Job ID = 6454124 SRX = SRX1837976 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:06:39 prefetch.2.10.7: 1) Downloading 'SRR3658917'... 2020-06-21T09:06:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:11:17 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:11:17 prefetch.2.10.7: 1) 'SRR3658917' was downloaded successfully 2020-06-21T09:11:17 prefetch.2.10.7: 'SRR3658917' has 0 unresolved dependencies Read 15707161 spots for SRR3658917/SRR3658917.sra Written 15707161 spots for SRR3658917/SRR3658917.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:11:20 15707161 reads; of these: 15707161 (100.00%) were unpaired; of these: 605829 (3.86%) aligned 0 times 12247585 (77.97%) aligned exactly 1 time 2853747 (18.17%) aligned >1 times 96.14% overall alignment rate Time searching: 00:11:20 Overall time: 00:11:20 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 2379573 / 15101332 = 0.1576 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 @ Sun, 21 Jun 2020 18:29:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1837976/SRX1837976.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1837976/SRX1837976.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1837976/SRX1837976.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1837976/SRX1837976.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 @ Sun, 21 Jun 2020 18:29:15: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:29:15: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:29:25: 1000000 INFO @ Sun, 21 Jun 2020 18:29:36: 2000000 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 @ Sun, 21 Jun 2020 18:29:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1837976/SRX1837976.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1837976/SRX1837976.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1837976/SRX1837976.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1837976/SRX1837976.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 @ Sun, 21 Jun 2020 18:29:45: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:29:45: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:29:46: 3000000 INFO @ Sun, 21 Jun 2020 18:29:56: 1000000 INFO @ Sun, 21 Jun 2020 18:29:57: 4000000 INFO @ Sun, 21 Jun 2020 18:30:06: 2000000 INFO @ Sun, 21 Jun 2020 18:30:09: 5000000 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 @ Sun, 21 Jun 2020 18:30:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1837976/SRX1837976.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1837976/SRX1837976.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1837976/SRX1837976.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1837976/SRX1837976.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 @ Sun, 21 Jun 2020 18:30:15: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:30:15: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:30:17: 3000000 INFO @ Sun, 21 Jun 2020 18:30:20: 6000000 INFO @ Sun, 21 Jun 2020 18:30:27: 1000000 INFO @ Sun, 21 Jun 2020 18:30:29: 4000000 INFO @ Sun, 21 Jun 2020 18:30:32: 7000000 INFO @ Sun, 21 Jun 2020 18:30:39: 2000000 INFO @ Sun, 21 Jun 2020 18:30:41: 5000000 INFO @ Sun, 21 Jun 2020 18:30:43: 8000000 INFO @ Sun, 21 Jun 2020 18:30:51: 3000000 INFO @ Sun, 21 Jun 2020 18:30:53: 6000000 INFO @ Sun, 21 Jun 2020 18:30:54: 9000000 INFO @ Sun, 21 Jun 2020 18:31:03: 4000000 INFO @ Sun, 21 Jun 2020 18:31:04: 7000000 INFO @ Sun, 21 Jun 2020 18:31:06: 10000000 INFO @ Sun, 21 Jun 2020 18:31:14: 5000000 INFO @ Sun, 21 Jun 2020 18:31:16: 8000000 INFO @ Sun, 21 Jun 2020 18:31:18: 11000000 INFO @ Sun, 21 Jun 2020 18:31:26: 6000000 INFO @ Sun, 21 Jun 2020 18:31:28: 9000000 INFO @ Sun, 21 Jun 2020 18:31:29: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:31:38: #1 tag size is determined as 149 bps INFO @ Sun, 21 Jun 2020 18:31:38: #1 tag size = 149 INFO @ Sun, 21 Jun 2020 18:31:38: #1 total tags in treatment: 12721759 INFO @ Sun, 21 Jun 2020 18:31:38: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:31:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:31:38: 7000000 INFO @ Sun, 21 Jun 2020 18:31:38: #1 tags after filtering in treatment: 12721624 INFO @ Sun, 21 Jun 2020 18:31:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:31:38: #1 finished! INFO @ Sun, 21 Jun 2020 18:31:38: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:31:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:31:39: #2 number of paired peaks: 826 WARNING @ Sun, 21 Jun 2020 18:31:39: Fewer paired peaks (826) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 826 pairs to build model! INFO @ Sun, 21 Jun 2020 18:31:39: start model_add_line... INFO @ Sun, 21 Jun 2020 18:31:39: start X-correlation... INFO @ Sun, 21 Jun 2020 18:31:39: end of X-cor INFO @ Sun, 21 Jun 2020 18:31:39: #2 finished! INFO @ Sun, 21 Jun 2020 18:31:39: #2 predicted fragment length is 154 bps INFO @ Sun, 21 Jun 2020 18:31:39: #2 alternative fragment length(s) may be 154 bps INFO @ Sun, 21 Jun 2020 18:31:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1837976/SRX1837976.05_model.r WARNING @ Sun, 21 Jun 2020 18:31:39: #2 Since the d (154) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:31:39: #2 You may need to consider one of the other alternative d(s): 154 WARNING @ Sun, 21 Jun 2020 18:31:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 18:31:39: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:31:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:31:39: 10000000 INFO @ Sun, 21 Jun 2020 18:31:48: 8000000 INFO @ Sun, 21 Jun 2020 18:31:49: 11000000 INFO @ Sun, 21 Jun 2020 18:31:57: 9000000 INFO @ Sun, 21 Jun 2020 18:31:59: 12000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:32:06: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:32:06: #1 tag size is determined as 149 bps INFO @ Sun, 21 Jun 2020 18:32:06: #1 tag size = 149 INFO @ Sun, 21 Jun 2020 18:32:06: #1 total tags in treatment: 12721759 INFO @ Sun, 21 Jun 2020 18:32:06: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:32:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:32:06: #1 tags after filtering in treatment: 12721624 INFO @ Sun, 21 Jun 2020 18:32:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:32:06: #1 finished! INFO @ Sun, 21 Jun 2020 18:32:06: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:32:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:32:07: 10000000 INFO @ Sun, 21 Jun 2020 18:32:07: #2 number of paired peaks: 826 WARNING @ Sun, 21 Jun 2020 18:32:07: Fewer paired peaks (826) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 826 pairs to build model! INFO @ Sun, 21 Jun 2020 18:32:07: start model_add_line... INFO @ Sun, 21 Jun 2020 18:32:07: start X-correlation... INFO @ Sun, 21 Jun 2020 18:32:07: end of X-cor INFO @ Sun, 21 Jun 2020 18:32:07: #2 finished! INFO @ Sun, 21 Jun 2020 18:32:07: #2 predicted fragment length is 154 bps INFO @ Sun, 21 Jun 2020 18:32:07: #2 alternative fragment length(s) may be 154 bps INFO @ Sun, 21 Jun 2020 18:32:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1837976/SRX1837976.10_model.r WARNING @ Sun, 21 Jun 2020 18:32:07: #2 Since the d (154) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:32:07: #2 You may need to consider one of the other alternative d(s): 154 WARNING @ Sun, 21 Jun 2020 18:32:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 18:32:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:32:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:32:15: 11000000 INFO @ Sun, 21 Jun 2020 18:32:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1837976/SRX1837976.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:32:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1837976/SRX1837976.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:32:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1837976/SRX1837976.05_summits.bed INFO @ Sun, 21 Jun 2020 18:32:20: Done! pass1 - making usageList (464 chroms): 4 millis pass2 - checking and writing primary data (25284 records, 4 fields): 32 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:32:24: 12000000 INFO @ Sun, 21 Jun 2020 18:32:30: #1 tag size is determined as 149 bps INFO @ Sun, 21 Jun 2020 18:32:30: #1 tag size = 149 INFO @ Sun, 21 Jun 2020 18:32:30: #1 total tags in treatment: 12721759 INFO @ Sun, 21 Jun 2020 18:32:30: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:32:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:32:31: #1 tags after filtering in treatment: 12721624 INFO @ Sun, 21 Jun 2020 18:32:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:32:31: #1 finished! INFO @ Sun, 21 Jun 2020 18:32:31: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:32:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:32:32: #2 number of paired peaks: 826 WARNING @ Sun, 21 Jun 2020 18:32:32: Fewer paired peaks (826) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 826 pairs to build model! INFO @ Sun, 21 Jun 2020 18:32:32: start model_add_line... INFO @ Sun, 21 Jun 2020 18:32:32: start X-correlation... INFO @ Sun, 21 Jun 2020 18:32:32: end of X-cor INFO @ Sun, 21 Jun 2020 18:32:32: #2 finished! INFO @ Sun, 21 Jun 2020 18:32:32: #2 predicted fragment length is 154 bps INFO @ Sun, 21 Jun 2020 18:32:32: #2 alternative fragment length(s) may be 154 bps INFO @ Sun, 21 Jun 2020 18:32:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1837976/SRX1837976.20_model.r WARNING @ Sun, 21 Jun 2020 18:32:32: #2 Since the d (154) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:32:32: #2 You may need to consider one of the other alternative d(s): 154 WARNING @ Sun, 21 Jun 2020 18:32:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 18:32:32: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:32:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:32:36: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:32:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1837976/SRX1837976.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:32:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1837976/SRX1837976.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:32:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1837976/SRX1837976.10_summits.bed INFO @ Sun, 21 Jun 2020 18:32:53: Done! pass1 - making usageList (373 chroms): 2 millis pass2 - checking and writing primary data (10360 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:33:01: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:33:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1837976/SRX1837976.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:33:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1837976/SRX1837976.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:33:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1837976/SRX1837976.20_summits.bed INFO @ Sun, 21 Jun 2020 18:33:17: Done! pass1 - making usageList (289 chroms): 1 millis pass2 - checking and writing primary data (2445 records, 4 fields): 10 millis CompletedMACS2peakCalling