Job ID = 6458743 SRX = SRX5431046 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:37:59 prefetch.2.10.7: 1) Downloading 'SRR8632345'... 2020-06-21T12:37:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:42:17 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:42:17 prefetch.2.10.7: 1) 'SRR8632345' was downloaded successfully Read 37573032 spots for SRR8632345/SRR8632345.sra Written 37573032 spots for SRR8632345/SRR8632345.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: 00:10:35 37573032 reads; of these: 37573032 (100.00%) were unpaired; of these: 3276694 (8.72%) aligned 0 times 24143547 (64.26%) aligned exactly 1 time 10152791 (27.02%) aligned >1 times 91.28% overall alignment rate Time searching: 00:10:35 Overall time: 00:10:35 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] 6119176 / 34296338 = 0.1784 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 22:01:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5431046/SRX5431046.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5431046/SRX5431046.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5431046/SRX5431046.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5431046/SRX5431046.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 22:01:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:01:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:01:45: 1000000 INFO @ Sun, 21 Jun 2020 22:01:50: 2000000 INFO @ Sun, 21 Jun 2020 22:01:54: 3000000 INFO @ Sun, 21 Jun 2020 22:01:59: 4000000 INFO @ Sun, 21 Jun 2020 22:02:04: 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 22:02:09: 6000000 INFO @ Sun, 21 Jun 2020 22:02:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5431046/SRX5431046.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5431046/SRX5431046.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5431046/SRX5431046.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5431046/SRX5431046.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 22:02:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:02:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:02:15: 7000000 INFO @ Sun, 21 Jun 2020 22:02:16: 1000000 INFO @ Sun, 21 Jun 2020 22:02:20: 8000000 INFO @ Sun, 21 Jun 2020 22:02:22: 2000000 INFO @ Sun, 21 Jun 2020 22:02:25: 9000000 INFO @ Sun, 21 Jun 2020 22:02:28: 3000000 INFO @ Sun, 21 Jun 2020 22:02:30: 10000000 INFO @ Sun, 21 Jun 2020 22:02:34: 4000000 INFO @ Sun, 21 Jun 2020 22:02:36: 11000000 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 22:02:40: 5000000 INFO @ Sun, 21 Jun 2020 22:02:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5431046/SRX5431046.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5431046/SRX5431046.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5431046/SRX5431046.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5431046/SRX5431046.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 22:02:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:02:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:02:41: 12000000 INFO @ Sun, 21 Jun 2020 22:02:45: 1000000 INFO @ Sun, 21 Jun 2020 22:02:46: 6000000 INFO @ Sun, 21 Jun 2020 22:02:46: 13000000 INFO @ Sun, 21 Jun 2020 22:02:51: 2000000 INFO @ Sun, 21 Jun 2020 22:02:52: 7000000 INFO @ Sun, 21 Jun 2020 22:02:52: 14000000 INFO @ Sun, 21 Jun 2020 22:02:56: 3000000 INFO @ Sun, 21 Jun 2020 22:02:57: 15000000 INFO @ Sun, 21 Jun 2020 22:02:58: 8000000 INFO @ Sun, 21 Jun 2020 22:03:02: 4000000 INFO @ Sun, 21 Jun 2020 22:03:03: 16000000 INFO @ Sun, 21 Jun 2020 22:03:04: 9000000 INFO @ Sun, 21 Jun 2020 22:03:07: 5000000 INFO @ Sun, 21 Jun 2020 22:03:08: 17000000 INFO @ Sun, 21 Jun 2020 22:03:10: 10000000 INFO @ Sun, 21 Jun 2020 22:03:13: 6000000 INFO @ Sun, 21 Jun 2020 22:03:13: 18000000 INFO @ Sun, 21 Jun 2020 22:03:15: 11000000 INFO @ Sun, 21 Jun 2020 22:03:18: 7000000 INFO @ Sun, 21 Jun 2020 22:03:19: 19000000 INFO @ Sun, 21 Jun 2020 22:03:21: 12000000 INFO @ Sun, 21 Jun 2020 22:03:24: 8000000 INFO @ Sun, 21 Jun 2020 22:03:24: 20000000 INFO @ Sun, 21 Jun 2020 22:03:27: 13000000 INFO @ Sun, 21 Jun 2020 22:03:29: 9000000 INFO @ Sun, 21 Jun 2020 22:03:30: 21000000 INFO @ Sun, 21 Jun 2020 22:03:33: 14000000 INFO @ Sun, 21 Jun 2020 22:03:35: 10000000 INFO @ Sun, 21 Jun 2020 22:03:35: 22000000 INFO @ Sun, 21 Jun 2020 22:03:39: 15000000 INFO @ Sun, 21 Jun 2020 22:03:40: 11000000 INFO @ Sun, 21 Jun 2020 22:03:41: 23000000 INFO @ Sun, 21 Jun 2020 22:03:45: 16000000 INFO @ Sun, 21 Jun 2020 22:03:45: 12000000 INFO @ Sun, 21 Jun 2020 22:03:47: 24000000 INFO @ Sun, 21 Jun 2020 22:03:51: 13000000 INFO @ Sun, 21 Jun 2020 22:03:51: 17000000 INFO @ Sun, 21 Jun 2020 22:03:52: 25000000 INFO @ Sun, 21 Jun 2020 22:03:56: 14000000 INFO @ Sun, 21 Jun 2020 22:03:57: 18000000 INFO @ Sun, 21 Jun 2020 22:03:57: 26000000 INFO @ Sun, 21 Jun 2020 22:04:02: 15000000 INFO @ Sun, 21 Jun 2020 22:04:03: 19000000 INFO @ Sun, 21 Jun 2020 22:04:03: 27000000 INFO @ Sun, 21 Jun 2020 22:04:07: 16000000 INFO @ Sun, 21 Jun 2020 22:04:09: 28000000 INFO @ Sun, 21 Jun 2020 22:04:09: 20000000 INFO @ Sun, 21 Jun 2020 22:04:10: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:04:10: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:04:10: #1 total tags in treatment: 28177162 INFO @ Sun, 21 Jun 2020 22:04:10: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:04:10: #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 22:04:11: #1 tags after filtering in treatment: 28177162 INFO @ Sun, 21 Jun 2020 22:04:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:04:11: #1 finished! INFO @ Sun, 21 Jun 2020 22:04:11: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:04:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:04:12: 17000000 INFO @ Sun, 21 Jun 2020 22:04:13: #2 number of paired peaks: 405 WARNING @ Sun, 21 Jun 2020 22:04:13: Fewer paired peaks (405) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 405 pairs to build model! INFO @ Sun, 21 Jun 2020 22:04:13: start model_add_line... INFO @ Sun, 21 Jun 2020 22:04:13: start X-correlation... INFO @ Sun, 21 Jun 2020 22:04:13: end of X-cor INFO @ Sun, 21 Jun 2020 22:04:13: #2 finished! INFO @ Sun, 21 Jun 2020 22:04:13: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 22:04:13: #2 alternative fragment length(s) may be 2 bps INFO @ Sun, 21 Jun 2020 22:04:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5431046/SRX5431046.05_model.r WARNING @ Sun, 21 Jun 2020 22:04:13: #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 22:04:13: #2 You may need to consider one of the other alternative d(s): 2 WARNING @ Sun, 21 Jun 2020 22:04:13: #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 22:04:13: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:04:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:04:15: 21000000 INFO @ Sun, 21 Jun 2020 22:04:18: 18000000 INFO @ Sun, 21 Jun 2020 22:04:20: 22000000 INFO @ Sun, 21 Jun 2020 22:04:23: 19000000 INFO @ Sun, 21 Jun 2020 22:04:27: 23000000 INFO @ Sun, 21 Jun 2020 22:04:28: 20000000 INFO @ Sun, 21 Jun 2020 22:04:32: 24000000 INFO @ Sun, 21 Jun 2020 22:04:33: 21000000 INFO @ Sun, 21 Jun 2020 22:04:38: 25000000 INFO @ Sun, 21 Jun 2020 22:04:39: 22000000 INFO @ Sun, 21 Jun 2020 22:04:44: 26000000 INFO @ Sun, 21 Jun 2020 22:04:44: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:04:50: 24000000 INFO @ Sun, 21 Jun 2020 22:04:50: 27000000 INFO @ Sun, 21 Jun 2020 22:04:55: 25000000 INFO @ Sun, 21 Jun 2020 22:04:56: 28000000 INFO @ Sun, 21 Jun 2020 22:04:57: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:04:57: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:04:57: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:04:57: #1 total tags in treatment: 28177162 INFO @ Sun, 21 Jun 2020 22:04:57: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:04:57: #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 22:04:58: #1 tags after filtering in treatment: 28177162 INFO @ Sun, 21 Jun 2020 22:04:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:04:58: #1 finished! INFO @ Sun, 21 Jun 2020 22:04:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:04:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:05:00: #2 number of paired peaks: 405 WARNING @ Sun, 21 Jun 2020 22:05:00: Fewer paired peaks (405) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 405 pairs to build model! INFO @ Sun, 21 Jun 2020 22:05:00: start model_add_line... INFO @ Sun, 21 Jun 2020 22:05:00: start X-correlation... INFO @ Sun, 21 Jun 2020 22:05:00: end of X-cor INFO @ Sun, 21 Jun 2020 22:05:00: #2 finished! INFO @ Sun, 21 Jun 2020 22:05:00: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 22:05:00: #2 alternative fragment length(s) may be 2 bps INFO @ Sun, 21 Jun 2020 22:05:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5431046/SRX5431046.10_model.r WARNING @ Sun, 21 Jun 2020 22:05:00: #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 22:05:00: #2 You may need to consider one of the other alternative d(s): 2 WARNING @ Sun, 21 Jun 2020 22:05:00: #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 22:05:00: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:05:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:05:00: 26000000 INFO @ Sun, 21 Jun 2020 22:05:05: 27000000 INFO @ Sun, 21 Jun 2020 22:05:10: 28000000 INFO @ Sun, 21 Jun 2020 22:05:11: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:05:11: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:05:11: #1 total tags in treatment: 28177162 INFO @ Sun, 21 Jun 2020 22:05:11: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:05:11: #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 22:05:12: #1 tags after filtering in treatment: 28177162 INFO @ Sun, 21 Jun 2020 22:05:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:05:12: #1 finished! INFO @ Sun, 21 Jun 2020 22:05:12: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:05:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:05:14: #2 number of paired peaks: 405 WARNING @ Sun, 21 Jun 2020 22:05:14: Fewer paired peaks (405) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 405 pairs to build model! INFO @ Sun, 21 Jun 2020 22:05:14: start model_add_line... INFO @ Sun, 21 Jun 2020 22:05:14: start X-correlation... INFO @ Sun, 21 Jun 2020 22:05:14: end of X-cor INFO @ Sun, 21 Jun 2020 22:05:14: #2 finished! INFO @ Sun, 21 Jun 2020 22:05:14: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 22:05:14: #2 alternative fragment length(s) may be 2 bps INFO @ Sun, 21 Jun 2020 22:05:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5431046/SRX5431046.20_model.r WARNING @ Sun, 21 Jun 2020 22:05:14: #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 22:05:14: #2 You may need to consider one of the other alternative d(s): 2 WARNING @ Sun, 21 Jun 2020 22:05:14: #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 22:05:14: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:05:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:05:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5431046/SRX5431046.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:05:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5431046/SRX5431046.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:05:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5431046/SRX5431046.05_summits.bed INFO @ Sun, 21 Jun 2020 22:05:17: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:05:44: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:05:57: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:06:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5431046/SRX5431046.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:06:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5431046/SRX5431046.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:06:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5431046/SRX5431046.10_summits.bed INFO @ Sun, 21 Jun 2020 22:06:03: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:06:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5431046/SRX5431046.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:06:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5431046/SRX5431046.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:06:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5431046/SRX5431046.20_summits.bed INFO @ Sun, 21 Jun 2020 22:06:17: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling