Job ID = 6458757 SRX = SRX5436035 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:45:10 prefetch.2.10.7: 1) Downloading 'SRR8637367'... 2020-06-21T12:45:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:49:27 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:49:27 prefetch.2.10.7: 1) 'SRR8637367' was downloaded successfully Read 35422362 spots for SRR8637367/SRR8637367.sra Written 35422362 spots for SRR8637367/SRR8637367.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: 00:10:25 35422362 reads; of these: 35422362 (100.00%) were unpaired; of these: 1364295 (3.85%) aligned 0 times 23506125 (66.36%) aligned exactly 1 time 10551942 (29.79%) aligned >1 times 96.15% overall alignment rate Time searching: 00:10:25 Overall time: 00:10:25 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] 6516925 / 34058067 = 0.1913 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 22:09:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5436035/SRX5436035.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5436035/SRX5436035.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5436035/SRX5436035.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5436035/SRX5436035.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 22:09:19: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:09:19: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:09:24: 1000000 INFO @ Sun, 21 Jun 2020 22:09:30: 2000000 INFO @ Sun, 21 Jun 2020 22:09:36: 3000000 INFO @ Sun, 21 Jun 2020 22:09:41: 4000000 INFO @ Sun, 21 Jun 2020 22:09:47: 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 22:09:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5436035/SRX5436035.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5436035/SRX5436035.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5436035/SRX5436035.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5436035/SRX5436035.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 22:09:49: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:09:49: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:09:53: 6000000 INFO @ Sun, 21 Jun 2020 22:09:55: 1000000 INFO @ Sun, 21 Jun 2020 22:09:59: 7000000 INFO @ Sun, 21 Jun 2020 22:10:01: 2000000 INFO @ Sun, 21 Jun 2020 22:10:05: 8000000 INFO @ Sun, 21 Jun 2020 22:10:08: 3000000 INFO @ Sun, 21 Jun 2020 22:10:12: 9000000 INFO @ Sun, 21 Jun 2020 22:10:14: 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 22:10:18: 10000000 INFO @ Sun, 21 Jun 2020 22:10:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5436035/SRX5436035.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5436035/SRX5436035.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5436035/SRX5436035.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5436035/SRX5436035.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 22:10:19: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:10:19: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:10:21: 5000000 INFO @ Sun, 21 Jun 2020 22:10:25: 11000000 INFO @ Sun, 21 Jun 2020 22:10:25: 1000000 INFO @ Sun, 21 Jun 2020 22:10:27: 6000000 INFO @ Sun, 21 Jun 2020 22:10:32: 12000000 INFO @ Sun, 21 Jun 2020 22:10:32: 2000000 INFO @ Sun, 21 Jun 2020 22:10:34: 7000000 INFO @ Sun, 21 Jun 2020 22:10:38: 13000000 INFO @ Sun, 21 Jun 2020 22:10:39: 3000000 INFO @ Sun, 21 Jun 2020 22:10:41: 8000000 INFO @ Sun, 21 Jun 2020 22:10:45: 14000000 INFO @ Sun, 21 Jun 2020 22:10:45: 4000000 INFO @ Sun, 21 Jun 2020 22:10:47: 9000000 INFO @ Sun, 21 Jun 2020 22:10:51: 15000000 INFO @ Sun, 21 Jun 2020 22:10:52: 5000000 INFO @ Sun, 21 Jun 2020 22:10:54: 10000000 INFO @ Sun, 21 Jun 2020 22:10:58: 16000000 INFO @ Sun, 21 Jun 2020 22:10:59: 6000000 INFO @ Sun, 21 Jun 2020 22:11:01: 11000000 INFO @ Sun, 21 Jun 2020 22:11:04: 17000000 INFO @ Sun, 21 Jun 2020 22:11:05: 7000000 INFO @ Sun, 21 Jun 2020 22:11:08: 12000000 INFO @ Sun, 21 Jun 2020 22:11:11: 18000000 INFO @ Sun, 21 Jun 2020 22:11:12: 8000000 INFO @ Sun, 21 Jun 2020 22:11:14: 13000000 INFO @ Sun, 21 Jun 2020 22:11:17: 19000000 INFO @ Sun, 21 Jun 2020 22:11:19: 9000000 INFO @ Sun, 21 Jun 2020 22:11:21: 14000000 INFO @ Sun, 21 Jun 2020 22:11:24: 20000000 INFO @ Sun, 21 Jun 2020 22:11:25: 10000000 INFO @ Sun, 21 Jun 2020 22:11:28: 15000000 INFO @ Sun, 21 Jun 2020 22:11:31: 21000000 INFO @ Sun, 21 Jun 2020 22:11:32: 11000000 INFO @ Sun, 21 Jun 2020 22:11:35: 16000000 INFO @ Sun, 21 Jun 2020 22:11:37: 22000000 INFO @ Sun, 21 Jun 2020 22:11:39: 12000000 INFO @ Sun, 21 Jun 2020 22:11:43: 17000000 INFO @ Sun, 21 Jun 2020 22:11:45: 23000000 INFO @ Sun, 21 Jun 2020 22:11:45: 13000000 INFO @ Sun, 21 Jun 2020 22:11:50: 18000000 INFO @ Sun, 21 Jun 2020 22:11:51: 24000000 INFO @ Sun, 21 Jun 2020 22:11:52: 14000000 INFO @ Sun, 21 Jun 2020 22:11:57: 19000000 INFO @ Sun, 21 Jun 2020 22:11:58: 25000000 INFO @ Sun, 21 Jun 2020 22:11:59: 15000000 INFO @ Sun, 21 Jun 2020 22:12:04: 20000000 INFO @ Sun, 21 Jun 2020 22:12:05: 26000000 INFO @ Sun, 21 Jun 2020 22:12:06: 16000000 INFO @ Sun, 21 Jun 2020 22:12:11: 21000000 INFO @ Sun, 21 Jun 2020 22:12:11: 27000000 INFO @ Sun, 21 Jun 2020 22:12:12: 17000000 INFO @ Sun, 21 Jun 2020 22:12:15: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:12:15: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:12:15: #1 total tags in treatment: 27541142 INFO @ Sun, 21 Jun 2020 22:12:15: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:12:15: #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 22:12:16: #1 tags after filtering in treatment: 27541086 INFO @ Sun, 21 Jun 2020 22:12:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:12:16: #1 finished! INFO @ Sun, 21 Jun 2020 22:12:16: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:12:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:12:17: 22000000 INFO @ Sun, 21 Jun 2020 22:12:18: #2 number of paired peaks: 1213 INFO @ Sun, 21 Jun 2020 22:12:18: start model_add_line... INFO @ Sun, 21 Jun 2020 22:12:18: start X-correlation... INFO @ Sun, 21 Jun 2020 22:12:18: end of X-cor INFO @ Sun, 21 Jun 2020 22:12:18: #2 finished! INFO @ Sun, 21 Jun 2020 22:12:18: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 22:12:18: #2 alternative fragment length(s) may be 1,29,579,585 bps INFO @ Sun, 21 Jun 2020 22:12:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5436035/SRX5436035.05_model.r WARNING @ Sun, 21 Jun 2020 22:12:18: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:12:18: #2 You may need to consider one of the other alternative d(s): 1,29,579,585 WARNING @ Sun, 21 Jun 2020 22:12:18: #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 22:12:18: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:12:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:12:19: 18000000 INFO @ Sun, 21 Jun 2020 22:12:25: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:12:26: 19000000 INFO @ Sun, 21 Jun 2020 22:12:32: 24000000 INFO @ Sun, 21 Jun 2020 22:12:33: 20000000 INFO @ Sun, 21 Jun 2020 22:12:39: 25000000 INFO @ Sun, 21 Jun 2020 22:12:40: 21000000 INFO @ Sun, 21 Jun 2020 22:12:46: 26000000 INFO @ Sun, 21 Jun 2020 22:12:47: 22000000 INFO @ Sun, 21 Jun 2020 22:12:53: 27000000 INFO @ Sun, 21 Jun 2020 22:12:54: 23000000 INFO @ Sun, 21 Jun 2020 22:12:57: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:12:57: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:12:57: #1 total tags in treatment: 27541142 INFO @ Sun, 21 Jun 2020 22:12:57: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:12:57: #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 22:12:58: #1 tags after filtering in treatment: 27541086 INFO @ Sun, 21 Jun 2020 22:12:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:12:58: #1 finished! INFO @ Sun, 21 Jun 2020 22:12:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:12:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:13:00: #2 number of paired peaks: 1213 INFO @ Sun, 21 Jun 2020 22:13:00: start model_add_line... INFO @ Sun, 21 Jun 2020 22:13:00: 24000000 INFO @ Sun, 21 Jun 2020 22:13:00: start X-correlation... INFO @ Sun, 21 Jun 2020 22:13:00: end of X-cor INFO @ Sun, 21 Jun 2020 22:13:00: #2 finished! INFO @ Sun, 21 Jun 2020 22:13:00: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 22:13:00: #2 alternative fragment length(s) may be 1,29,579,585 bps INFO @ Sun, 21 Jun 2020 22:13:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5436035/SRX5436035.10_model.r WARNING @ Sun, 21 Jun 2020 22:13:00: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:13:00: #2 You may need to consider one of the other alternative d(s): 1,29,579,585 WARNING @ Sun, 21 Jun 2020 22:13:00: #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 22:13:00: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:13:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:13:04: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:13:06: 25000000 INFO @ Sun, 21 Jun 2020 22:13:12: 26000000 INFO @ Sun, 21 Jun 2020 22:13:19: 27000000 INFO @ Sun, 21 Jun 2020 22:13:22: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:13:22: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:13:22: #1 total tags in treatment: 27541142 INFO @ Sun, 21 Jun 2020 22:13:22: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:13:22: #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 22:13:23: #1 tags after filtering in treatment: 27541086 INFO @ Sun, 21 Jun 2020 22:13:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:13:23: #1 finished! INFO @ Sun, 21 Jun 2020 22:13:23: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:13:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:13:25: #2 number of paired peaks: 1213 INFO @ Sun, 21 Jun 2020 22:13:25: start model_add_line... INFO @ Sun, 21 Jun 2020 22:13:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5436035/SRX5436035.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:13:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5436035/SRX5436035.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:13:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5436035/SRX5436035.05_summits.bed INFO @ Sun, 21 Jun 2020 22:13:25: Done! INFO @ Sun, 21 Jun 2020 22:13:25: start X-correlation... INFO @ Sun, 21 Jun 2020 22:13:25: end of X-cor INFO @ Sun, 21 Jun 2020 22:13:25: #2 finished! INFO @ Sun, 21 Jun 2020 22:13:25: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 22:13:25: #2 alternative fragment length(s) may be 1,29,579,585 bps INFO @ Sun, 21 Jun 2020 22:13:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5436035/SRX5436035.20_model.r WARNING @ Sun, 21 Jun 2020 22:13:25: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:13:25: #2 You may need to consider one of the other alternative d(s): 1,29,579,585 WARNING @ Sun, 21 Jun 2020 22:13:25: #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 22:13:25: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:13:25: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:13:45: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:14:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5436035/SRX5436035.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:14:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5436035/SRX5436035.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:14:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5436035/SRX5436035.10_summits.bed INFO @ Sun, 21 Jun 2020 22:14:06: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:14:10: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:14:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5436035/SRX5436035.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:14:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5436035/SRX5436035.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:14:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5436035/SRX5436035.20_summits.bed INFO @ Sun, 21 Jun 2020 22:14:31: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling