Job ID = 16439342 SRX = SRX13453874 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 9412073 spots for SRR17276264/SRR17276264.sra Written 9412073 spots for SRR17276264/SRR17276264.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439519 ("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: 00:26:23 9412073 reads; of these: 9412073 (100.00%) were paired; of these: 448470 (4.76%) aligned concordantly 0 times 7165252 (76.13%) aligned concordantly exactly 1 time 1798351 (19.11%) aligned concordantly >1 times ---- 448470 pairs aligned concordantly 0 times; of these: 85245 (19.01%) aligned discordantly 1 time ---- 363225 pairs aligned 0 times concordantly or discordantly; of these: 726450 mates make up the pairs; of these: 445556 (61.33%) aligned 0 times 189732 (26.12%) aligned exactly 1 time 91162 (12.55%) aligned >1 times 97.63% overall alignment rate Time searching: 00:26:23 Overall time: 00:26:23 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 8 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] 50519 / 8934186 = 0.0057 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 15:32:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX13453874/SRX13453874.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX13453874/SRX13453874.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX13453874/SRX13453874.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX13453874/SRX13453874.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 @ Tue, 02 Aug 2022 15:32:05: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:32:05: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:32:13: 1000000 INFO @ Tue, 02 Aug 2022 15:32:21: 2000000 INFO @ Tue, 02 Aug 2022 15:32:30: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 15:32:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX13453874/SRX13453874.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX13453874/SRX13453874.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX13453874/SRX13453874.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX13453874/SRX13453874.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 @ Tue, 02 Aug 2022 15:32:34: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:32:34: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:32:38: 4000000 INFO @ Tue, 02 Aug 2022 15:32:42: 1000000 INFO @ Tue, 02 Aug 2022 15:32:47: 5000000 INFO @ Tue, 02 Aug 2022 15:32:51: 2000000 INFO @ Tue, 02 Aug 2022 15:32:56: 6000000 INFO @ Tue, 02 Aug 2022 15:33:00: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 15:33:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX13453874/SRX13453874.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX13453874/SRX13453874.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX13453874/SRX13453874.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX13453874/SRX13453874.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 @ Tue, 02 Aug 2022 15:33:04: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:33:04: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:33:05: 7000000 INFO @ Tue, 02 Aug 2022 15:33:09: 4000000 INFO @ Tue, 02 Aug 2022 15:33:12: 1000000 INFO @ Tue, 02 Aug 2022 15:33:15: 8000000 INFO @ Tue, 02 Aug 2022 15:33:18: 5000000 INFO @ Tue, 02 Aug 2022 15:33:20: 2000000 INFO @ Tue, 02 Aug 2022 15:33:24: 9000000 INFO @ Tue, 02 Aug 2022 15:33:26: 6000000 INFO @ Tue, 02 Aug 2022 15:33:28: 3000000 INFO @ Tue, 02 Aug 2022 15:33:33: 10000000 INFO @ Tue, 02 Aug 2022 15:33:35: 7000000 INFO @ Tue, 02 Aug 2022 15:33:36: 4000000 INFO @ Tue, 02 Aug 2022 15:33:42: 11000000 INFO @ Tue, 02 Aug 2022 15:33:44: 8000000 INFO @ Tue, 02 Aug 2022 15:33:44: 5000000 INFO @ Tue, 02 Aug 2022 15:33:51: 12000000 INFO @ Tue, 02 Aug 2022 15:33:53: 9000000 INFO @ Tue, 02 Aug 2022 15:33:53: 6000000 INFO @ Tue, 02 Aug 2022 15:33:59: 13000000 INFO @ Tue, 02 Aug 2022 15:34:01: 10000000 INFO @ Tue, 02 Aug 2022 15:34:02: 7000000 INFO @ Tue, 02 Aug 2022 15:34:09: 14000000 INFO @ Tue, 02 Aug 2022 15:34:10: 11000000 INFO @ Tue, 02 Aug 2022 15:34:11: 8000000 INFO @ Tue, 02 Aug 2022 15:34:17: 15000000 INFO @ Tue, 02 Aug 2022 15:34:19: 12000000 INFO @ Tue, 02 Aug 2022 15:34:20: 9000000 INFO @ Tue, 02 Aug 2022 15:34:27: 16000000 INFO @ Tue, 02 Aug 2022 15:34:28: 13000000 INFO @ Tue, 02 Aug 2022 15:34:28: 10000000 INFO @ Tue, 02 Aug 2022 15:34:37: 17000000 INFO @ Tue, 02 Aug 2022 15:34:37: 14000000 INFO @ Tue, 02 Aug 2022 15:34:37: 11000000 INFO @ Tue, 02 Aug 2022 15:34:46: 15000000 INFO @ Tue, 02 Aug 2022 15:34:46: 18000000 INFO @ Tue, 02 Aug 2022 15:34:46: 12000000 INFO @ Tue, 02 Aug 2022 15:34:49: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 15:34:49: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 15:34:49: #1 total tags in treatment: 8913177 INFO @ Tue, 02 Aug 2022 15:34:49: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:34:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 15:34:49: #1 tags after filtering in treatment: 8673940 INFO @ Tue, 02 Aug 2022 15:34:49: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 02 Aug 2022 15:34:49: #1 finished! INFO @ Tue, 02 Aug 2022 15:34:49: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:34:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:34:49: #2 number of paired peaks: 105 WARNING @ Tue, 02 Aug 2022 15:34:49: Fewer paired peaks (105) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 105 pairs to build model! INFO @ Tue, 02 Aug 2022 15:34:49: start model_add_line... INFO @ Tue, 02 Aug 2022 15:34:49: start X-correlation... INFO @ Tue, 02 Aug 2022 15:34:50: end of X-cor INFO @ Tue, 02 Aug 2022 15:34:50: #2 finished! INFO @ Tue, 02 Aug 2022 15:34:50: #2 predicted fragment length is 164 bps INFO @ Tue, 02 Aug 2022 15:34:50: #2 alternative fragment length(s) may be 164 bps INFO @ Tue, 02 Aug 2022 15:34:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX13453874/SRX13453874.05_model.r INFO @ Tue, 02 Aug 2022 15:34:50: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:34:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:34:55: 16000000 INFO @ Tue, 02 Aug 2022 15:34:55: 13000000 INFO @ Tue, 02 Aug 2022 15:35:04: 17000000 INFO @ Tue, 02 Aug 2022 15:35:04: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 15:35:06: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:35:13: 18000000 INFO @ Tue, 02 Aug 2022 15:35:13: 15000000 INFO @ Tue, 02 Aug 2022 15:35:15: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 15:35:15: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 15:35:15: #1 total tags in treatment: 8913177 INFO @ Tue, 02 Aug 2022 15:35:15: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:35:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 15:35:15: #1 tags after filtering in treatment: 8673940 INFO @ Tue, 02 Aug 2022 15:35:15: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 02 Aug 2022 15:35:15: #1 finished! INFO @ Tue, 02 Aug 2022 15:35:15: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:35:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:35:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX13453874/SRX13453874.05_peaks.xls INFO @ Tue, 02 Aug 2022 15:35:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX13453874/SRX13453874.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:35:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX13453874/SRX13453874.05_summits.bed INFO @ Tue, 02 Aug 2022 15:35:16: Done! INFO @ Tue, 02 Aug 2022 15:35:16: #2 number of paired peaks: 105 WARNING @ Tue, 02 Aug 2022 15:35:16: Fewer paired peaks (105) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 105 pairs to build model! INFO @ Tue, 02 Aug 2022 15:35:16: start model_add_line... INFO @ Tue, 02 Aug 2022 15:35:16: start X-correlation... INFO @ Tue, 02 Aug 2022 15:35:16: end of X-cor INFO @ Tue, 02 Aug 2022 15:35:16: #2 finished! INFO @ Tue, 02 Aug 2022 15:35:16: #2 predicted fragment length is 164 bps INFO @ Tue, 02 Aug 2022 15:35:16: #2 alternative fragment length(s) may be 164 bps INFO @ Tue, 02 Aug 2022 15:35:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX13453874/SRX13453874.10_model.r pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1401 records, 4 fields): 27 millis INFO @ Tue, 02 Aug 2022 15:35:16: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:35:16: #3 Pre-compute pvalue-qvalue table... CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:35:22: 16000000 INFO @ Tue, 02 Aug 2022 15:35:31: 17000000 INFO @ Tue, 02 Aug 2022 15:35:33: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:35:40: 18000000 INFO @ Tue, 02 Aug 2022 15:35:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX13453874/SRX13453874.10_peaks.xls INFO @ Tue, 02 Aug 2022 15:35:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX13453874/SRX13453874.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:35:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX13453874/SRX13453874.10_summits.bed INFO @ Tue, 02 Aug 2022 15:35:43: Done! INFO @ Tue, 02 Aug 2022 15:35:43: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 15:35:43: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 15:35:43: #1 total tags in treatment: 8913177 INFO @ Tue, 02 Aug 2022 15:35:43: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:35:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) pass1 - making usageList (11 chroms): 1 millis INFO @ Tue, 02 Aug 2022 15:35:43: #1 tags after filtering in treatment: 8673940 INFO @ Tue, 02 Aug 2022 15:35:43: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 02 Aug 2022 15:35:43: #1 finished! INFO @ Tue, 02 Aug 2022 15:35:43: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:35:43: #2 looking for paired plus/minus strand peaks... pass2 - checking and writing primary data (643 records, 4 fields): 64 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:35:44: #2 number of paired peaks: 105 WARNING @ Tue, 02 Aug 2022 15:35:44: Fewer paired peaks (105) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 105 pairs to build model! INFO @ Tue, 02 Aug 2022 15:35:44: start model_add_line... INFO @ Tue, 02 Aug 2022 15:35:44: start X-correlation... INFO @ Tue, 02 Aug 2022 15:35:44: end of X-cor INFO @ Tue, 02 Aug 2022 15:35:44: #2 finished! INFO @ Tue, 02 Aug 2022 15:35:44: #2 predicted fragment length is 164 bps INFO @ Tue, 02 Aug 2022 15:35:44: #2 alternative fragment length(s) may be 164 bps INFO @ Tue, 02 Aug 2022 15:35:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX13453874/SRX13453874.20_model.r INFO @ Tue, 02 Aug 2022 15:35:44: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:35:44: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 15:36:01: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:36:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX13453874/SRX13453874.20_peaks.xls INFO @ Tue, 02 Aug 2022 15:36:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX13453874/SRX13453874.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:36:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX13453874/SRX13453874.20_summits.bed INFO @ Tue, 02 Aug 2022 15:36:10: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (262 records, 4 fields): 72 millis CompletedMACS2peakCalling