Job ID = 14171424 SRX = SRX9711631 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 17151975 spots for SRR13282246/SRR13282246.sra Written 17151975 spots for SRR13282246/SRR13282246.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172022 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:31:04 17151975 reads; of these: 17151975 (100.00%) were paired; of these: 2410235 (14.05%) aligned concordantly 0 times 11931494 (69.56%) aligned concordantly exactly 1 time 2810246 (16.38%) aligned concordantly >1 times ---- 2410235 pairs aligned concordantly 0 times; of these: 777327 (32.25%) aligned discordantly 1 time ---- 1632908 pairs aligned 0 times concordantly or discordantly; of these: 3265816 mates make up the pairs; of these: 2443518 (74.82%) aligned 0 times 406504 (12.45%) aligned exactly 1 time 415794 (12.73%) aligned >1 times 92.88% overall alignment rate Time searching: 00:31:05 Overall time: 00:31:05 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] 2636259 / 15410351 = 0.1711 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 12:17:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9711631/SRX9711631.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9711631/SRX9711631.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9711631/SRX9711631.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9711631/SRX9711631.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 12:17:27: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:17:27: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:17:32: 1000000 INFO @ Sat, 11 Dec 2021 12:17:37: 2000000 INFO @ Sat, 11 Dec 2021 12:17:42: 3000000 INFO @ Sat, 11 Dec 2021 12:17:47: 4000000 INFO @ Sat, 11 Dec 2021 12:17:52: 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 12:17:57: 6000000 INFO @ Sat, 11 Dec 2021 12:17:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9711631/SRX9711631.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9711631/SRX9711631.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9711631/SRX9711631.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9711631/SRX9711631.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 12:17:57: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:17:57: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:18:02: 7000000 INFO @ Sat, 11 Dec 2021 12:18:02: 1000000 INFO @ Sat, 11 Dec 2021 12:18:07: 8000000 INFO @ Sat, 11 Dec 2021 12:18:07: 2000000 INFO @ Sat, 11 Dec 2021 12:18:12: 9000000 INFO @ Sat, 11 Dec 2021 12:18:13: 3000000 INFO @ Sat, 11 Dec 2021 12:18:17: 10000000 INFO @ Sat, 11 Dec 2021 12:18:18: 4000000 INFO @ Sat, 11 Dec 2021 12:18:22: 11000000 INFO @ Sat, 11 Dec 2021 12:18:23: 5000000 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 12:18:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9711631/SRX9711631.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9711631/SRX9711631.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9711631/SRX9711631.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9711631/SRX9711631.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 12:18:27: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:18:27: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:18:28: 12000000 INFO @ Sat, 11 Dec 2021 12:18:28: 6000000 INFO @ Sat, 11 Dec 2021 12:18:32: 1000000 INFO @ Sat, 11 Dec 2021 12:18:33: 13000000 INFO @ Sat, 11 Dec 2021 12:18:33: 7000000 INFO @ Sat, 11 Dec 2021 12:18:37: 2000000 INFO @ Sat, 11 Dec 2021 12:18:38: 14000000 INFO @ Sat, 11 Dec 2021 12:18:39: 8000000 INFO @ Sat, 11 Dec 2021 12:18:42: 3000000 INFO @ Sat, 11 Dec 2021 12:18:43: 15000000 INFO @ Sat, 11 Dec 2021 12:18:44: 9000000 INFO @ Sat, 11 Dec 2021 12:18:47: 4000000 INFO @ Sat, 11 Dec 2021 12:18:48: 16000000 INFO @ Sat, 11 Dec 2021 12:18:49: 10000000 INFO @ Sat, 11 Dec 2021 12:18:52: 5000000 INFO @ Sat, 11 Dec 2021 12:18:53: 17000000 INFO @ Sat, 11 Dec 2021 12:18:54: 11000000 INFO @ Sat, 11 Dec 2021 12:18:58: 6000000 INFO @ Sat, 11 Dec 2021 12:18:58: 18000000 INFO @ Sat, 11 Dec 2021 12:18:59: 12000000 INFO @ Sat, 11 Dec 2021 12:19:03: 7000000 INFO @ Sat, 11 Dec 2021 12:19:04: 19000000 INFO @ Sat, 11 Dec 2021 12:19:04: 13000000 INFO @ Sat, 11 Dec 2021 12:19:08: 8000000 INFO @ Sat, 11 Dec 2021 12:19:09: 20000000 INFO @ Sat, 11 Dec 2021 12:19:10: 14000000 INFO @ Sat, 11 Dec 2021 12:19:13: 9000000 INFO @ Sat, 11 Dec 2021 12:19:14: 21000000 INFO @ Sat, 11 Dec 2021 12:19:15: 15000000 INFO @ Sat, 11 Dec 2021 12:19:18: 10000000 INFO @ Sat, 11 Dec 2021 12:19:19: 22000000 INFO @ Sat, 11 Dec 2021 12:19:20: 16000000 INFO @ Sat, 11 Dec 2021 12:19:23: 11000000 INFO @ Sat, 11 Dec 2021 12:19:24: 23000000 INFO @ Sat, 11 Dec 2021 12:19:25: 17000000 INFO @ Sat, 11 Dec 2021 12:19:28: 12000000 INFO @ Sat, 11 Dec 2021 12:19:29: 24000000 INFO @ Sat, 11 Dec 2021 12:19:30: 18000000 INFO @ Sat, 11 Dec 2021 12:19:33: 13000000 INFO @ Sat, 11 Dec 2021 12:19:34: 25000000 INFO @ Sat, 11 Dec 2021 12:19:35: 19000000 INFO @ Sat, 11 Dec 2021 12:19:38: 14000000 INFO @ Sat, 11 Dec 2021 12:19:40: 26000000 INFO @ Sat, 11 Dec 2021 12:19:40: 20000000 INFO @ Sat, 11 Dec 2021 12:19:43: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 12:19:43: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 12:19:43: #1 total tags in treatment: 12195613 INFO @ Sat, 11 Dec 2021 12:19:43: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:19:43: #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 12:19:43: #1 tags after filtering in treatment: 11565446 INFO @ Sat, 11 Dec 2021 12:19:43: #1 Redundant rate of treatment: 0.05 INFO @ Sat, 11 Dec 2021 12:19:43: #1 finished! INFO @ Sat, 11 Dec 2021 12:19:43: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:19:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:19:43: 15000000 INFO @ Sat, 11 Dec 2021 12:19:44: #2 number of paired peaks: 304 WARNING @ Sat, 11 Dec 2021 12:19:44: Fewer paired peaks (304) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 304 pairs to build model! INFO @ Sat, 11 Dec 2021 12:19:44: start model_add_line... INFO @ Sat, 11 Dec 2021 12:19:44: start X-correlation... INFO @ Sat, 11 Dec 2021 12:19:44: end of X-cor INFO @ Sat, 11 Dec 2021 12:19:44: #2 finished! INFO @ Sat, 11 Dec 2021 12:19:44: #2 predicted fragment length is 236 bps INFO @ Sat, 11 Dec 2021 12:19:44: #2 alternative fragment length(s) may be 236 bps INFO @ Sat, 11 Dec 2021 12:19:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9711631/SRX9711631.05_model.r INFO @ Sat, 11 Dec 2021 12:19:44: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:19:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:19:46: 21000000 INFO @ Sat, 11 Dec 2021 12:19:49: 16000000 INFO @ Sat, 11 Dec 2021 12:19:51: 22000000 INFO @ Sat, 11 Dec 2021 12:19:54: 17000000 INFO @ Sat, 11 Dec 2021 12:19:56: 23000000 INFO @ Sat, 11 Dec 2021 12:19:59: 18000000 INFO @ Sat, 11 Dec 2021 12:20:01: 24000000 INFO @ Sat, 11 Dec 2021 12:20:04: 19000000 INFO @ Sat, 11 Dec 2021 12:20:06: 25000000 INFO @ Sat, 11 Dec 2021 12:20:08: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:20:09: 20000000 INFO @ Sat, 11 Dec 2021 12:20:11: 26000000 INFO @ Sat, 11 Dec 2021 12:20:14: 21000000 INFO @ Sat, 11 Dec 2021 12:20:14: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 12:20:14: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 12:20:14: #1 total tags in treatment: 12195613 INFO @ Sat, 11 Dec 2021 12:20:14: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:20:14: #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 12:20:14: #1 tags after filtering in treatment: 11565446 INFO @ Sat, 11 Dec 2021 12:20:14: #1 Redundant rate of treatment: 0.05 INFO @ Sat, 11 Dec 2021 12:20:14: #1 finished! INFO @ Sat, 11 Dec 2021 12:20:14: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:20:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:20:15: #2 number of paired peaks: 304 WARNING @ Sat, 11 Dec 2021 12:20:15: Fewer paired peaks (304) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 304 pairs to build model! INFO @ Sat, 11 Dec 2021 12:20:15: start model_add_line... INFO @ Sat, 11 Dec 2021 12:20:15: start X-correlation... INFO @ Sat, 11 Dec 2021 12:20:15: end of X-cor INFO @ Sat, 11 Dec 2021 12:20:15: #2 finished! INFO @ Sat, 11 Dec 2021 12:20:15: #2 predicted fragment length is 236 bps INFO @ Sat, 11 Dec 2021 12:20:15: #2 alternative fragment length(s) may be 236 bps INFO @ Sat, 11 Dec 2021 12:20:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9711631/SRX9711631.10_model.r INFO @ Sat, 11 Dec 2021 12:20:15: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:20:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:20:19: 22000000 INFO @ Sat, 11 Dec 2021 12:20:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9711631/SRX9711631.05_peaks.xls INFO @ Sat, 11 Dec 2021 12:20:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9711631/SRX9711631.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:20:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9711631/SRX9711631.05_summits.bed INFO @ Sat, 11 Dec 2021 12:20:19: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1722 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 12:20:24: 23000000 INFO @ Sat, 11 Dec 2021 12:20:29: 24000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 12:20:34: 25000000 INFO @ Sat, 11 Dec 2021 12:20:39: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:20:39: 26000000 INFO @ Sat, 11 Dec 2021 12:20:42: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 12:20:42: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 12:20:42: #1 total tags in treatment: 12195613 INFO @ Sat, 11 Dec 2021 12:20:42: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:20:42: #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 12:20:42: #1 tags after filtering in treatment: 11565446 INFO @ Sat, 11 Dec 2021 12:20:42: #1 Redundant rate of treatment: 0.05 INFO @ Sat, 11 Dec 2021 12:20:42: #1 finished! INFO @ Sat, 11 Dec 2021 12:20:42: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:20:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:20:43: #2 number of paired peaks: 304 WARNING @ Sat, 11 Dec 2021 12:20:43: Fewer paired peaks (304) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 304 pairs to build model! INFO @ Sat, 11 Dec 2021 12:20:43: start model_add_line... INFO @ Sat, 11 Dec 2021 12:20:43: start X-correlation... INFO @ Sat, 11 Dec 2021 12:20:43: end of X-cor INFO @ Sat, 11 Dec 2021 12:20:43: #2 finished! INFO @ Sat, 11 Dec 2021 12:20:43: #2 predicted fragment length is 236 bps INFO @ Sat, 11 Dec 2021 12:20:43: #2 alternative fragment length(s) may be 236 bps INFO @ Sat, 11 Dec 2021 12:20:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9711631/SRX9711631.20_model.r INFO @ Sat, 11 Dec 2021 12:20:43: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:20:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:20:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9711631/SRX9711631.10_peaks.xls INFO @ Sat, 11 Dec 2021 12:20:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9711631/SRX9711631.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:20:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9711631/SRX9711631.10_summits.bed INFO @ Sat, 11 Dec 2021 12:20:50: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (748 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 12:21:07: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:21:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9711631/SRX9711631.20_peaks.xls INFO @ Sat, 11 Dec 2021 12:21:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9711631/SRX9711631.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:21:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9711631/SRX9711631.20_summits.bed INFO @ Sat, 11 Dec 2021 12:21:18: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (352 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。