Job ID = 12265529 SRX = SRX7277015 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 16659964 spots for SRR10597280/SRR10597280.sra Written 16659964 spots for SRR10597280/SRR10597280.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265780 ("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: 00:31:43 16659964 reads; of these: 16659964 (100.00%) were paired; of these: 6175548 (37.07%) aligned concordantly 0 times 6486693 (38.94%) aligned concordantly exactly 1 time 3997723 (24.00%) aligned concordantly >1 times ---- 6175548 pairs aligned concordantly 0 times; of these: 1804940 (29.23%) aligned discordantly 1 time ---- 4370608 pairs aligned 0 times concordantly or discordantly; of these: 8741216 mates make up the pairs; of these: 6529350 (74.70%) aligned 0 times 471403 (5.39%) aligned exactly 1 time 1740463 (19.91%) aligned >1 times 80.40% overall alignment rate Time searching: 00:31:43 Overall time: 00:31:43 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 12 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] 1936938 / 12203259 = 0.1587 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 08:13:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7277015/SRX7277015.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7277015/SRX7277015.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7277015/SRX7277015.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7277015/SRX7277015.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, 03 Apr 2021 08:13:07: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:13:07: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:13:15: 1000000 INFO @ Sat, 03 Apr 2021 08:13:23: 2000000 INFO @ Sat, 03 Apr 2021 08:13:31: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 08:13:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7277015/SRX7277015.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7277015/SRX7277015.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7277015/SRX7277015.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7277015/SRX7277015.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, 03 Apr 2021 08:13:37: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:13:37: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:13:39: 4000000 INFO @ Sat, 03 Apr 2021 08:13:45: 1000000 INFO @ Sat, 03 Apr 2021 08:13:47: 5000000 INFO @ Sat, 03 Apr 2021 08:13:53: 2000000 INFO @ Sat, 03 Apr 2021 08:13:55: 6000000 INFO @ Sat, 03 Apr 2021 08:14:00: 3000000 INFO @ Sat, 03 Apr 2021 08:14:03: 7000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 08:14:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7277015/SRX7277015.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7277015/SRX7277015.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7277015/SRX7277015.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7277015/SRX7277015.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, 03 Apr 2021 08:14:07: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:14:07: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:14:08: 4000000 INFO @ Sat, 03 Apr 2021 08:14:12: 8000000 INFO @ Sat, 03 Apr 2021 08:14:16: 1000000 INFO @ Sat, 03 Apr 2021 08:14:17: 5000000 INFO @ Sat, 03 Apr 2021 08:14:21: 9000000 INFO @ Sat, 03 Apr 2021 08:14:25: 2000000 INFO @ Sat, 03 Apr 2021 08:14:26: 6000000 INFO @ Sat, 03 Apr 2021 08:14:29: 10000000 INFO @ Sat, 03 Apr 2021 08:14:35: 3000000 INFO @ Sat, 03 Apr 2021 08:14:36: 7000000 INFO @ Sat, 03 Apr 2021 08:14:38: 11000000 INFO @ Sat, 03 Apr 2021 08:14:44: 4000000 INFO @ Sat, 03 Apr 2021 08:14:45: 8000000 INFO @ Sat, 03 Apr 2021 08:14:46: 12000000 INFO @ Sat, 03 Apr 2021 08:14:54: 5000000 INFO @ Sat, 03 Apr 2021 08:14:55: 9000000 INFO @ Sat, 03 Apr 2021 08:14:55: 13000000 INFO @ Sat, 03 Apr 2021 08:15:03: 6000000 INFO @ Sat, 03 Apr 2021 08:15:03: 14000000 INFO @ Sat, 03 Apr 2021 08:15:04: 10000000 INFO @ Sat, 03 Apr 2021 08:15:12: 7000000 INFO @ Sat, 03 Apr 2021 08:15:12: 15000000 INFO @ Sat, 03 Apr 2021 08:15:13: 11000000 INFO @ Sat, 03 Apr 2021 08:15:20: 16000000 INFO @ Sat, 03 Apr 2021 08:15:20: 8000000 INFO @ Sat, 03 Apr 2021 08:15:21: 12000000 INFO @ Sat, 03 Apr 2021 08:15:28: 17000000 INFO @ Sat, 03 Apr 2021 08:15:29: 9000000 INFO @ Sat, 03 Apr 2021 08:15:30: 13000000 INFO @ Sat, 03 Apr 2021 08:15:37: 18000000 INFO @ Sat, 03 Apr 2021 08:15:38: 10000000 INFO @ Sat, 03 Apr 2021 08:15:39: 14000000 INFO @ Sat, 03 Apr 2021 08:15:46: 19000000 INFO @ Sat, 03 Apr 2021 08:15:47: 11000000 INFO @ Sat, 03 Apr 2021 08:15:48: 15000000 INFO @ Sat, 03 Apr 2021 08:15:55: 20000000 INFO @ Sat, 03 Apr 2021 08:15:56: 12000000 INFO @ Sat, 03 Apr 2021 08:15:57: 16000000 INFO @ Sat, 03 Apr 2021 08:16:03: 21000000 INFO @ Sat, 03 Apr 2021 08:16:05: 13000000 INFO @ Sat, 03 Apr 2021 08:16:06: 17000000 INFO @ Sat, 03 Apr 2021 08:16:12: 22000000 INFO @ Sat, 03 Apr 2021 08:16:14: 14000000 INFO @ Sat, 03 Apr 2021 08:16:15: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 08:16:20: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 08:16:20: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 08:16:20: #1 total tags in treatment: 8594664 INFO @ Sat, 03 Apr 2021 08:16:20: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:16:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 08:16:20: #1 tags after filtering in treatment: 7003806 INFO @ Sat, 03 Apr 2021 08:16:20: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 03 Apr 2021 08:16:20: #1 finished! INFO @ Sat, 03 Apr 2021 08:16:20: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:16:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:16:20: #2 number of paired peaks: 611 WARNING @ Sat, 03 Apr 2021 08:16:20: Fewer paired peaks (611) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 611 pairs to build model! INFO @ Sat, 03 Apr 2021 08:16:20: start model_add_line... INFO @ Sat, 03 Apr 2021 08:16:20: start X-correlation... INFO @ Sat, 03 Apr 2021 08:16:20: end of X-cor INFO @ Sat, 03 Apr 2021 08:16:20: #2 finished! INFO @ Sat, 03 Apr 2021 08:16:20: #2 predicted fragment length is 89 bps INFO @ Sat, 03 Apr 2021 08:16:20: #2 alternative fragment length(s) may be 89 bps INFO @ Sat, 03 Apr 2021 08:16:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7277015/SRX7277015.05_model.r WARNING @ Sat, 03 Apr 2021 08:16:20: #2 Since the d (89) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:16:20: #2 You may need to consider one of the other alternative d(s): 89 WARNING @ Sat, 03 Apr 2021 08:16:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 08:16:20: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:16:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:16:23: 15000000 INFO @ Sat, 03 Apr 2021 08:16:24: 19000000 INFO @ Sat, 03 Apr 2021 08:16:31: 16000000 INFO @ Sat, 03 Apr 2021 08:16:32: 20000000 INFO @ Sat, 03 Apr 2021 08:16:34: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:16:38: 17000000 INFO @ Sat, 03 Apr 2021 08:16:40: 21000000 INFO @ Sat, 03 Apr 2021 08:16:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7277015/SRX7277015.05_peaks.xls INFO @ Sat, 03 Apr 2021 08:16:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7277015/SRX7277015.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:16:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7277015/SRX7277015.05_summits.bed INFO @ Sat, 03 Apr 2021 08:16:42: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2645 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 08:16:46: 18000000 INFO @ Sat, 03 Apr 2021 08:16:49: 22000000 INFO @ Sat, 03 Apr 2021 08:16:54: 19000000 INFO @ Sat, 03 Apr 2021 08:16:56: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 08:16:56: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 08:16:56: #1 total tags in treatment: 8594664 INFO @ Sat, 03 Apr 2021 08:16:56: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:16:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 08:16:56: #1 tags after filtering in treatment: 7003806 INFO @ Sat, 03 Apr 2021 08:16:56: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 03 Apr 2021 08:16:56: #1 finished! INFO @ Sat, 03 Apr 2021 08:16:56: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:16:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:16:57: #2 number of paired peaks: 611 WARNING @ Sat, 03 Apr 2021 08:16:57: Fewer paired peaks (611) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 611 pairs to build model! INFO @ Sat, 03 Apr 2021 08:16:57: start model_add_line... INFO @ Sat, 03 Apr 2021 08:16:57: start X-correlation... INFO @ Sat, 03 Apr 2021 08:16:57: end of X-cor INFO @ Sat, 03 Apr 2021 08:16:57: #2 finished! INFO @ Sat, 03 Apr 2021 08:16:57: #2 predicted fragment length is 89 bps INFO @ Sat, 03 Apr 2021 08:16:57: #2 alternative fragment length(s) may be 89 bps INFO @ Sat, 03 Apr 2021 08:16:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7277015/SRX7277015.10_model.r WARNING @ Sat, 03 Apr 2021 08:16:57: #2 Since the d (89) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:16:57: #2 You may need to consider one of the other alternative d(s): 89 WARNING @ Sat, 03 Apr 2021 08:16:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 08:16:57: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:16:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:17:01: 20000000 BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 08:17:09: 21000000 INFO @ Sat, 03 Apr 2021 08:17:11: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:17:16: 22000000 INFO @ Sat, 03 Apr 2021 08:17:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7277015/SRX7277015.10_peaks.xls INFO @ Sat, 03 Apr 2021 08:17:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7277015/SRX7277015.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:17:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7277015/SRX7277015.10_summits.bed INFO @ Sat, 03 Apr 2021 08:17:18: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (704 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 08:17:23: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 08:17:23: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 08:17:23: #1 total tags in treatment: 8594664 INFO @ Sat, 03 Apr 2021 08:17:23: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:17:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 08:17:23: #1 tags after filtering in treatment: 7003806 INFO @ Sat, 03 Apr 2021 08:17:23: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 03 Apr 2021 08:17:23: #1 finished! INFO @ Sat, 03 Apr 2021 08:17:23: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:17:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:17:24: #2 number of paired peaks: 611 WARNING @ Sat, 03 Apr 2021 08:17:24: Fewer paired peaks (611) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 611 pairs to build model! INFO @ Sat, 03 Apr 2021 08:17:24: start model_add_line... INFO @ Sat, 03 Apr 2021 08:17:24: start X-correlation... INFO @ Sat, 03 Apr 2021 08:17:24: end of X-cor INFO @ Sat, 03 Apr 2021 08:17:24: #2 finished! INFO @ Sat, 03 Apr 2021 08:17:24: #2 predicted fragment length is 89 bps INFO @ Sat, 03 Apr 2021 08:17:24: #2 alternative fragment length(s) may be 89 bps INFO @ Sat, 03 Apr 2021 08:17:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7277015/SRX7277015.20_model.r WARNING @ Sat, 03 Apr 2021 08:17:24: #2 Since the d (89) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:17:24: #2 You may need to consider one of the other alternative d(s): 89 WARNING @ Sat, 03 Apr 2021 08:17:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 08:17:24: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:17:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:17:38: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:17:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7277015/SRX7277015.20_peaks.xls INFO @ Sat, 03 Apr 2021 08:17:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7277015/SRX7277015.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:17:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7277015/SRX7277015.20_summits.bed INFO @ Sat, 03 Apr 2021 08:17:45: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (169 records, 4 fields): 1 millis CompletedMACS2peakCalling