Job ID = 6456154 SRX = SRX3270980 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:33:04 prefetch.2.10.7: 1) Downloading 'SRR6159391'... 2020-06-21T10:33:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:35:28 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:35:28 prefetch.2.10.7: 'SRR6159391' is valid 2020-06-21T10:35:28 prefetch.2.10.7: 1) 'SRR6159391' was downloaded successfully 2020-06-21T10:35:28 prefetch.2.10.7: 'SRR6159391' has 0 unresolved dependencies Read 18955656 spots for SRR6159391/SRR6159391.sra Written 18955656 spots for SRR6159391/SRR6159391.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: 00:05:39 18955656 reads; of these: 18955656 (100.00%) were unpaired; of these: 1440687 (7.60%) aligned 0 times 11567052 (61.02%) aligned exactly 1 time 5947917 (31.38%) aligned >1 times 92.40% overall alignment rate Time searching: 00:05:39 Overall time: 00:05:39 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] 2951153 / 17514969 = 0.1685 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 19:46:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3270980/SRX3270980.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3270980/SRX3270980.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3270980/SRX3270980.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3270980/SRX3270980.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 19:46:37: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:46:37: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:46:44: 1000000 INFO @ Sun, 21 Jun 2020 19:46:50: 2000000 INFO @ Sun, 21 Jun 2020 19:46:57: 3000000 INFO @ Sun, 21 Jun 2020 19:47:03: 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 19:47:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3270980/SRX3270980.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3270980/SRX3270980.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3270980/SRX3270980.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3270980/SRX3270980.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 19:47:07: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:47:07: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:47:10: 5000000 INFO @ Sun, 21 Jun 2020 19:47:14: 1000000 INFO @ Sun, 21 Jun 2020 19:47:17: 6000000 INFO @ Sun, 21 Jun 2020 19:47:20: 2000000 INFO @ Sun, 21 Jun 2020 19:47:24: 7000000 INFO @ Sun, 21 Jun 2020 19:47:27: 3000000 INFO @ Sun, 21 Jun 2020 19:47:31: 8000000 INFO @ Sun, 21 Jun 2020 19:47:33: 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 19:47:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3270980/SRX3270980.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3270980/SRX3270980.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3270980/SRX3270980.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3270980/SRX3270980.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 19:47:37: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:47:37: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:47:38: 9000000 INFO @ Sun, 21 Jun 2020 19:47:39: 5000000 INFO @ Sun, 21 Jun 2020 19:47:44: 1000000 INFO @ Sun, 21 Jun 2020 19:47:45: 10000000 INFO @ Sun, 21 Jun 2020 19:47:46: 6000000 INFO @ Sun, 21 Jun 2020 19:47:50: 2000000 INFO @ Sun, 21 Jun 2020 19:47:52: 11000000 INFO @ Sun, 21 Jun 2020 19:47:52: 7000000 INFO @ Sun, 21 Jun 2020 19:47:57: 3000000 INFO @ Sun, 21 Jun 2020 19:47:59: 8000000 INFO @ Sun, 21 Jun 2020 19:47:59: 12000000 INFO @ Sun, 21 Jun 2020 19:48:03: 4000000 INFO @ Sun, 21 Jun 2020 19:48:06: 9000000 INFO @ Sun, 21 Jun 2020 19:48:06: 13000000 INFO @ Sun, 21 Jun 2020 19:48:10: 5000000 INFO @ Sun, 21 Jun 2020 19:48:12: 10000000 INFO @ Sun, 21 Jun 2020 19:48:13: 14000000 INFO @ Sun, 21 Jun 2020 19:48:16: 6000000 INFO @ Sun, 21 Jun 2020 19:48:17: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:48:17: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:48:17: #1 total tags in treatment: 14563816 INFO @ Sun, 21 Jun 2020 19:48:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:48:17: #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 19:48:18: #1 tags after filtering in treatment: 14563815 INFO @ Sun, 21 Jun 2020 19:48:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:48:18: #1 finished! INFO @ Sun, 21 Jun 2020 19:48:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:48:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:48:19: 11000000 INFO @ Sun, 21 Jun 2020 19:48:19: #2 number of paired peaks: 953 WARNING @ Sun, 21 Jun 2020 19:48:19: Fewer paired peaks (953) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 953 pairs to build model! INFO @ Sun, 21 Jun 2020 19:48:19: start model_add_line... INFO @ Sun, 21 Jun 2020 19:48:19: start X-correlation... INFO @ Sun, 21 Jun 2020 19:48:19: end of X-cor INFO @ Sun, 21 Jun 2020 19:48:19: #2 finished! INFO @ Sun, 21 Jun 2020 19:48:19: #2 predicted fragment length is 53 bps INFO @ Sun, 21 Jun 2020 19:48:19: #2 alternative fragment length(s) may be 4,53 bps INFO @ Sun, 21 Jun 2020 19:48:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3270980/SRX3270980.05_model.r WARNING @ Sun, 21 Jun 2020 19:48:19: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:48:19: #2 You may need to consider one of the other alternative d(s): 4,53 WARNING @ Sun, 21 Jun 2020 19:48:19: #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 19:48:19: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:48:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:48:23: 7000000 INFO @ Sun, 21 Jun 2020 19:48:25: 12000000 INFO @ Sun, 21 Jun 2020 19:48:29: 8000000 INFO @ Sun, 21 Jun 2020 19:48:31: 13000000 INFO @ Sun, 21 Jun 2020 19:48:35: 9000000 INFO @ Sun, 21 Jun 2020 19:48:38: 14000000 INFO @ Sun, 21 Jun 2020 19:48:41: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:48:41: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:48:41: #1 total tags in treatment: 14563816 INFO @ Sun, 21 Jun 2020 19:48:41: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:48:41: #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 19:48:41: 10000000 INFO @ Sun, 21 Jun 2020 19:48:42: #1 tags after filtering in treatment: 14563815 INFO @ Sun, 21 Jun 2020 19:48:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:48:42: #1 finished! INFO @ Sun, 21 Jun 2020 19:48:42: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:48:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:48:43: #2 number of paired peaks: 953 WARNING @ Sun, 21 Jun 2020 19:48:43: Fewer paired peaks (953) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 953 pairs to build model! INFO @ Sun, 21 Jun 2020 19:48:43: start model_add_line... INFO @ Sun, 21 Jun 2020 19:48:43: start X-correlation... INFO @ Sun, 21 Jun 2020 19:48:43: end of X-cor INFO @ Sun, 21 Jun 2020 19:48:43: #2 finished! INFO @ Sun, 21 Jun 2020 19:48:43: #2 predicted fragment length is 53 bps INFO @ Sun, 21 Jun 2020 19:48:43: #2 alternative fragment length(s) may be 4,53 bps INFO @ Sun, 21 Jun 2020 19:48:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3270980/SRX3270980.10_model.r WARNING @ Sun, 21 Jun 2020 19:48:43: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:48:43: #2 You may need to consider one of the other alternative d(s): 4,53 WARNING @ Sun, 21 Jun 2020 19:48:43: #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 19:48:43: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:48:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:48:46: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:48:47: 11000000 INFO @ Sun, 21 Jun 2020 19:48:53: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:48:59: 13000000 INFO @ Sun, 21 Jun 2020 19:49:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3270980/SRX3270980.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:49:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3270980/SRX3270980.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:49:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3270980/SRX3270980.05_summits.bed INFO @ Sun, 21 Jun 2020 19:49:00: Done! pass1 - making usageList (793 chroms): 1 millis pass2 - checking and writing primary data (3515 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:49:04: 14000000 INFO @ Sun, 21 Jun 2020 19:49:08: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:49:08: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:49:08: #1 total tags in treatment: 14563816 INFO @ Sun, 21 Jun 2020 19:49:08: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:49:08: #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 19:49:08: #1 tags after filtering in treatment: 14563815 INFO @ Sun, 21 Jun 2020 19:49:08: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:49:08: #1 finished! INFO @ Sun, 21 Jun 2020 19:49:08: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:49:08: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:49:09: #2 number of paired peaks: 953 WARNING @ Sun, 21 Jun 2020 19:49:09: Fewer paired peaks (953) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 953 pairs to build model! INFO @ Sun, 21 Jun 2020 19:49:09: start model_add_line... INFO @ Sun, 21 Jun 2020 19:49:09: start X-correlation... INFO @ Sun, 21 Jun 2020 19:49:09: end of X-cor INFO @ Sun, 21 Jun 2020 19:49:09: #2 finished! INFO @ Sun, 21 Jun 2020 19:49:09: #2 predicted fragment length is 53 bps INFO @ Sun, 21 Jun 2020 19:49:09: #2 alternative fragment length(s) may be 4,53 bps INFO @ Sun, 21 Jun 2020 19:49:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3270980/SRX3270980.20_model.r WARNING @ Sun, 21 Jun 2020 19:49:09: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:49:09: #2 You may need to consider one of the other alternative d(s): 4,53 WARNING @ Sun, 21 Jun 2020 19:49:09: #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 19:49:09: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:49:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:49:11: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:49:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3270980/SRX3270980.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:49:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3270980/SRX3270980.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:49:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3270980/SRX3270980.10_summits.bed INFO @ Sun, 21 Jun 2020 19:49:25: Done! pass1 - making usageList (643 chroms): 1 millis pass2 - checking and writing primary data (2501 records, 4 fields): 18 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:49:37: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:49:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3270980/SRX3270980.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:49:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3270980/SRX3270980.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:49:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3270980/SRX3270980.20_summits.bed INFO @ Sun, 21 Jun 2020 19:49:50: Done! pass1 - making usageList (427 chroms): 1 millis pass2 - checking and writing primary data (1081 records, 4 fields): 13 millis CompletedMACS2peakCalling