16:54: 11000000 INFO @ Sat, 11 Dec 2021 14:16:58: 9000000 INFO @ Sat, 11 Dec 2021 14:17:00: 5000000 INFO @ Sat, 11 Dec 2021 14:17:02: 12000000 INFO @ Sat, 11 Dec 2021 14:17:05: 10000000 INFO @ Sat, 11 Dec 2021 14:17:07: 6000000 INFO @ Sat, 11 Dec 2021 14:17:10: 13000000 INFO @ Sat, 11 Dec 2021 14:17:12: 11000000 INFO @ Sat, 11 Dec 2021 14:17:14: 7000000 INFO @ Sat, 11 Dec 2021 14:17:18: 14000000 INFO @ Sat, 11 Dec 2021 14:17:19: 12000000 INFO @ Sat, 11 Dec 2021 14:17:21: 8000000 INFO @ Sat, 11 Dec 2021 14:17:26: 13000000 INFO @ Sat, 11 Dec 2021 14:17:26: 15000000 INFO @ Sat, 11 Dec 2021 14:17:28: 9000000 INFO @ Sat, 11 Dec 2021 14:17:33: 14000000 INFO @ Sat, 11 Dec 2021 14:17:34: 16000000 INFO @ Sat, 11 Dec 2021 14:17:35: 10000000 INFO @ Sat, 11 Dec 2021 14:17:40: 15000000 INFO @ Sat, 11 Dec 2021 14:17:42: 11000000 INFO @ Sat, 11 Dec 2021 14:17:42: 17000000 INFO @ Sat, 11 Dec 2021 14:17:47: 16000000 INFO @ Sat, 11 Dec 2021 14:17:49: 12000000 INFO @ Sat, 11 Dec 2021 14:17:51: 18000000 INFO @ Sat, 11 Dec 2021 14:17:54: 17000000 INFO @ Sat, 11 Dec 2021 14:17:56: 13000000 INFO @ Sat, 11 Dec 2021 14:17:59: 19000000 INFO @ Sat, 11 Dec 2021 14:18:01: 18000000 INFO @ Sat, 11 Dec 2021 14:18:03: 14000000 INFO @ Sat, 11 Dec 2021 14:18:07: 20000000 INFO @ Sat, 11 Dec 2021 14:18:08: 19000000 INFO @ Sat, 11 Dec 2021 14:18:10: 15000000 INFO @ Sat, 11 Dec 2021 14:18:15: 21000000 INFO @ Sat, 11 Dec 2021 14:18:15: 20000000 INFO @ Sat, 11 Dec 2021 14:18:17: 16000000 INFO @ Sat, 11 Dec 2021 14:18:22: 21000000 INFO @ Sat, 11 Dec 2021 14:18:23: 22000000 INFO @ Sat, 11 Dec 2021 14:18:24: 17000000 INFO @ Sat, 11 Dec 2021 14:18:29: 22000000 INFO @ Sat, 11 Dec 2021 14:18:31: 23000000 INFO @ Sat, 11 Dec 2021 14:18:31: 18000000 INFO @ Sat, 11 Dec 2021 14:18:36: 23000000 INFO @ Sat, 11 Dec 2021 14:18:38: 19000000 INFO @ Sat, 11 Dec 2021 14:18:39: 24000000 INFO @ Sat, 11 Dec 2021 14:18:42: 24000000 INFO @ Sat, 11 Dec 2021 14:18:45: 20000000 INFO @ Sat, 11 Dec 2021 14:18:47: 25000000 INFO @ Sat, 11 Dec 2021 14:18:49: 25000000 INFO @ Sat, 11 Dec 2021 14:18:52: 21000000 INFO @ Sat, 11 Dec 2021 14:18:55: 26000000 INFO @ Sat, 11 Dec 2021 14:18:56: 26000000 INFO @ Sat, 11 Dec 2021 14:18:58: 22000000 INFO @ Sat, 11 Dec 2021 14:19:03: 27000000 INFO @ Sat, 11 Dec 2021 14:19:04: 27000000 INFO @ Sat, 11 Dec 2021 14:19:05: 23000000 INFO @ Sat, 11 Dec 2021 14:19:11: 28000000 INFO @ Sat, 11 Dec 2021 14:19:12: 24000000 INFO @ Sat, 11 Dec 2021 14:19:12: 28000000 INFO @ Sat, 11 Dec 2021 14:19:19: 25000000 INFO @ Sat, 11 Dec 2021 14:19:19: 29000000 INFO @ Sat, 11 Dec 2021 14:19:20: 29000000 INFO @ Sat, 11 Dec 2021 14:19:26: 26000000 INFO @ Sat, 11 Dec 2021 14:19:27: 30000000 INFO @ Sat, 11 Dec 2021 14:19:28: 30000000 INFO @ Sat, 11 Dec 2021 14:19:33: 27000000 INFO @ Sat, 11 Dec 2021 14:19:36: 31000000 INFO @ Sat, 11 Dec 2021 14:19:36: 31000000 INFO @ Sat, 11 Dec 2021 14:19:39: 28000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 14:19:44: 32000000 INFO @ Sat, 11 Dec 2021 14:19:45: 32000000 INFO @ Sat, 11 Dec 2021 14:19:46: 29000000 INFO @ Sat, 11 Dec 2021 14:19:52: 33000000 INFO @ Sat, 11 Dec 2021 14:19:53: 33000000 INFO @ Sat, 11 Dec 2021 14:19:53: 30000000 INFO @ Sat, 11 Dec 2021 14:20:00: 31000000 INFO @ Sat, 11 Dec 2021 14:20:00: 34000000 INFO @ Sat, 11 Dec 2021 14:20:01: 34000000 INFO @ Sat, 11 Dec 2021 14:20:07: 32000000 INFO @ Sat, 11 Dec 2021 14:20:08: 35000000 INFO @ Sat, 11 Dec 2021 14:20:09: 35000000 INFO @ Sat, 11 Dec 2021 14:20:14: 33000000 INFO @ Sat, 11 Dec 2021 14:20:16: 36000000 INFO @ Sat, 11 Dec 2021 14:20:17: 36000000 INFO @ Sat, 11 Dec 2021 14:20:21: 34000000 INFO @ Sat, 11 Dec 2021 14:20:24: 37000000 INFO @ Sat, 11 Dec 2021 14:20:24: 37000000 INFO @ Sat, 11 Dec 2021 14:20:28: 35000000 INFO @ Sat, 11 Dec 2021 14:20:31: 38000000 INFO @ Sat, 11 Dec 2021 14:20:32: 38000000 INFO @ Sat, 11 Dec 2021 14:20:34: 36000000 INFO @ Sat, 11 Dec 2021 14:20:39: 39000000 INFO @ Sat, 11 Dec 2021 14:20:40: 39000000 INFO @ Sat, 11 Dec 2021 14:20:41: 37000000 INFO @ Sat, 11 Dec 2021 14:20:48: 40000000 INFO @ Sat, 11 Dec 2021 14:20:48: 38000000 INFO @ Sat, 11 Dec 2021 14:20:48: 40000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 14:20:55: 39000000 INFO @ Sat, 11 Dec 2021 14:20:56: 41000000 INFO @ Sat, 11 Dec 2021 14:20:57: 41000000 INFO @ Sat, 11 Dec 2021 14:21:02: 40000000 INFO @ Sat, 11 Dec 2021 14:21:02: #1 tag size is determined as 100 bps INFO @ Sat, 11 Dec 2021 14:21:02: #1 tag size = 100 INFO @ Sat, 11 Dec 2021 14:21:02: #1 total tags in treatment: 18777745 INFO @ Sat, 11 Dec 2021 14:21:02: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:21:02: #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 14:21:02: #1 tags after filtering in treatment: 17125484 INFO @ Sat, 11 Dec 2021 14:21:02: #1 Redundant rate of treatment: 0.09 INFO @ Sat, 11 Dec 2021 14:21:02: #1 finished! INFO @ Sat, 11 Dec 2021 14:21:02: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:21:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:21:02: #1 tag size is determined as 100 bps INFO @ Sat, 11 Dec 2021 14:21:02: #1 tag size = 100 INFO @ Sat, 11 Dec 2021 14:21:02: #1 total tags in treatment: 18777745 INFO @ Sat, 11 Dec 2021 14:21:02: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:21:02: #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 14:21:03: #1 tags after filtering in treatment: 17125484 INFO @ Sat, 11 Dec 2021 14:21:03: #1 Redundant rate of treatment: 0.09 INFO @ Sat, 11 Dec 2021 14:21:03: #1 finished! INFO @ Sat, 11 Dec 2021 14:21:03: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:21:03: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:21:03: #2 number of paired peaks: 695 WARNING @ Sat, 11 Dec 2021 14:21:03: Fewer paired peaks (695) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 695 pairs to build model! INFO @ Sat, 11 Dec 2021 14:21:03: start model_add_line... INFO @ Sat, 11 Dec 2021 14:21:03: start X-correlation... INFO @ Sat, 11 Dec 2021 14:21:03: end of X-cor INFO @ Sat, 11 Dec 2021 14:21:03: #2 finished! INFO @ Sat, 11 Dec 2021 14:21:03: #2 predicted fragment length is 257 bps INFO @ Sat, 11 Dec 2021 14:21:03: #2 alternative fragment length(s) may be 257 bps INFO @ Sat, 11 Dec 2021 14:21:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10971118/SRX10971118.05_model.r INFO @ Sat, 11 Dec 2021 14:21:03: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:21:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:21:04: #2 number of paired peaks: 695 WARNING @ Sat, 11 Dec 2021 14:21:04: Fewer paired peaks (695) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 695 pairs to build model! INFO @ Sat, 11 Dec 2021 14:21:04: start model_add_line... INFO @ Sat, 11 Dec 2021 14:21:04: start X-correlation... INFO @ Sat, 11 Dec 2021 14:21:04: end of X-cor INFO @ Sat, 11 Dec 2021 14:21:04: #2 finished! INFO @ Sat, 11 Dec 2021 14:21:04: #2 predicted fragment length is 257 bps INFO @ Sat, 11 Dec 2021 14:21:04: #2 alternative fragment length(s) may be 257 bps INFO @ Sat, 11 Dec 2021 14:21:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10971118/SRX10971118.10_model.r INFO @ Sat, 11 Dec 2021 14:21:04: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:21:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:21:08: 41000000 INFO @ Sat, 11 Dec 2021 14:21:12: #1 tag size is determined as 100 bps INFO @ Sat, 11 Dec 2021 14:21:12: #1 tag size = 100 INFO @ Sat, 11 Dec 2021 14:21:12: #1 total tags in treatment: 18777745 INFO @ Sat, 11 Dec 2021 14:21:12: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:21:12: #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 14:21:13: #1 tags after filtering in treatment: 17125484 INFO @ Sat, 11 Dec 2021 14:21:13: #1 Redundant rate of treatment: 0.09 INFO @ Sat, 11 Dec 2021 14:21:13: #1 finished! INFO @ Sat, 11 Dec 2021 14:21:13: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:21:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:21:14: #2 number of paired peaks: 695 WARNING @ Sat, 11 Dec 2021 14:21:14: Fewer paired peaks (695) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 695 pairs to build model! INFO @ Sat, 11 Dec 2021 14:21:14: start model_add_line... INFO @ Sat, 11 Dec 2021 14:21:14: start X-correlation... INFO @ Sat, 11 Dec 2021 14:21:14: end of X-cor INFO @ Sat, 11 Dec 2021 14:21:14: #2 finished! INFO @ Sat, 11 Dec 2021 14:21:14: #2 predicted fragment length is 257 bps INFO @ Sat, 11 Dec 2021 14:21:14: #2 alternative fragment length(s) may be 257 bps INFO @ Sat, 11 Dec 2021 14:21:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10971118/SRX10971118.20_model.r INFO @ Sat, 11 Dec 2021 14:21:14: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:21:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:21:38: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:21:39: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:21:49: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:21:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10971118/SRX10971118.05_peaks.xls INFO @ Sat, 11 Dec 2021 14:21:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10971118/SRX10971118.10_peaks.xls INFO @ Sat, 11 Dec 2021 14:21:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10971118/SRX10971118.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:21:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10971118/SRX10971118.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:21:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10971118/SRX10971118.10_summits.bed INFO @ Sat, 11 Dec 2021 14:21:56: Done! INFO @ Sat, 11 Dec 2021 14:21:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10971118/SRX10971118.05_summits.bed INFO @ Sat, 11 Dec 2021 14:21:56: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2503 records, 4 fields): 8 millis pass1 - making usageList (14 chroms): 1 millis CompletedMACS2peakCalling pass2 - checking and writing primary data (3387 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 14:22:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10971118/SRX10971118.20_peaks.xls INFO @ Sat, 11 Dec 2021 14:22:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10971118/SRX10971118.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:22:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10971118/SRX10971118.20_summits.bed INFO @ Sat, 11 Dec 2021 14:22:05: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1810 records, 4 fields): 3 millis CompletedMACS2peakCalling