Job ID = 6455175 SRX = SRX2804233 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:51:10 prefetch.2.10.7: 1) Downloading 'SRR5534661'... 2020-06-21T09:51:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:55:21 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:55:21 prefetch.2.10.7: 1) 'SRR5534661' was downloaded successfully 2020-06-21T09:55:21 prefetch.2.10.7: 'SRR5534661' has 0 unresolved dependencies Read 40256499 spots for SRR5534661/SRR5534661.sra Written 40256499 spots for SRR5534661/SRR5534661.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: 00:12:03 40256499 reads; of these: 40256499 (100.00%) were unpaired; of these: 1661204 (4.13%) aligned 0 times 27198047 (67.56%) aligned exactly 1 time 11397248 (28.31%) aligned >1 times 95.87% overall alignment rate Time searching: 00:12:03 Overall time: 00:12:03 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 16 files... [bam_rmdupse_core] 7693837 / 38595295 = 0.1993 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 19:18:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2804233/SRX2804233.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2804233/SRX2804233.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2804233/SRX2804233.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2804233/SRX2804233.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 19:18:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:18:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:18:43: 1000000 INFO @ Sun, 21 Jun 2020 19:18:48: 2000000 INFO @ Sun, 21 Jun 2020 19:18:53: 3000000 INFO @ Sun, 21 Jun 2020 19:18:57: 4000000 INFO @ Sun, 21 Jun 2020 19:19:02: 5000000 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 19:19:07: 6000000 INFO @ Sun, 21 Jun 2020 19:19:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2804233/SRX2804233.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2804233/SRX2804233.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2804233/SRX2804233.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2804233/SRX2804233.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 19:19:08: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:19:08: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:19:13: 7000000 INFO @ Sun, 21 Jun 2020 19:19:13: 1000000 INFO @ Sun, 21 Jun 2020 19:19:18: 8000000 INFO @ Sun, 21 Jun 2020 19:19:19: 2000000 INFO @ Sun, 21 Jun 2020 19:19:24: 9000000 INFO @ Sun, 21 Jun 2020 19:19:24: 3000000 INFO @ Sun, 21 Jun 2020 19:19:29: 10000000 INFO @ Sun, 21 Jun 2020 19:19:30: 4000000 INFO @ Sun, 21 Jun 2020 19:19:35: 11000000 INFO @ Sun, 21 Jun 2020 19:19:35: 5000000 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 19:19:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2804233/SRX2804233.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2804233/SRX2804233.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2804233/SRX2804233.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2804233/SRX2804233.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 19:19:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:19:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:19:40: 12000000 INFO @ Sun, 21 Jun 2020 19:19:41: 6000000 INFO @ Sun, 21 Jun 2020 19:19:44: 1000000 INFO @ Sun, 21 Jun 2020 19:19:46: 13000000 INFO @ Sun, 21 Jun 2020 19:19:47: 7000000 INFO @ Sun, 21 Jun 2020 19:19:50: 2000000 INFO @ Sun, 21 Jun 2020 19:19:52: 14000000 INFO @ Sun, 21 Jun 2020 19:19:53: 8000000 INFO @ Sun, 21 Jun 2020 19:19:56: 3000000 INFO @ Sun, 21 Jun 2020 19:19:58: 15000000 INFO @ Sun, 21 Jun 2020 19:20:00: 9000000 INFO @ Sun, 21 Jun 2020 19:20:03: 4000000 INFO @ Sun, 21 Jun 2020 19:20:04: 16000000 INFO @ Sun, 21 Jun 2020 19:20:06: 10000000 INFO @ Sun, 21 Jun 2020 19:20:09: 5000000 INFO @ Sun, 21 Jun 2020 19:20:10: 17000000 INFO @ Sun, 21 Jun 2020 19:20:12: 11000000 INFO @ Sun, 21 Jun 2020 19:20:15: 6000000 INFO @ Sun, 21 Jun 2020 19:20:16: 18000000 INFO @ Sun, 21 Jun 2020 19:20:18: 12000000 INFO @ Sun, 21 Jun 2020 19:20:21: 7000000 INFO @ Sun, 21 Jun 2020 19:20:22: 19000000 INFO @ Sun, 21 Jun 2020 19:20:24: 13000000 INFO @ Sun, 21 Jun 2020 19:20:27: 8000000 INFO @ Sun, 21 Jun 2020 19:20:28: 20000000 INFO @ Sun, 21 Jun 2020 19:20:30: 14000000 INFO @ Sun, 21 Jun 2020 19:20:33: 9000000 INFO @ Sun, 21 Jun 2020 19:20:34: 21000000 INFO @ Sun, 21 Jun 2020 19:20:36: 15000000 INFO @ Sun, 21 Jun 2020 19:20:40: 10000000 INFO @ Sun, 21 Jun 2020 19:20:40: 22000000 INFO @ Sun, 21 Jun 2020 19:20:42: 16000000 INFO @ Sun, 21 Jun 2020 19:20:46: 23000000 INFO @ Sun, 21 Jun 2020 19:20:46: 11000000 INFO @ Sun, 21 Jun 2020 19:20:48: 17000000 INFO @ Sun, 21 Jun 2020 19:20:52: 24000000 INFO @ Sun, 21 Jun 2020 19:20:52: 12000000 INFO @ Sun, 21 Jun 2020 19:20:54: 18000000 INFO @ Sun, 21 Jun 2020 19:20:58: 13000000 INFO @ Sun, 21 Jun 2020 19:20:58: 25000000 INFO @ Sun, 21 Jun 2020 19:21:00: 19000000 INFO @ Sun, 21 Jun 2020 19:21:04: 14000000 INFO @ Sun, 21 Jun 2020 19:21:05: 26000000 INFO @ Sun, 21 Jun 2020 19:21:06: 20000000 INFO @ Sun, 21 Jun 2020 19:21:10: 15000000 INFO @ Sun, 21 Jun 2020 19:21:11: 27000000 INFO @ Sun, 21 Jun 2020 19:21:12: 21000000 INFO @ Sun, 21 Jun 2020 19:21:16: 16000000 INFO @ Sun, 21 Jun 2020 19:21:17: 28000000 INFO @ Sun, 21 Jun 2020 19:21:18: 22000000 INFO @ Sun, 21 Jun 2020 19:21:22: 17000000 INFO @ Sun, 21 Jun 2020 19:21:23: 29000000 INFO @ Sun, 21 Jun 2020 19:21:24: 23000000 INFO @ Sun, 21 Jun 2020 19:21:28: 18000000 INFO @ Sun, 21 Jun 2020 19:21:29: 30000000 INFO @ Sun, 21 Jun 2020 19:21:30: 24000000 INFO @ Sun, 21 Jun 2020 19:21:35: 19000000 INFO @ Sun, 21 Jun 2020 19:21:36: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:21:36: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:21:36: #1 total tags in treatment: 30901458 INFO @ Sun, 21 Jun 2020 19:21:36: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:21:36: #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 19:21:37: #1 tags after filtering in treatment: 30901458 INFO @ Sun, 21 Jun 2020 19:21:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:21:37: #1 finished! INFO @ Sun, 21 Jun 2020 19:21:37: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:21:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:21:37: 25000000 INFO @ Sun, 21 Jun 2020 19:21:39: #2 number of paired peaks: 303 WARNING @ Sun, 21 Jun 2020 19:21:39: Fewer paired peaks (303) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 303 pairs to build model! INFO @ Sun, 21 Jun 2020 19:21:39: start model_add_line... INFO @ Sun, 21 Jun 2020 19:21:39: start X-correlation... INFO @ Sun, 21 Jun 2020 19:21:39: end of X-cor INFO @ Sun, 21 Jun 2020 19:21:39: #2 finished! INFO @ Sun, 21 Jun 2020 19:21:39: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 19:21:39: #2 alternative fragment length(s) may be 2 bps INFO @ Sun, 21 Jun 2020 19:21:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2804233/SRX2804233.05_model.r WARNING @ Sun, 21 Jun 2020 19:21:39: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:21:39: #2 You may need to consider one of the other alternative d(s): 2 WARNING @ Sun, 21 Jun 2020 19:21:39: #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 19:21:39: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:21:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:21:40: 20000000 INFO @ Sun, 21 Jun 2020 19:21:43: 26000000 INFO @ Sun, 21 Jun 2020 19:21:46: 21000000 INFO @ Sun, 21 Jun 2020 19:21:50: 27000000 INFO @ Sun, 21 Jun 2020 19:21:51: 22000000 INFO @ Sun, 21 Jun 2020 19:21:56: 28000000 INFO @ Sun, 21 Jun 2020 19:21:56: 23000000 INFO @ Sun, 21 Jun 2020 19:22:02: 24000000 INFO @ Sun, 21 Jun 2020 19:22:02: 29000000 INFO @ Sun, 21 Jun 2020 19:22:08: 30000000 INFO @ Sun, 21 Jun 2020 19:22:08: 25000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:22:14: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:22:14: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:22:14: #1 total tags in treatment: 30901458 INFO @ Sun, 21 Jun 2020 19:22:14: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:22:14: #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 19:22:14: 26000000 INFO @ Sun, 21 Jun 2020 19:22:15: #1 tags after filtering in treatment: 30901458 INFO @ Sun, 21 Jun 2020 19:22:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:22:15: #1 finished! INFO @ Sun, 21 Jun 2020 19:22:15: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:22:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:22:17: #2 number of paired peaks: 303 WARNING @ Sun, 21 Jun 2020 19:22:17: Fewer paired peaks (303) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 303 pairs to build model! INFO @ Sun, 21 Jun 2020 19:22:17: start model_add_line... INFO @ Sun, 21 Jun 2020 19:22:17: start X-correlation... INFO @ Sun, 21 Jun 2020 19:22:17: end of X-cor INFO @ Sun, 21 Jun 2020 19:22:17: #2 finished! INFO @ Sun, 21 Jun 2020 19:22:17: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 19:22:17: #2 alternative fragment length(s) may be 2 bps INFO @ Sun, 21 Jun 2020 19:22:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2804233/SRX2804233.10_model.r WARNING @ Sun, 21 Jun 2020 19:22:17: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:22:17: #2 You may need to consider one of the other alternative d(s): 2 WARNING @ Sun, 21 Jun 2020 19:22:17: #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 19:22:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:22:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:22:19: 27000000 INFO @ Sun, 21 Jun 2020 19:22:23: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:22:25: 28000000 INFO @ Sun, 21 Jun 2020 19:22:30: 29000000 INFO @ Sun, 21 Jun 2020 19:22:36: 30000000 INFO @ Sun, 21 Jun 2020 19:22:41: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:22:41: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:22:41: #1 total tags in treatment: 30901458 INFO @ Sun, 21 Jun 2020 19:22:41: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:22:41: #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 19:22:42: #1 tags after filtering in treatment: 30901458 INFO @ Sun, 21 Jun 2020 19:22:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:22:42: #1 finished! INFO @ Sun, 21 Jun 2020 19:22:42: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:22:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:22:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2804233/SRX2804233.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:22:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2804233/SRX2804233.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:22:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2804233/SRX2804233.05_summits.bed INFO @ Sun, 21 Jun 2020 19:22:43: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:22:44: #2 number of paired peaks: 303 WARNING @ Sun, 21 Jun 2020 19:22:44: Fewer paired peaks (303) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 303 pairs to build model! INFO @ Sun, 21 Jun 2020 19:22:44: start model_add_line... INFO @ Sun, 21 Jun 2020 19:22:44: start X-correlation... INFO @ Sun, 21 Jun 2020 19:22:44: end of X-cor INFO @ Sun, 21 Jun 2020 19:22:44: #2 finished! INFO @ Sun, 21 Jun 2020 19:22:44: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 19:22:44: #2 alternative fragment length(s) may be 2 bps INFO @ Sun, 21 Jun 2020 19:22:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2804233/SRX2804233.20_model.r WARNING @ Sun, 21 Jun 2020 19:22:44: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:22:44: #2 You may need to consider one of the other alternative d(s): 2 WARNING @ Sun, 21 Jun 2020 19:22:44: #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 19:22:44: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:22:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:23:01: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:23:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2804233/SRX2804233.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:23:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2804233/SRX2804233.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:23:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2804233/SRX2804233.10_summits.bed INFO @ Sun, 21 Jun 2020 19:23:22: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:23:29: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:23:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2804233/SRX2804233.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:23:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2804233/SRX2804233.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:23:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2804233/SRX2804233.20_summits.bed INFO @ Sun, 21 Jun 2020 19:23:49: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling