Job ID = 6627014 SRX = SRX8325345 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 3540578 spots for SRR11772151/SRR11772151.sra Written 3540578 spots for SRR11772151/SRR11772151.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627188 ("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: 00:11:47 3540578 reads; of these: 3540578 (100.00%) were paired; of these: 1111025 (31.38%) aligned concordantly 0 times 1756756 (49.62%) aligned concordantly exactly 1 time 672797 (19.00%) aligned concordantly >1 times ---- 1111025 pairs aligned concordantly 0 times; of these: 388274 (34.95%) aligned discordantly 1 time ---- 722751 pairs aligned 0 times concordantly or discordantly; of these: 1445502 mates make up the pairs; of these: 708847 (49.04%) aligned 0 times 353636 (24.46%) aligned exactly 1 time 383019 (26.50%) aligned >1 times 89.99% overall alignment rate Time searching: 00:11:47 Overall time: 00:11:47 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] 984610 / 2707428 = 0.3637 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 09:39:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8325345/SRX8325345.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8325345/SRX8325345.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8325345/SRX8325345.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8325345/SRX8325345.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, 14 Jul 2020 09:39:07: #1 read tag files... INFO @ Tue, 14 Jul 2020 09:39:07: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 09:39:15: 1000000 INFO @ Tue, 14 Jul 2020 09:39:23: 2000000 INFO @ Tue, 14 Jul 2020 09:39:31: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 09:39:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8325345/SRX8325345.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8325345/SRX8325345.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8325345/SRX8325345.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8325345/SRX8325345.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, 14 Jul 2020 09:39:37: #1 read tag files... INFO @ Tue, 14 Jul 2020 09:39:37: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 09:39:40: 4000000 INFO @ Tue, 14 Jul 2020 09:39:43: #1 tag size is determined as 115 bps INFO @ Tue, 14 Jul 2020 09:39:43: #1 tag size = 115 INFO @ Tue, 14 Jul 2020 09:39:43: #1 total tags in treatment: 1556236 INFO @ Tue, 14 Jul 2020 09:39:43: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 09:39:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 09:39:43: #1 tags after filtering in treatment: 1443716 INFO @ Tue, 14 Jul 2020 09:39:43: #1 Redundant rate of treatment: 0.07 INFO @ Tue, 14 Jul 2020 09:39:43: #1 finished! INFO @ Tue, 14 Jul 2020 09:39:43: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 09:39:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 09:39:43: #2 number of paired peaks: 460 WARNING @ Tue, 14 Jul 2020 09:39:43: Fewer paired peaks (460) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 460 pairs to build model! INFO @ Tue, 14 Jul 2020 09:39:43: start model_add_line... INFO @ Tue, 14 Jul 2020 09:39:44: start X-correlation... INFO @ Tue, 14 Jul 2020 09:39:44: end of X-cor INFO @ Tue, 14 Jul 2020 09:39:44: #2 finished! INFO @ Tue, 14 Jul 2020 09:39:44: #2 predicted fragment length is 164 bps INFO @ Tue, 14 Jul 2020 09:39:44: #2 alternative fragment length(s) may be 164 bps INFO @ Tue, 14 Jul 2020 09:39:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8325345/SRX8325345.05_model.r WARNING @ Tue, 14 Jul 2020 09:39:44: #2 Since the d (164) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 09:39:44: #2 You may need to consider one of the other alternative d(s): 164 WARNING @ Tue, 14 Jul 2020 09:39:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 09:39:44: #3 Call peaks... INFO @ Tue, 14 Jul 2020 09:39:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 09:39:46: 1000000 INFO @ Tue, 14 Jul 2020 09:39:47: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 09:39:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8325345/SRX8325345.05_peaks.xls INFO @ Tue, 14 Jul 2020 09:39:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8325345/SRX8325345.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 09:39:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8325345/SRX8325345.05_summits.bed INFO @ Tue, 14 Jul 2020 09:39:49: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (547 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 09:39:54: 2000000 INFO @ Tue, 14 Jul 2020 09:40:03: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 09:40:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8325345/SRX8325345.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8325345/SRX8325345.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8325345/SRX8325345.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8325345/SRX8325345.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, 14 Jul 2020 09:40:07: #1 read tag files... INFO @ Tue, 14 Jul 2020 09:40:07: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 09:40:11: 4000000 INFO @ Tue, 14 Jul 2020 09:40:15: #1 tag size is determined as 115 bps INFO @ Tue, 14 Jul 2020 09:40:15: #1 tag size = 115 INFO @ Tue, 14 Jul 2020 09:40:15: #1 total tags in treatment: 1556236 INFO @ Tue, 14 Jul 2020 09:40:15: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 09:40:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 09:40:15: #1 tags after filtering in treatment: 1443716 INFO @ Tue, 14 Jul 2020 09:40:15: #1 Redundant rate of treatment: 0.07 INFO @ Tue, 14 Jul 2020 09:40:15: #1 finished! INFO @ Tue, 14 Jul 2020 09:40:15: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 09:40:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 09:40:15: #2 number of paired peaks: 460 WARNING @ Tue, 14 Jul 2020 09:40:15: Fewer paired peaks (460) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 460 pairs to build model! INFO @ Tue, 14 Jul 2020 09:40:15: start model_add_line... INFO @ Tue, 14 Jul 2020 09:40:15: start X-correlation... INFO @ Tue, 14 Jul 2020 09:40:15: end of X-cor INFO @ Tue, 14 Jul 2020 09:40:15: #2 finished! INFO @ Tue, 14 Jul 2020 09:40:15: #2 predicted fragment length is 164 bps INFO @ Tue, 14 Jul 2020 09:40:15: #2 alternative fragment length(s) may be 164 bps INFO @ Tue, 14 Jul 2020 09:40:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8325345/SRX8325345.10_model.r WARNING @ Tue, 14 Jul 2020 09:40:15: #2 Since the d (164) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 09:40:15: #2 You may need to consider one of the other alternative d(s): 164 WARNING @ Tue, 14 Jul 2020 09:40:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 09:40:15: #3 Call peaks... INFO @ Tue, 14 Jul 2020 09:40:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 09:40:16: 1000000 INFO @ Tue, 14 Jul 2020 09:40:19: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 09:40:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8325345/SRX8325345.10_peaks.xls INFO @ Tue, 14 Jul 2020 09:40:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8325345/SRX8325345.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 09:40:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8325345/SRX8325345.10_summits.bed INFO @ Tue, 14 Jul 2020 09:40:21: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (293 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 09:40:25: 2000000 INFO @ Tue, 14 Jul 2020 09:40:33: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 09:40:42: 4000000 INFO @ Tue, 14 Jul 2020 09:40:45: #1 tag size is determined as 115 bps INFO @ Tue, 14 Jul 2020 09:40:45: #1 tag size = 115 INFO @ Tue, 14 Jul 2020 09:40:45: #1 total tags in treatment: 1556236 INFO @ Tue, 14 Jul 2020 09:40:45: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 09:40:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 09:40:45: #1 tags after filtering in treatment: 1443716 INFO @ Tue, 14 Jul 2020 09:40:45: #1 Redundant rate of treatment: 0.07 INFO @ Tue, 14 Jul 2020 09:40:45: #1 finished! INFO @ Tue, 14 Jul 2020 09:40:45: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 09:40:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 09:40:46: #2 number of paired peaks: 460 WARNING @ Tue, 14 Jul 2020 09:40:46: Fewer paired peaks (460) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 460 pairs to build model! INFO @ Tue, 14 Jul 2020 09:40:46: start model_add_line... INFO @ Tue, 14 Jul 2020 09:40:46: start X-correlation... INFO @ Tue, 14 Jul 2020 09:40:46: end of X-cor INFO @ Tue, 14 Jul 2020 09:40:46: #2 finished! INFO @ Tue, 14 Jul 2020 09:40:46: #2 predicted fragment length is 164 bps INFO @ Tue, 14 Jul 2020 09:40:46: #2 alternative fragment length(s) may be 164 bps INFO @ Tue, 14 Jul 2020 09:40:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8325345/SRX8325345.20_model.r WARNING @ Tue, 14 Jul 2020 09:40:46: #2 Since the d (164) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 09:40:46: #2 You may need to consider one of the other alternative d(s): 164 WARNING @ Tue, 14 Jul 2020 09:40:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 09:40:46: #3 Call peaks... INFO @ Tue, 14 Jul 2020 09:40:46: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 09:40:50: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 09:40:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8325345/SRX8325345.20_peaks.xls INFO @ Tue, 14 Jul 2020 09:40:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8325345/SRX8325345.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 09:40:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8325345/SRX8325345.20_summits.bed INFO @ Tue, 14 Jul 2020 09:40:51: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (176 records, 4 fields): 1 millis CompletedMACS2peakCalling