Job ID = 14167075 SRX = SRX10412057 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 15734888 spots for SRR14035721/SRR14035721.sra Written 15734888 spots for SRR14035721/SRR14035721.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167658 ("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: 01:07:14 15734888 reads; of these: 15734888 (100.00%) were paired; of these: 1665829 (10.59%) aligned concordantly 0 times 9698775 (61.64%) aligned concordantly exactly 1 time 4370284 (27.77%) aligned concordantly >1 times ---- 1665829 pairs aligned concordantly 0 times; of these: 270078 (16.21%) aligned discordantly 1 time ---- 1395751 pairs aligned 0 times concordantly or discordantly; of these: 2791502 mates make up the pairs; of these: 2087561 (74.78%) aligned 0 times 264080 (9.46%) aligned exactly 1 time 439861 (15.76%) aligned >1 times 93.37% overall alignment rate Time searching: 01:07:14 Overall time: 01:07:14 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 24 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] 3242587 / 14282893 = 0.2270 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 @ Fri, 10 Dec 2021 10:55:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10412057/SRX10412057.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10412057/SRX10412057.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10412057/SRX10412057.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10412057/SRX10412057.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 @ Fri, 10 Dec 2021 10:55:39: #1 read tag files... INFO @ Fri, 10 Dec 2021 10:55:39: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 10:55:47: 1000000 INFO @ Fri, 10 Dec 2021 10:55:55: 2000000 INFO @ Fri, 10 Dec 2021 10:56:03: 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 @ Fri, 10 Dec 2021 10:56:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10412057/SRX10412057.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10412057/SRX10412057.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10412057/SRX10412057.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10412057/SRX10412057.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 @ Fri, 10 Dec 2021 10:56:09: #1 read tag files... INFO @ Fri, 10 Dec 2021 10:56:09: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 10:56:12: 4000000 INFO @ Fri, 10 Dec 2021 10:56:19: 1000000 INFO @ Fri, 10 Dec 2021 10:56:22: 5000000 INFO @ Fri, 10 Dec 2021 10:56:28: 2000000 INFO @ Fri, 10 Dec 2021 10:56:31: 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 @ Fri, 10 Dec 2021 10:56:38: 3000000 INFO @ Fri, 10 Dec 2021 10:56:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10412057/SRX10412057.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10412057/SRX10412057.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10412057/SRX10412057.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10412057/SRX10412057.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 @ Fri, 10 Dec 2021 10:56:39: #1 read tag files... INFO @ Fri, 10 Dec 2021 10:56:39: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 10:56:41: 7000000 INFO @ Fri, 10 Dec 2021 10:56:49: 4000000 INFO @ Fri, 10 Dec 2021 10:56:52: 1000000 INFO @ Fri, 10 Dec 2021 10:56:52: 8000000 INFO @ Fri, 10 Dec 2021 10:57:00: 5000000 INFO @ Fri, 10 Dec 2021 10:57:03: 9000000 INFO @ Fri, 10 Dec 2021 10:57:05: 2000000 INFO @ Fri, 10 Dec 2021 10:57:11: 6000000 INFO @ Fri, 10 Dec 2021 10:57:14: 10000000 INFO @ Fri, 10 Dec 2021 10:57:18: 3000000 INFO @ Fri, 10 Dec 2021 10:57:22: 7000000 INFO @ Fri, 10 Dec 2021 10:57:25: 11000000 INFO @ Fri, 10 Dec 2021 10:57:30: 4000000 INFO @ Fri, 10 Dec 2021 10:57:33: 8000000 INFO @ Fri, 10 Dec 2021 10:57:36: 12000000 INFO @ Fri, 10 Dec 2021 10:57:43: 5000000 INFO @ Fri, 10 Dec 2021 10:57:45: 9000000 INFO @ Fri, 10 Dec 2021 10:57:47: 13000000 INFO @ Fri, 10 Dec 2021 10:57:56: 6000000 INFO @ Fri, 10 Dec 2021 10:57:56: 10000000 INFO @ Fri, 10 Dec 2021 10:57:58: 14000000 INFO @ Fri, 10 Dec 2021 10:58:07: 11000000 INFO @ Fri, 10 Dec 2021 10:58:08: 7000000 INFO @ Fri, 10 Dec 2021 10:58:10: 15000000 INFO @ Fri, 10 Dec 2021 10:58:18: 12000000 INFO @ Fri, 10 Dec 2021 10:58:20: 16000000 INFO @ Fri, 10 Dec 2021 10:58:21: 8000000 INFO @ Fri, 10 Dec 2021 10:58:29: 13000000 INFO @ Fri, 10 Dec 2021 10:58:31: 17000000 INFO @ Fri, 10 Dec 2021 10:58:33: 9000000 INFO @ Fri, 10 Dec 2021 10:58:39: 14000000 INFO @ Fri, 10 Dec 2021 10:58:42: 18000000 INFO @ Fri, 10 Dec 2021 10:58:46: 10000000 INFO @ Fri, 10 Dec 2021 10:58:50: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 10:58:53: 19000000 INFO @ Fri, 10 Dec 2021 10:58:58: 11000000 INFO @ Fri, 10 Dec 2021 10:59:01: 16000000 INFO @ Fri, 10 Dec 2021 10:59:04: 20000000 INFO @ Fri, 10 Dec 2021 10:59:10: 12000000 INFO @ Fri, 10 Dec 2021 10:59:12: 17000000 INFO @ Fri, 10 Dec 2021 10:59:15: 21000000 INFO @ Fri, 10 Dec 2021 10:59:23: 18000000 INFO @ Fri, 10 Dec 2021 10:59:23: 13000000 INFO @ Fri, 10 Dec 2021 10:59:26: 22000000 INFO @ Fri, 10 Dec 2021 10:59:33: 19000000 INFO @ Fri, 10 Dec 2021 10:59:35: 14000000 INFO @ Fri, 10 Dec 2021 10:59:36: #1 tag size is determined as 150 bps INFO @ Fri, 10 Dec 2021 10:59:36: #1 tag size = 150 INFO @ Fri, 10 Dec 2021 10:59:36: #1 total tags in treatment: 10872469 INFO @ Fri, 10 Dec 2021 10:59:36: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 10:59:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 10:59:36: #1 tags after filtering in treatment: 10225921 INFO @ Fri, 10 Dec 2021 10:59:36: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 10 Dec 2021 10:59:36: #1 finished! INFO @ Fri, 10 Dec 2021 10:59:36: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 10:59:36: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 10:59:36: #2 number of paired peaks: 291 WARNING @ Fri, 10 Dec 2021 10:59:36: Fewer paired peaks (291) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 291 pairs to build model! INFO @ Fri, 10 Dec 2021 10:59:36: start model_add_line... INFO @ Fri, 10 Dec 2021 10:59:36: start X-correlation... INFO @ Fri, 10 Dec 2021 10:59:36: end of X-cor INFO @ Fri, 10 Dec 2021 10:59:36: #2 finished! INFO @ Fri, 10 Dec 2021 10:59:36: #2 predicted fragment length is 183 bps INFO @ Fri, 10 Dec 2021 10:59:36: #2 alternative fragment length(s) may be 183 bps INFO @ Fri, 10 Dec 2021 10:59:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10412057/SRX10412057.05_model.r WARNING @ Fri, 10 Dec 2021 10:59:37: #2 Since the d (183) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 10:59:37: #2 You may need to consider one of the other alternative d(s): 183 WARNING @ Fri, 10 Dec 2021 10:59:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 10:59:37: #3 Call peaks... INFO @ Fri, 10 Dec 2021 10:59:37: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 10:59:44: 20000000 INFO @ Fri, 10 Dec 2021 10:59:48: 15000000 INFO @ Fri, 10 Dec 2021 10:59:54: 21000000 INFO @ Fri, 10 Dec 2021 10:59:58: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:00:00: 16000000 INFO @ Fri, 10 Dec 2021 11:00:04: 22000000 INFO @ Fri, 10 Dec 2021 11:00:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10412057/SRX10412057.05_peaks.xls INFO @ Fri, 10 Dec 2021 11:00:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10412057/SRX10412057.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:00:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10412057/SRX10412057.05_summits.bed INFO @ Fri, 10 Dec 2021 11:00:09: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4014 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:00:12: 17000000 INFO @ Fri, 10 Dec 2021 11:00:13: #1 tag size is determined as 150 bps INFO @ Fri, 10 Dec 2021 11:00:13: #1 tag size = 150 INFO @ Fri, 10 Dec 2021 11:00:13: #1 total tags in treatment: 10872469 INFO @ Fri, 10 Dec 2021 11:00:13: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:00:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 11:00:13: #1 tags after filtering in treatment: 10225921 INFO @ Fri, 10 Dec 2021 11:00:13: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 10 Dec 2021 11:00:13: #1 finished! INFO @ Fri, 10 Dec 2021 11:00:13: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:00:13: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:00:14: #2 number of paired peaks: 291 WARNING @ Fri, 10 Dec 2021 11:00:14: Fewer paired peaks (291) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 291 pairs to build model! INFO @ Fri, 10 Dec 2021 11:00:14: start model_add_line... INFO @ Fri, 10 Dec 2021 11:00:14: start X-correlation... INFO @ Fri, 10 Dec 2021 11:00:14: end of X-cor INFO @ Fri, 10 Dec 2021 11:00:14: #2 finished! INFO @ Fri, 10 Dec 2021 11:00:14: #2 predicted fragment length is 183 bps INFO @ Fri, 10 Dec 2021 11:00:14: #2 alternative fragment length(s) may be 183 bps INFO @ Fri, 10 Dec 2021 11:00:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10412057/SRX10412057.10_model.r WARNING @ Fri, 10 Dec 2021 11:00:14: #2 Since the d (183) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:00:14: #2 You may need to consider one of the other alternative d(s): 183 WARNING @ Fri, 10 Dec 2021 11:00:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 11:00:14: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:00:14: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:00:24: 18000000 INFO @ Fri, 10 Dec 2021 11:00:35: 19000000 INFO @ Fri, 10 Dec 2021 11:00:35: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:00:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10412057/SRX10412057.10_peaks.xls INFO @ Fri, 10 Dec 2021 11:00:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10412057/SRX10412057.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:00:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10412057/SRX10412057.10_summits.bed INFO @ Fri, 10 Dec 2021 11:00:45: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1838 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:00:46: 20000000 INFO @ Fri, 10 Dec 2021 11:00:57: 21000000 INFO @ Fri, 10 Dec 2021 11:01:08: 22000000 INFO @ Fri, 10 Dec 2021 11:01:18: #1 tag size is determined as 150 bps INFO @ Fri, 10 Dec 2021 11:01:18: #1 tag size = 150 INFO @ Fri, 10 Dec 2021 11:01:18: #1 total tags in treatment: 10872469 INFO @ Fri, 10 Dec 2021 11:01:18: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:01:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 11:01:18: #1 tags after filtering in treatment: 10225921 INFO @ Fri, 10 Dec 2021 11:01:18: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 10 Dec 2021 11:01:18: #1 finished! INFO @ Fri, 10 Dec 2021 11:01:18: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:01:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:01:19: #2 number of paired peaks: 291 WARNING @ Fri, 10 Dec 2021 11:01:19: Fewer paired peaks (291) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 291 pairs to build model! INFO @ Fri, 10 Dec 2021 11:01:19: start model_add_line... INFO @ Fri, 10 Dec 2021 11:01:19: start X-correlation... INFO @ Fri, 10 Dec 2021 11:01:19: end of X-cor INFO @ Fri, 10 Dec 2021 11:01:19: #2 finished! INFO @ Fri, 10 Dec 2021 11:01:19: #2 predicted fragment length is 183 bps INFO @ Fri, 10 Dec 2021 11:01:19: #2 alternative fragment length(s) may be 183 bps INFO @ Fri, 10 Dec 2021 11:01:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10412057/SRX10412057.20_model.r WARNING @ Fri, 10 Dec 2021 11:01:19: #2 Since the d (183) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:01:19: #2 You may need to consider one of the other alternative d(s): 183 WARNING @ Fri, 10 Dec 2021 11:01:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 11:01:19: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:01:19: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:01:42: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:01:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10412057/SRX10412057.20_peaks.xls INFO @ Fri, 10 Dec 2021 11:01:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10412057/SRX10412057.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:01:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10412057/SRX10412057.20_summits.bed INFO @ Fri, 10 Dec 2021 11:01:54: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (776 records, 4 fields): 2 millis CompletedMACS2peakCalling