Job ID = 6459415 SRX = SRX6747981 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T13:12:34 prefetch.2.10.7: 1) Downloading 'SRR10009756'... 2020-06-21T13:12:34 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:14:34 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:14:34 prefetch.2.10.7: 1) 'SRR10009756' was downloaded successfully 2020-06-21T13:14:34 prefetch.2.10.7: 'SRR10009756' has 0 unresolved dependencies Read 19970393 spots for SRR10009756/SRR10009756.sra Written 19970393 spots for SRR10009756/SRR10009756.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: 00:07:34 19970393 reads; of these: 19970393 (100.00%) were unpaired; of these: 437676 (2.19%) aligned 0 times 14440314 (72.31%) aligned exactly 1 time 5092403 (25.50%) aligned >1 times 97.81% overall alignment rate Time searching: 00:07:34 Overall time: 00:07:34 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] 2213111 / 19532717 = 0.1133 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 22:29:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6747981/SRX6747981.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6747981/SRX6747981.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6747981/SRX6747981.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6747981/SRX6747981.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 22:29:04: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:29:04: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:29:10: 1000000 INFO @ Sun, 21 Jun 2020 22:29:16: 2000000 INFO @ Sun, 21 Jun 2020 22:29:22: 3000000 INFO @ Sun, 21 Jun 2020 22:29:28: 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 22:29:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6747981/SRX6747981.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6747981/SRX6747981.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6747981/SRX6747981.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6747981/SRX6747981.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 22:29:34: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:29:34: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:29:35: 5000000 INFO @ Sun, 21 Jun 2020 22:29:41: 6000000 INFO @ Sun, 21 Jun 2020 22:29:42: 1000000 INFO @ Sun, 21 Jun 2020 22:29:48: 7000000 INFO @ Sun, 21 Jun 2020 22:29:50: 2000000 INFO @ Sun, 21 Jun 2020 22:29:54: 8000000 INFO @ Sun, 21 Jun 2020 22:29:58: 3000000 INFO @ Sun, 21 Jun 2020 22:30:01: 9000000 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 22:30:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6747981/SRX6747981.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6747981/SRX6747981.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6747981/SRX6747981.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6747981/SRX6747981.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 22:30:04: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:30:04: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:30:06: 4000000 INFO @ Sun, 21 Jun 2020 22:30:08: 10000000 INFO @ Sun, 21 Jun 2020 22:30:11: 1000000 INFO @ Sun, 21 Jun 2020 22:30:13: 5000000 INFO @ Sun, 21 Jun 2020 22:30:14: 11000000 INFO @ Sun, 21 Jun 2020 22:30:17: 2000000 INFO @ Sun, 21 Jun 2020 22:30:21: 12000000 INFO @ Sun, 21 Jun 2020 22:30:21: 6000000 INFO @ Sun, 21 Jun 2020 22:30:24: 3000000 INFO @ Sun, 21 Jun 2020 22:30:28: 13000000 INFO @ Sun, 21 Jun 2020 22:30:29: 7000000 INFO @ Sun, 21 Jun 2020 22:30:31: 4000000 INFO @ Sun, 21 Jun 2020 22:30:34: 14000000 INFO @ Sun, 21 Jun 2020 22:30:37: 8000000 INFO @ Sun, 21 Jun 2020 22:30:37: 5000000 INFO @ Sun, 21 Jun 2020 22:30:41: 15000000 INFO @ Sun, 21 Jun 2020 22:30:44: 6000000 INFO @ Sun, 21 Jun 2020 22:30:45: 9000000 INFO @ Sun, 21 Jun 2020 22:30:48: 16000000 INFO @ Sun, 21 Jun 2020 22:30:51: 7000000 INFO @ Sun, 21 Jun 2020 22:30:53: 10000000 INFO @ Sun, 21 Jun 2020 22:30:55: 17000000 INFO @ Sun, 21 Jun 2020 22:30:57: #1 tag size is determined as 68 bps INFO @ Sun, 21 Jun 2020 22:30:57: #1 tag size = 68 INFO @ Sun, 21 Jun 2020 22:30:57: #1 total tags in treatment: 17319606 INFO @ Sun, 21 Jun 2020 22:30:57: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:30:57: #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 22:30:57: 8000000 INFO @ Sun, 21 Jun 2020 22:30:57: #1 tags after filtering in treatment: 17319489 INFO @ Sun, 21 Jun 2020 22:30:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:30:57: #1 finished! INFO @ Sun, 21 Jun 2020 22:30:57: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:30:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:30:59: #2 number of paired peaks: 877 WARNING @ Sun, 21 Jun 2020 22:30:59: Fewer paired peaks (877) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 877 pairs to build model! INFO @ Sun, 21 Jun 2020 22:30:59: start model_add_line... INFO @ Sun, 21 Jun 2020 22:30:59: start X-correlation... INFO @ Sun, 21 Jun 2020 22:30:59: end of X-cor INFO @ Sun, 21 Jun 2020 22:30:59: #2 finished! INFO @ Sun, 21 Jun 2020 22:30:59: #2 predicted fragment length is 90 bps INFO @ Sun, 21 Jun 2020 22:30:59: #2 alternative fragment length(s) may be 4,90 bps INFO @ Sun, 21 Jun 2020 22:30:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6747981/SRX6747981.05_model.r WARNING @ Sun, 21 Jun 2020 22:30:59: #2 Since the d (90) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:30:59: #2 You may need to consider one of the other alternative d(s): 4,90 WARNING @ Sun, 21 Jun 2020 22:30:59: #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 22:30:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:30:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:31:00: 11000000 INFO @ Sun, 21 Jun 2020 22:31:04: 9000000 INFO @ Sun, 21 Jun 2020 22:31:08: 12000000 INFO @ Sun, 21 Jun 2020 22:31:10: 10000000 INFO @ Sun, 21 Jun 2020 22:31:16: 13000000 INFO @ Sun, 21 Jun 2020 22:31:17: 11000000 INFO @ Sun, 21 Jun 2020 22:31:23: 12000000 INFO @ Sun, 21 Jun 2020 22:31:24: 14000000 INFO @ Sun, 21 Jun 2020 22:31:30: 13000000 INFO @ Sun, 21 Jun 2020 22:31:32: 15000000 INFO @ Sun, 21 Jun 2020 22:31:36: 14000000 INFO @ Sun, 21 Jun 2020 22:31:39: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:31:40: 16000000 INFO @ Sun, 21 Jun 2020 22:31:43: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:31:47: 17000000 INFO @ Sun, 21 Jun 2020 22:31:50: 16000000 INFO @ Sun, 21 Jun 2020 22:31:50: #1 tag size is determined as 68 bps INFO @ Sun, 21 Jun 2020 22:31:50: #1 tag size = 68 INFO @ Sun, 21 Jun 2020 22:31:50: #1 total tags in treatment: 17319606 INFO @ Sun, 21 Jun 2020 22:31:50: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:31:50: #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 22:31:51: #1 tags after filtering in treatment: 17319489 INFO @ Sun, 21 Jun 2020 22:31:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:31:51: #1 finished! INFO @ Sun, 21 Jun 2020 22:31:51: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:31:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:31:52: #2 number of paired peaks: 877 WARNING @ Sun, 21 Jun 2020 22:31:52: Fewer paired peaks (877) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 877 pairs to build model! INFO @ Sun, 21 Jun 2020 22:31:52: start model_add_line... INFO @ Sun, 21 Jun 2020 22:31:52: start X-correlation... INFO @ Sun, 21 Jun 2020 22:31:52: end of X-cor INFO @ Sun, 21 Jun 2020 22:31:52: #2 finished! INFO @ Sun, 21 Jun 2020 22:31:52: #2 predicted fragment length is 90 bps INFO @ Sun, 21 Jun 2020 22:31:52: #2 alternative fragment length(s) may be 4,90 bps INFO @ Sun, 21 Jun 2020 22:31:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6747981/SRX6747981.10_model.r WARNING @ Sun, 21 Jun 2020 22:31:52: #2 Since the d (90) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:31:52: #2 You may need to consider one of the other alternative d(s): 4,90 WARNING @ Sun, 21 Jun 2020 22:31:52: #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 22:31:52: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:31:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:31:56: 17000000 INFO @ Sun, 21 Jun 2020 22:31:58: #1 tag size is determined as 68 bps INFO @ Sun, 21 Jun 2020 22:31:58: #1 tag size = 68 INFO @ Sun, 21 Jun 2020 22:31:58: #1 total tags in treatment: 17319606 INFO @ Sun, 21 Jun 2020 22:31:58: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:31:58: #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 22:31:59: #1 tags after filtering in treatment: 17319489 INFO @ Sun, 21 Jun 2020 22:31:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:31:59: #1 finished! INFO @ Sun, 21 Jun 2020 22:31:59: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:31:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:31:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6747981/SRX6747981.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:31:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6747981/SRX6747981.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:31:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6747981/SRX6747981.05_summits.bed INFO @ Sun, 21 Jun 2020 22:31:59: Done! pass1 - making usageList (633 chroms): 1 millis pass2 - checking and writing primary data (4323 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:32:00: #2 number of paired peaks: 877 WARNING @ Sun, 21 Jun 2020 22:32:00: Fewer paired peaks (877) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 877 pairs to build model! INFO @ Sun, 21 Jun 2020 22:32:00: start model_add_line... INFO @ Sun, 21 Jun 2020 22:32:00: start X-correlation... INFO @ Sun, 21 Jun 2020 22:32:00: end of X-cor INFO @ Sun, 21 Jun 2020 22:32:00: #2 finished! INFO @ Sun, 21 Jun 2020 22:32:00: #2 predicted fragment length is 90 bps INFO @ Sun, 21 Jun 2020 22:32:00: #2 alternative fragment length(s) may be 4,90 bps INFO @ Sun, 21 Jun 2020 22:32:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6747981/SRX6747981.20_model.r WARNING @ Sun, 21 Jun 2020 22:32:00: #2 Since the d (90) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:32:00: #2 You may need to consider one of the other alternative d(s): 4,90 WARNING @ Sun, 21 Jun 2020 22:32:00: #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 22:32:00: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:32:00: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:32:34: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:32:38: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:32:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6747981/SRX6747981.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:32:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6747981/SRX6747981.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:32:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6747981/SRX6747981.10_summits.bed INFO @ Sun, 21 Jun 2020 22:32:54: Done! pass1 - making usageList (477 chroms): 2 millis pass2 - checking and writing primary data (1840 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:32:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6747981/SRX6747981.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:32:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6747981/SRX6747981.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:32:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6747981/SRX6747981.20_summits.bed INFO @ Sun, 21 Jun 2020 22:32:57: Done! pass1 - making usageList (239 chroms): 1 millis pass2 - checking and writing primary data (629 records, 4 fields): 10 millis CompletedMACS2peakCalling