Job ID = 6458440 SRX = SRX5226994 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:24:37 prefetch.2.10.7: 1) Downloading 'SRR8417909'... 2020-06-21T12:24:37 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:26:39 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:26:40 prefetch.2.10.7: 'SRR8417909' is valid 2020-06-21T12:26:40 prefetch.2.10.7: 1) 'SRR8417909' was downloaded successfully 2020-06-21T12:26:40 prefetch.2.10.7: 'SRR8417909' has 0 unresolved dependencies Read 11846198 spots for SRR8417909/SRR8417909.sra Written 11846198 spots for SRR8417909/SRR8417909.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: 00:04:01 11846198 reads; of these: 11846198 (100.00%) were unpaired; of these: 2610494 (22.04%) aligned 0 times 6497526 (54.85%) aligned exactly 1 time 2738178 (23.11%) aligned >1 times 77.96% overall alignment rate Time searching: 00:04:01 Overall time: 00:04:01 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_rmdupse_core] 1022115 / 9235704 = 0.1107 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 21:35:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5226994/SRX5226994.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5226994/SRX5226994.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5226994/SRX5226994.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5226994/SRX5226994.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 21:35:08: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:35:08: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:35:14: 1000000 INFO @ Sun, 21 Jun 2020 21:35:21: 2000000 INFO @ Sun, 21 Jun 2020 21:35:28: 3000000 INFO @ Sun, 21 Jun 2020 21:35:36: 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 21:35:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5226994/SRX5226994.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5226994/SRX5226994.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5226994/SRX5226994.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5226994/SRX5226994.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 21:35:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:35:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:35:43: 5000000 INFO @ Sun, 21 Jun 2020 21:35:46: 1000000 INFO @ Sun, 21 Jun 2020 21:35:51: 6000000 INFO @ Sun, 21 Jun 2020 21:35:54: 2000000 INFO @ Sun, 21 Jun 2020 21:36:00: 7000000 INFO @ Sun, 21 Jun 2020 21:36:02: 3000000 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 21:36:08: 8000000 INFO @ Sun, 21 Jun 2020 21:36:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5226994/SRX5226994.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5226994/SRX5226994.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5226994/SRX5226994.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5226994/SRX5226994.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 21:36:08: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:36:08: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:36:09: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 21:36:09: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 21:36:09: #1 total tags in treatment: 8213589 INFO @ Sun, 21 Jun 2020 21:36:09: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:36:09: #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 21:36:10: 4000000 INFO @ Sun, 21 Jun 2020 21:36:10: #1 tags after filtering in treatment: 8213423 INFO @ Sun, 21 Jun 2020 21:36:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:36:10: #1 finished! INFO @ Sun, 21 Jun 2020 21:36:10: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:36:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:36:10: #2 number of paired peaks: 1534 INFO @ Sun, 21 Jun 2020 21:36:10: start model_add_line... INFO @ Sun, 21 Jun 2020 21:36:10: start X-correlation... INFO @ Sun, 21 Jun 2020 21:36:10: end of X-cor INFO @ Sun, 21 Jun 2020 21:36:10: #2 finished! INFO @ Sun, 21 Jun 2020 21:36:10: #2 predicted fragment length is 98 bps INFO @ Sun, 21 Jun 2020 21:36:10: #2 alternative fragment length(s) may be 98 bps INFO @ Sun, 21 Jun 2020 21:36:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5226994/SRX5226994.05_model.r WARNING @ Sun, 21 Jun 2020 21:36:10: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:36:10: #2 You may need to consider one of the other alternative d(s): 98 WARNING @ Sun, 21 Jun 2020 21:36:10: #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 21:36:10: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:36:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:36:16: 1000000 INFO @ Sun, 21 Jun 2020 21:36:18: 5000000 INFO @ Sun, 21 Jun 2020 21:36:24: 2000000 INFO @ Sun, 21 Jun 2020 21:36:26: 6000000 INFO @ Sun, 21 Jun 2020 21:36:31: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:36:32: 3000000 INFO @ Sun, 21 Jun 2020 21:36:34: 7000000 INFO @ Sun, 21 Jun 2020 21:36:40: 4000000 INFO @ Sun, 21 Jun 2020 21:36:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5226994/SRX5226994.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:36:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5226994/SRX5226994.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:36:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5226994/SRX5226994.05_summits.bed INFO @ Sun, 21 Jun 2020 21:36:42: Done! pass1 - making usageList (507 chroms): 2 millis pass2 - checking and writing primary data (3259 records, 4 fields): 39 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:36:42: 8000000 INFO @ Sun, 21 Jun 2020 21:36:44: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 21:36:44: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 21:36:44: #1 total tags in treatment: 8213589 INFO @ Sun, 21 Jun 2020 21:36:44: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:36:44: #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 21:36:44: #1 tags after filtering in treatment: 8213423 INFO @ Sun, 21 Jun 2020 21:36:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:36:44: #1 finished! INFO @ Sun, 21 Jun 2020 21:36:44: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:36:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:36:45: #2 number of paired peaks: 1534 INFO @ Sun, 21 Jun 2020 21:36:45: start model_add_line... INFO @ Sun, 21 Jun 2020 21:36:45: start X-correlation... INFO @ Sun, 21 Jun 2020 21:36:45: end of X-cor INFO @ Sun, 21 Jun 2020 21:36:45: #2 finished! INFO @ Sun, 21 Jun 2020 21:36:45: #2 predicted fragment length is 98 bps INFO @ Sun, 21 Jun 2020 21:36:45: #2 alternative fragment length(s) may be 98 bps INFO @ Sun, 21 Jun 2020 21:36:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5226994/SRX5226994.10_model.r WARNING @ Sun, 21 Jun 2020 21:36:45: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:36:45: #2 You may need to consider one of the other alternative d(s): 98 WARNING @ Sun, 21 Jun 2020 21:36:45: #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 21:36:45: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:36:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:36:47: 5000000 INFO @ Sun, 21 Jun 2020 21:36:55: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:37:02: 7000000 INFO @ Sun, 21 Jun 2020 21:37:05: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:37:09: 8000000 INFO @ Sun, 21 Jun 2020 21:37:11: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 21:37:11: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 21:37:11: #1 total tags in treatment: 8213589 INFO @ Sun, 21 Jun 2020 21:37:11: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:37:11: #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 21:37:11: #1 tags after filtering in treatment: 8213423 INFO @ Sun, 21 Jun 2020 21:37:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:37:11: #1 finished! INFO @ Sun, 21 Jun 2020 21:37:11: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:37:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:37:12: #2 number of paired peaks: 1534 INFO @ Sun, 21 Jun 2020 21:37:12: start model_add_line... INFO @ Sun, 21 Jun 2020 21:37:12: start X-correlation... INFO @ Sun, 21 Jun 2020 21:37:12: end of X-cor INFO @ Sun, 21 Jun 2020 21:37:12: #2 finished! INFO @ Sun, 21 Jun 2020 21:37:12: #2 predicted fragment length is 98 bps INFO @ Sun, 21 Jun 2020 21:37:12: #2 alternative fragment length(s) may be 98 bps INFO @ Sun, 21 Jun 2020 21:37:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5226994/SRX5226994.20_model.r WARNING @ Sun, 21 Jun 2020 21:37:12: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:37:12: #2 You may need to consider one of the other alternative d(s): 98 WARNING @ Sun, 21 Jun 2020 21:37:12: #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 21:37:12: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:37:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:37:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5226994/SRX5226994.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:37:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5226994/SRX5226994.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:37:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5226994/SRX5226994.10_summits.bed INFO @ Sun, 21 Jun 2020 21:37:15: Done! pass1 - making usageList (327 chroms): 1 millis pass2 - checking and writing primary data (1576 records, 4 fields): 12 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:37:31: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:37:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5226994/SRX5226994.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:37:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5226994/SRX5226994.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:37:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5226994/SRX5226994.20_summits.bed INFO @ Sun, 21 Jun 2020 21:37:41: Done! pass1 - making usageList (199 chroms): 1 millis pass2 - checking and writing primary data (635 records, 4 fields): 7 millis CompletedMACS2peakCalling