Job ID = 6454693 SRX = SRX2520642 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:13:54 prefetch.2.10.7: 1) Downloading 'SRR5206761'... 2020-06-21T09:13:54 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:17:04 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:17:05 prefetch.2.10.7: 'SRR5206761' is valid 2020-06-21T09:17:05 prefetch.2.10.7: 1) 'SRR5206761' was downloaded successfully Read 22611246 spots for SRR5206761/SRR5206761.sra Written 22611246 spots for SRR5206761/SRR5206761.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: 00:06:49 22611246 reads; of these: 22611246 (100.00%) were unpaired; of these: 1095622 (4.85%) aligned 0 times 16314594 (72.15%) aligned exactly 1 time 5201030 (23.00%) aligned >1 times 95.15% overall alignment rate Time searching: 00:06:49 Overall time: 00:06:49 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] 2334732 / 21515624 = 0.1085 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 18:31:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2520642/SRX2520642.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2520642/SRX2520642.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2520642/SRX2520642.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2520642/SRX2520642.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 18:31:05: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:31:05: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:31:11: 1000000 INFO @ Sun, 21 Jun 2020 18:31:18: 2000000 INFO @ Sun, 21 Jun 2020 18:31:25: 3000000 INFO @ Sun, 21 Jun 2020 18:31:31: 4000000 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 18:31:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2520642/SRX2520642.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2520642/SRX2520642.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2520642/SRX2520642.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2520642/SRX2520642.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 18:31:35: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:31:35: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:31:38: 5000000 INFO @ Sun, 21 Jun 2020 18:31:42: 1000000 INFO @ Sun, 21 Jun 2020 18:31:45: 6000000 INFO @ Sun, 21 Jun 2020 18:31:49: 2000000 INFO @ Sun, 21 Jun 2020 18:31:52: 7000000 INFO @ Sun, 21 Jun 2020 18:31:57: 3000000 INFO @ Sun, 21 Jun 2020 18:31:59: 8000000 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 18:32:04: 4000000 INFO @ Sun, 21 Jun 2020 18:32:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2520642/SRX2520642.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2520642/SRX2520642.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2520642/SRX2520642.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2520642/SRX2520642.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 18:32:05: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:32:05: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:32:06: 9000000 INFO @ Sun, 21 Jun 2020 18:32:11: 5000000 INFO @ Sun, 21 Jun 2020 18:32:11: 1000000 INFO @ Sun, 21 Jun 2020 18:32:13: 10000000 INFO @ Sun, 21 Jun 2020 18:32:17: 2000000 INFO @ Sun, 21 Jun 2020 18:32:18: 6000000 INFO @ Sun, 21 Jun 2020 18:32:20: 11000000 INFO @ Sun, 21 Jun 2020 18:32:23: 3000000 INFO @ Sun, 21 Jun 2020 18:32:25: 7000000 INFO @ Sun, 21 Jun 2020 18:32:27: 12000000 INFO @ Sun, 21 Jun 2020 18:32:29: 4000000 INFO @ Sun, 21 Jun 2020 18:32:32: 8000000 INFO @ Sun, 21 Jun 2020 18:32:33: 13000000 INFO @ Sun, 21 Jun 2020 18:32:36: 5000000 INFO @ Sun, 21 Jun 2020 18:32:38: 9000000 INFO @ Sun, 21 Jun 2020 18:32:40: 14000000 INFO @ Sun, 21 Jun 2020 18:32:42: 6000000 INFO @ Sun, 21 Jun 2020 18:32:45: 10000000 INFO @ Sun, 21 Jun 2020 18:32:47: 15000000 INFO @ Sun, 21 Jun 2020 18:32:48: 7000000 INFO @ Sun, 21 Jun 2020 18:32:52: 11000000 INFO @ Sun, 21 Jun 2020 18:32:53: 8000000 INFO @ Sun, 21 Jun 2020 18:32:55: 16000000 INFO @ Sun, 21 Jun 2020 18:32:59: 12000000 INFO @ Sun, 21 Jun 2020 18:32:59: 9000000 INFO @ Sun, 21 Jun 2020 18:33:01: 17000000 INFO @ Sun, 21 Jun 2020 18:33:05: 10000000 INFO @ Sun, 21 Jun 2020 18:33:06: 13000000 INFO @ Sun, 21 Jun 2020 18:33:08: 18000000 INFO @ Sun, 21 Jun 2020 18:33:11: 11000000 INFO @ Sun, 21 Jun 2020 18:33:13: 14000000 INFO @ Sun, 21 Jun 2020 18:33:15: 19000000 INFO @ Sun, 21 Jun 2020 18:33:17: 12000000 INFO @ Sun, 21 Jun 2020 18:33:17: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:33:17: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:33:17: #1 total tags in treatment: 19180892 INFO @ Sun, 21 Jun 2020 18:33:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:33:17: #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 18:33:18: #1 tags after filtering in treatment: 19180823 INFO @ Sun, 21 Jun 2020 18:33:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:33:18: #1 finished! INFO @ Sun, 21 Jun 2020 18:33:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:33:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:33:19: #2 number of paired peaks: 348 WARNING @ Sun, 21 Jun 2020 18:33:19: Fewer paired peaks (348) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 348 pairs to build model! INFO @ Sun, 21 Jun 2020 18:33:19: start model_add_line... INFO @ Sun, 21 Jun 2020 18:33:19: start X-correlation... INFO @ Sun, 21 Jun 2020 18:33:19: end of X-cor INFO @ Sun, 21 Jun 2020 18:33:19: #2 finished! INFO @ Sun, 21 Jun 2020 18:33:19: #2 predicted fragment length is 50 bps INFO @ Sun, 21 Jun 2020 18:33:19: #2 alternative fragment length(s) may be 2,50,532,582 bps INFO @ Sun, 21 Jun 2020 18:33:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2520642/SRX2520642.05_model.r WARNING @ Sun, 21 Jun 2020 18:33:19: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:33:19: #2 You may need to consider one of the other alternative d(s): 2,50,532,582 WARNING @ Sun, 21 Jun 2020 18:33:19: #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 18:33:19: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:33:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:33:19: 15000000 INFO @ Sun, 21 Jun 2020 18:33:23: 13000000 INFO @ Sun, 21 Jun 2020 18:33:27: 16000000 INFO @ Sun, 21 Jun 2020 18:33:29: 14000000 INFO @ Sun, 21 Jun 2020 18:33:34: 17000000 INFO @ Sun, 21 Jun 2020 18:33:34: 15000000 INFO @ Sun, 21 Jun 2020 18:33:41: 18000000 INFO @ Sun, 21 Jun 2020 18:33:41: 16000000 INFO @ Sun, 21 Jun 2020 18:33:47: 17000000 INFO @ Sun, 21 Jun 2020 18:33:49: 19000000 INFO @ Sun, 21 Jun 2020 18:33:50: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:33:50: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:33:50: #1 total tags in treatment: 19180892 INFO @ Sun, 21 Jun 2020 18:33:50: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:33:50: #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 18:33:52: #1 tags after filtering in treatment: 19180823 INFO @ Sun, 21 Jun 2020 18:33:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:33:52: #1 finished! INFO @ Sun, 21 Jun 2020 18:33:52: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:33:52: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:33:53: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:33:53: #2 number of paired peaks: 348 WARNING @ Sun, 21 Jun 2020 18:33:53: Fewer paired peaks (348) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 348 pairs to build model! INFO @ Sun, 21 Jun 2020 18:33:53: start model_add_line... INFO @ Sun, 21 Jun 2020 18:33:53: start X-correlation... INFO @ Sun, 21 Jun 2020 18:33:53: 18000000 INFO @ Sun, 21 Jun 2020 18:33:53: end of X-cor INFO @ Sun, 21 Jun 2020 18:33:53: #2 finished! INFO @ Sun, 21 Jun 2020 18:33:53: #2 predicted fragment length is 50 bps INFO @ Sun, 21 Jun 2020 18:33:53: #2 alternative fragment length(s) may be 2,50,532,582 bps INFO @ Sun, 21 Jun 2020 18:33:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2520642/SRX2520642.10_model.r WARNING @ Sun, 21 Jun 2020 18:33:53: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:33:53: #2 You may need to consider one of the other alternative d(s): 2,50,532,582 WARNING @ Sun, 21 Jun 2020 18:33:53: #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 18:33:53: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:33:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:33:59: 19000000 INFO @ Sun, 21 Jun 2020 18:34:01: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:34:01: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:34:01: #1 total tags in treatment: 19180892 INFO @ Sun, 21 Jun 2020 18:34:01: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:34:01: #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 18:34:01: #1 tags after filtering in treatment: 19180823 INFO @ Sun, 21 Jun 2020 18:34:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:34:01: #1 finished! INFO @ Sun, 21 Jun 2020 18:34:01: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:34:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:34:03: #2 number of paired peaks: 348 WARNING @ Sun, 21 Jun 2020 18:34:03: Fewer paired peaks (348) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 348 pairs to build model! INFO @ Sun, 21 Jun 2020 18:34:03: start model_add_line... INFO @ Sun, 21 Jun 2020 18:34:03: start X-correlation... INFO @ Sun, 21 Jun 2020 18:34:03: end of X-cor INFO @ Sun, 21 Jun 2020 18:34:03: #2 finished! INFO @ Sun, 21 Jun 2020 18:34:03: #2 predicted fragment length is 50 bps INFO @ Sun, 21 Jun 2020 18:34:03: #2 alternative fragment length(s) may be 2,50,532,582 bps INFO @ Sun, 21 Jun 2020 18:34:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2520642/SRX2520642.20_model.r WARNING @ Sun, 21 Jun 2020 18:34:03: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:34:03: #2 You may need to consider one of the other alternative d(s): 2,50,532,582 WARNING @ Sun, 21 Jun 2020 18:34:03: #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 18:34:03: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:34:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:34:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2520642/SRX2520642.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:34:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2520642/SRX2520642.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:34:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2520642/SRX2520642.05_summits.bed INFO @ Sun, 21 Jun 2020 18:34:10: Done! pass1 - making usageList (498 chroms): 2 millis pass2 - checking and writing primary data (2105 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:34:26: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:34:36: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:34:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2520642/SRX2520642.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:34:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2520642/SRX2520642.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:34:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2520642/SRX2520642.10_summits.bed INFO @ Sun, 21 Jun 2020 18:34:43: Done! pass1 - making usageList (342 chroms): 2 millis pass2 - checking and writing primary data (896 records, 4 fields): 20 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:34:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2520642/SRX2520642.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:34:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2520642/SRX2520642.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:34:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2520642/SRX2520642.20_summits.bed INFO @ Sun, 21 Jun 2020 18:34:53: Done! pass1 - making usageList (116 chroms): 1 millis pass2 - checking and writing primary data (265 records, 4 fields): 8 millis CompletedMACS2peakCalling