Job ID = 6458773 SRX = SRX5436046 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:47:40 prefetch.2.10.7: 1) Downloading 'SRR8637378'... 2020-06-21T12:47:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:51:11 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:51:11 prefetch.2.10.7: 1) 'SRR8637378' was downloaded successfully Read 34097513 spots for SRR8637378/SRR8637378.sra Written 34097513 spots for SRR8637378/SRR8637378.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: 00:09:08 34097513 reads; of these: 34097513 (100.00%) were unpaired; of these: 1404348 (4.12%) aligned 0 times 22726888 (66.65%) aligned exactly 1 time 9966277 (29.23%) aligned >1 times 95.88% overall alignment rate Time searching: 00:09:08 Overall time: 00:09:08 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] 5442458 / 32693165 = 0.1665 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 22:08:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5436046/SRX5436046.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5436046/SRX5436046.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5436046/SRX5436046.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5436046/SRX5436046.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 22:08:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:08:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:09:04: 1000000 INFO @ Sun, 21 Jun 2020 22:09:10: 2000000 INFO @ Sun, 21 Jun 2020 22:09:16: 3000000 INFO @ Sun, 21 Jun 2020 22:09:22: 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 22:09:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5436046/SRX5436046.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5436046/SRX5436046.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5436046/SRX5436046.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5436046/SRX5436046.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 22:09:27: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:09:27: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:09:29: 5000000 INFO @ Sun, 21 Jun 2020 22:09:36: 1000000 INFO @ Sun, 21 Jun 2020 22:09:37: 6000000 INFO @ Sun, 21 Jun 2020 22:09:44: 2000000 INFO @ Sun, 21 Jun 2020 22:09:44: 7000000 INFO @ Sun, 21 Jun 2020 22:09:52: 3000000 INFO @ Sun, 21 Jun 2020 22:09:52: 8000000 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 22:09:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5436046/SRX5436046.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5436046/SRX5436046.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5436046/SRX5436046.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5436046/SRX5436046.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 22:09:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:09:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:10:00: 9000000 INFO @ Sun, 21 Jun 2020 22:10:00: 4000000 INFO @ Sun, 21 Jun 2020 22:10:05: 1000000 INFO @ Sun, 21 Jun 2020 22:10:08: 10000000 INFO @ Sun, 21 Jun 2020 22:10:08: 5000000 INFO @ Sun, 21 Jun 2020 22:10:13: 2000000 INFO @ Sun, 21 Jun 2020 22:10:16: 11000000 INFO @ Sun, 21 Jun 2020 22:10:16: 6000000 INFO @ Sun, 21 Jun 2020 22:10:21: 3000000 INFO @ Sun, 21 Jun 2020 22:10:23: 12000000 INFO @ Sun, 21 Jun 2020 22:10:24: 7000000 INFO @ Sun, 21 Jun 2020 22:10:29: 4000000 INFO @ Sun, 21 Jun 2020 22:10:31: 13000000 INFO @ Sun, 21 Jun 2020 22:10:32: 8000000 INFO @ Sun, 21 Jun 2020 22:10:37: 5000000 INFO @ Sun, 21 Jun 2020 22:10:39: 14000000 INFO @ Sun, 21 Jun 2020 22:10:40: 9000000 INFO @ Sun, 21 Jun 2020 22:10:44: 6000000 INFO @ Sun, 21 Jun 2020 22:10:46: 15000000 INFO @ Sun, 21 Jun 2020 22:10:48: 10000000 INFO @ Sun, 21 Jun 2020 22:10:52: 7000000 INFO @ Sun, 21 Jun 2020 22:10:54: 16000000 INFO @ Sun, 21 Jun 2020 22:10:57: 11000000 INFO @ Sun, 21 Jun 2020 22:11:00: 8000000 INFO @ Sun, 21 Jun 2020 22:11:02: 17000000 INFO @ Sun, 21 Jun 2020 22:11:05: 12000000 INFO @ Sun, 21 Jun 2020 22:11:07: 9000000 INFO @ Sun, 21 Jun 2020 22:11:09: 18000000 INFO @ Sun, 21 Jun 2020 22:11:13: 13000000 INFO @ Sun, 21 Jun 2020 22:11:15: 10000000 INFO @ Sun, 21 Jun 2020 22:11:17: 19000000 INFO @ Sun, 21 Jun 2020 22:11:21: 14000000 INFO @ Sun, 21 Jun 2020 22:11:23: 11000000 INFO @ Sun, 21 Jun 2020 22:11:24: 20000000 INFO @ Sun, 21 Jun 2020 22:11:29: 15000000 INFO @ Sun, 21 Jun 2020 22:11:30: 12000000 INFO @ Sun, 21 Jun 2020 22:11:32: 21000000 INFO @ Sun, 21 Jun 2020 22:11:38: 16000000 INFO @ Sun, 21 Jun 2020 22:11:38: 13000000 INFO @ Sun, 21 Jun 2020 22:11:40: 22000000 INFO @ Sun, 21 Jun 2020 22:11:46: 17000000 INFO @ Sun, 21 Jun 2020 22:11:46: 14000000 INFO @ Sun, 21 Jun 2020 22:11:48: 23000000 INFO @ Sun, 21 Jun 2020 22:11:54: 18000000 INFO @ Sun, 21 Jun 2020 22:11:54: 15000000 INFO @ Sun, 21 Jun 2020 22:11:56: 24000000 INFO @ Sun, 21 Jun 2020 22:12:02: 16000000 INFO @ Sun, 21 Jun 2020 22:12:02: 19000000 INFO @ Sun, 21 Jun 2020 22:12:04: 25000000 INFO @ Sun, 21 Jun 2020 22:12:10: 17000000 INFO @ Sun, 21 Jun 2020 22:12:10: 20000000 INFO @ Sun, 21 Jun 2020 22:12:12: 26000000 INFO @ Sun, 21 Jun 2020 22:12:18: 18000000 INFO @ Sun, 21 Jun 2020 22:12:19: 21000000 INFO @ Sun, 21 Jun 2020 22:12:20: 27000000 INFO @ Sun, 21 Jun 2020 22:12:22: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:12:22: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:12:22: #1 total tags in treatment: 27250707 INFO @ Sun, 21 Jun 2020 22:12:22: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:12:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:12:22: #1 tags after filtering in treatment: 27250659 INFO @ Sun, 21 Jun 2020 22:12:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:12:22: #1 finished! INFO @ Sun, 21 Jun 2020 22:12:22: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:12:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:12:24: #2 number of paired peaks: 869 WARNING @ Sun, 21 Jun 2020 22:12:24: Fewer paired peaks (869) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 869 pairs to build model! INFO @ Sun, 21 Jun 2020 22:12:24: start model_add_line... INFO @ Sun, 21 Jun 2020 22:12:24: start X-correlation... INFO @ Sun, 21 Jun 2020 22:12:24: end of X-cor INFO @ Sun, 21 Jun 2020 22:12:24: #2 finished! INFO @ Sun, 21 Jun 2020 22:12:24: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 22:12:24: #2 alternative fragment length(s) may be 1,44 bps INFO @ Sun, 21 Jun 2020 22:12:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5436046/SRX5436046.05_model.r WARNING @ Sun, 21 Jun 2020 22:12:24: #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 22:12:24: #2 You may need to consider one of the other alternative d(s): 1,44 WARNING @ Sun, 21 Jun 2020 22:12:24: #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 22:12:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:12:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:12:25: 19000000 INFO @ Sun, 21 Jun 2020 22:12:28: 22000000 INFO @ Sun, 21 Jun 2020 22:12:33: 20000000 INFO @ Sun, 21 Jun 2020 22:12:37: 23000000 INFO @ Sun, 21 Jun 2020 22:12:41: 21000000 INFO @ Sun, 21 Jun 2020 22:12:45: 24000000 INFO @ Sun, 21 Jun 2020 22:12:48: 22000000 INFO @ Sun, 21 Jun 2020 22:12:54: 25000000 INFO @ Sun, 21 Jun 2020 22:12:57: 23000000 INFO @ Sun, 21 Jun 2020 22:13:02: 26000000 INFO @ Sun, 21 Jun 2020 22:13:04: 24000000 INFO @ Sun, 21 Jun 2020 22:13:10: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:13:11: 27000000 INFO @ Sun, 21 Jun 2020 22:13:12: 25000000 INFO @ Sun, 21 Jun 2020 22:13:13: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:13:13: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:13:13: #1 total tags in treatment: 27250707 INFO @ Sun, 21 Jun 2020 22:13:13: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:13:13: #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 22:13:14: #1 tags after filtering in treatment: 27250659 INFO @ Sun, 21 Jun 2020 22:13:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:13:14: #1 finished! INFO @ Sun, 21 Jun 2020 22:13:14: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:13:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:13:16: #2 number of paired peaks: 869 WARNING @ Sun, 21 Jun 2020 22:13:16: Fewer paired peaks (869) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 869 pairs to build model! INFO @ Sun, 21 Jun 2020 22:13:16: start model_add_line... INFO @ Sun, 21 Jun 2020 22:13:16: start X-correlation... INFO @ Sun, 21 Jun 2020 22:13:16: end of X-cor INFO @ Sun, 21 Jun 2020 22:13:16: #2 finished! INFO @ Sun, 21 Jun 2020 22:13:16: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 22:13:16: #2 alternative fragment length(s) may be 1,44 bps INFO @ Sun, 21 Jun 2020 22:13:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5436046/SRX5436046.10_model.r WARNING @ Sun, 21 Jun 2020 22:13:16: #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 22:13:16: #2 You may need to consider one of the other alternative d(s): 1,44 WARNING @ Sun, 21 Jun 2020 22:13:16: #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 22:13:16: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:13:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:13:19: 26000000 INFO @ Sun, 21 Jun 2020 22:13:25: 27000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:13:27: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:13:27: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:13:27: #1 total tags in treatment: 27250707 INFO @ Sun, 21 Jun 2020 22:13:27: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:13:27: #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 22:13:28: #1 tags after filtering in treatment: 27250659 INFO @ Sun, 21 Jun 2020 22:13:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:13:28: #1 finished! INFO @ Sun, 21 Jun 2020 22:13:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:13:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:13:30: #2 number of paired peaks: 869 WARNING @ Sun, 21 Jun 2020 22:13:30: Fewer paired peaks (869) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 869 pairs to build model! INFO @ Sun, 21 Jun 2020 22:13:30: start model_add_line... INFO @ Sun, 21 Jun 2020 22:13:30: start X-correlation... INFO @ Sun, 21 Jun 2020 22:13:30: end of X-cor INFO @ Sun, 21 Jun 2020 22:13:30: #2 finished! INFO @ Sun, 21 Jun 2020 22:13:30: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 22:13:30: #2 alternative fragment length(s) may be 1,44 bps INFO @ Sun, 21 Jun 2020 22:13:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5436046/SRX5436046.20_model.r WARNING @ Sun, 21 Jun 2020 22:13:30: #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 22:13:30: #2 You may need to consider one of the other alternative d(s): 1,44 WARNING @ Sun, 21 Jun 2020 22:13:30: #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 22:13:30: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:13:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:13:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5436046/SRX5436046.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:13:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5436046/SRX5436046.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:13:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5436046/SRX5436046.05_summits.bed INFO @ Sun, 21 Jun 2020 22:13:31: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:14:02: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:14:13: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:14:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5436046/SRX5436046.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:14:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5436046/SRX5436046.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:14:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5436046/SRX5436046.10_summits.bed INFO @ Sun, 21 Jun 2020 22:14:22: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:14:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5436046/SRX5436046.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:14:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5436046/SRX5436046.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:14:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5436046/SRX5436046.20_summits.bed INFO @ Sun, 21 Jun 2020 22:14:34: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling