Job ID = 6456660 SRX = SRX3909722 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:04:31 prefetch.2.10.7: 1) Downloading 'SRR6967849'... 2020-06-21T11:04:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:11:39 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:11:39 prefetch.2.10.7: 1) 'SRR6967849' was downloaded successfully Read 26707041 spots for SRR6967849/SRR6967849.sra Written 26707041 spots for SRR6967849/SRR6967849.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: 00:05:56 26707041 reads; of these: 26707041 (100.00%) were unpaired; of these: 8888805 (33.28%) aligned 0 times 13655166 (51.13%) aligned exactly 1 time 4163070 (15.59%) aligned >1 times 66.72% overall alignment rate Time searching: 00:05:56 Overall time: 00:05:56 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 8 files... [bam_rmdupse_core] 5544092 / 17818236 = 0.3111 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 20:23:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3909722/SRX3909722.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3909722/SRX3909722.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3909722/SRX3909722.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3909722/SRX3909722.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 20:23:14: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:23:14: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:23:19: 1000000 INFO @ Sun, 21 Jun 2020 20:23:25: 2000000 INFO @ Sun, 21 Jun 2020 20:23:31: 3000000 INFO @ Sun, 21 Jun 2020 20:23:36: 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 20:23:42: 5000000 INFO @ Sun, 21 Jun 2020 20:23:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3909722/SRX3909722.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3909722/SRX3909722.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3909722/SRX3909722.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3909722/SRX3909722.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 20:23:44: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:23:44: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:23:48: 6000000 INFO @ Sun, 21 Jun 2020 20:23:50: 1000000 INFO @ Sun, 21 Jun 2020 20:23:54: 7000000 INFO @ Sun, 21 Jun 2020 20:23:56: 2000000 INFO @ Sun, 21 Jun 2020 20:24:00: 8000000 INFO @ Sun, 21 Jun 2020 20:24:02: 3000000 INFO @ Sun, 21 Jun 2020 20:24:07: 9000000 INFO @ Sun, 21 Jun 2020 20:24:09: 4000000 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 20:24:13: 10000000 INFO @ Sun, 21 Jun 2020 20:24:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3909722/SRX3909722.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3909722/SRX3909722.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3909722/SRX3909722.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3909722/SRX3909722.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 20:24:14: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:24:14: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:24:15: 5000000 INFO @ Sun, 21 Jun 2020 20:24:19: 11000000 INFO @ Sun, 21 Jun 2020 20:24:20: 1000000 INFO @ Sun, 21 Jun 2020 20:24:21: 6000000 INFO @ Sun, 21 Jun 2020 20:24:25: 12000000 INFO @ Sun, 21 Jun 2020 20:24:26: 2000000 INFO @ Sun, 21 Jun 2020 20:24:27: 7000000 INFO @ Sun, 21 Jun 2020 20:24:27: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:24:27: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:24:27: #1 total tags in treatment: 12274144 INFO @ Sun, 21 Jun 2020 20:24:27: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:24:27: #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 20:24:28: #1 tags after filtering in treatment: 12274142 INFO @ Sun, 21 Jun 2020 20:24:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:24:28: #1 finished! INFO @ Sun, 21 Jun 2020 20:24:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:24:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:24:28: #2 number of paired peaks: 314 WARNING @ Sun, 21 Jun 2020 20:24:28: Fewer paired peaks (314) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 314 pairs to build model! INFO @ Sun, 21 Jun 2020 20:24:28: start model_add_line... INFO @ Sun, 21 Jun 2020 20:24:29: start X-correlation... INFO @ Sun, 21 Jun 2020 20:24:29: end of X-cor INFO @ Sun, 21 Jun 2020 20:24:29: #2 finished! INFO @ Sun, 21 Jun 2020 20:24:29: #2 predicted fragment length is 69 bps INFO @ Sun, 21 Jun 2020 20:24:29: #2 alternative fragment length(s) may be 4,69 bps INFO @ Sun, 21 Jun 2020 20:24:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3909722/SRX3909722.05_model.r WARNING @ Sun, 21 Jun 2020 20:24:29: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:24:29: #2 You may need to consider one of the other alternative d(s): 4,69 WARNING @ Sun, 21 Jun 2020 20:24:29: #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 20:24:29: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:24:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:24:32: 3000000 INFO @ Sun, 21 Jun 2020 20:24:33: 8000000 INFO @ Sun, 21 Jun 2020 20:24:38: 4000000 INFO @ Sun, 21 Jun 2020 20:24:40: 9000000 INFO @ Sun, 21 Jun 2020 20:24:45: 5000000 INFO @ Sun, 21 Jun 2020 20:24:47: 10000000 INFO @ Sun, 21 Jun 2020 20:24:51: 6000000 INFO @ Sun, 21 Jun 2020 20:24:52: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:24:53: 11000000 INFO @ Sun, 21 Jun 2020 20:24:58: 7000000 INFO @ Sun, 21 Jun 2020 20:25:00: 12000000 INFO @ Sun, 21 Jun 2020 20:25:02: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:25:02: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:25:02: #1 total tags in treatment: 12274144 INFO @ Sun, 21 Jun 2020 20:25:02: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:25:02: #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 20:25:02: #1 tags after filtering in treatment: 12274142 INFO @ Sun, 21 Jun 2020 20:25:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:25:02: #1 finished! INFO @ Sun, 21 Jun 2020 20:25:02: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:25:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:25:03: #2 number of paired peaks: 314 WARNING @ Sun, 21 Jun 2020 20:25:03: Fewer paired peaks (314) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 314 pairs to build model! INFO @ Sun, 21 Jun 2020 20:25:03: start model_add_line... INFO @ Sun, 21 Jun 2020 20:25:03: start X-correlation... INFO @ Sun, 21 Jun 2020 20:25:03: end of X-cor INFO @ Sun, 21 Jun 2020 20:25:03: #2 finished! INFO @ Sun, 21 Jun 2020 20:25:03: #2 predicted fragment length is 69 bps INFO @ Sun, 21 Jun 2020 20:25:03: #2 alternative fragment length(s) may be 4,69 bps INFO @ Sun, 21 Jun 2020 20:25:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3909722/SRX3909722.10_model.r WARNING @ Sun, 21 Jun 2020 20:25:03: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:25:03: #2 You may need to consider one of the other alternative d(s): 4,69 WARNING @ Sun, 21 Jun 2020 20:25:03: #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 20:25:03: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:25:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:25:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3909722/SRX3909722.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:25:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3909722/SRX3909722.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:25:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3909722/SRX3909722.05_summits.bed INFO @ Sun, 21 Jun 2020 20:25:04: Done! pass1 - making usageList (612 chroms): 1 millis pass2 - checking and writing primary data (2206 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:25:04: 8000000 INFO @ Sun, 21 Jun 2020 20:25:10: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:25:16: 10000000 INFO @ Sun, 21 Jun 2020 20:25:22: 11000000 INFO @ Sun, 21 Jun 2020 20:25:27: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:25:27: 12000000 INFO @ Sun, 21 Jun 2020 20:25:29: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:25:29: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:25:29: #1 total tags in treatment: 12274144 INFO @ Sun, 21 Jun 2020 20:25:29: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:25:29: #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 20:25:30: #1 tags after filtering in treatment: 12274142 INFO @ Sun, 21 Jun 2020 20:25:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:25:30: #1 finished! INFO @ Sun, 21 Jun 2020 20:25:30: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:25:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:25:30: #2 number of paired peaks: 314 WARNING @ Sun, 21 Jun 2020 20:25:30: Fewer paired peaks (314) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 314 pairs to build model! INFO @ Sun, 21 Jun 2020 20:25:30: start model_add_line... INFO @ Sun, 21 Jun 2020 20:25:30: start X-correlation... INFO @ Sun, 21 Jun 2020 20:25:30: end of X-cor INFO @ Sun, 21 Jun 2020 20:25:30: #2 finished! INFO @ Sun, 21 Jun 2020 20:25:30: #2 predicted fragment length is 69 bps INFO @ Sun, 21 Jun 2020 20:25:30: #2 alternative fragment length(s) may be 4,69 bps INFO @ Sun, 21 Jun 2020 20:25:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3909722/SRX3909722.20_model.r WARNING @ Sun, 21 Jun 2020 20:25:30: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:25:30: #2 You may need to consider one of the other alternative d(s): 4,69 WARNING @ Sun, 21 Jun 2020 20:25:30: #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 20:25:30: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:25:30: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:25:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3909722/SRX3909722.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:25:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3909722/SRX3909722.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:25:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3909722/SRX3909722.10_summits.bed INFO @ Sun, 21 Jun 2020 20:25:39: Done! pass1 - making usageList (453 chroms): 1 millis pass2 - checking and writing primary data (1205 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:25:54: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:26:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3909722/SRX3909722.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:26:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3909722/SRX3909722.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:26:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3909722/SRX3909722.20_summits.bed INFO @ Sun, 21 Jun 2020 20:26:06: Done! pass1 - making usageList (179 chroms): 1 millis pass2 - checking and writing primary data (349 records, 4 fields): 7 millis CompletedMACS2peakCalling