Job ID = 6458742 SRX = SRX5431045 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:48:55 prefetch.2.10.7: 1) Downloading 'SRR8632344'... 2020-06-21T12:48:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:53:30 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:53:30 prefetch.2.10.7: 1) 'SRR8632344' was downloaded successfully Read 30324004 spots for SRR8632344/SRR8632344.sra Written 30324004 spots for SRR8632344/SRR8632344.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: 00:08:53 30324004 reads; of these: 30324004 (100.00%) were unpaired; of these: 2087568 (6.88%) aligned 0 times 19710577 (65.00%) aligned exactly 1 time 8525859 (28.12%) aligned >1 times 93.12% overall alignment rate Time searching: 00:08:53 Overall time: 00:08:53 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 12 files... [bam_rmdupse_core] 4565285 / 28236436 = 0.1617 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 22:11:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5431045/SRX5431045.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5431045/SRX5431045.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5431045/SRX5431045.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5431045/SRX5431045.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 22:11:53: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:11:53: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:11:59: 1000000 INFO @ Sun, 21 Jun 2020 22:12:05: 2000000 INFO @ Sun, 21 Jun 2020 22:12:10: 3000000 INFO @ Sun, 21 Jun 2020 22:12:16: 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 22:12:21: 5000000 INFO @ Sun, 21 Jun 2020 22:12:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5431045/SRX5431045.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5431045/SRX5431045.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5431045/SRX5431045.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5431045/SRX5431045.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 22:12:23: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:12:23: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:12:27: 6000000 INFO @ Sun, 21 Jun 2020 22:12:30: 1000000 INFO @ Sun, 21 Jun 2020 22:12:33: 7000000 INFO @ Sun, 21 Jun 2020 22:12:36: 2000000 INFO @ Sun, 21 Jun 2020 22:12:39: 8000000 INFO @ Sun, 21 Jun 2020 22:12:42: 3000000 INFO @ Sun, 21 Jun 2020 22:12:45: 9000000 INFO @ Sun, 21 Jun 2020 22:12:48: 4000000 BedGraph に変換中... INFO @ Sun, 21 Jun 2020 22:12:51: 10000000 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 22:12:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5431045/SRX5431045.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5431045/SRX5431045.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5431045/SRX5431045.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5431045/SRX5431045.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 22:12:54: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:12:54: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:12:54: 5000000 INFO @ Sun, 21 Jun 2020 22:12:57: 11000000 INFO @ Sun, 21 Jun 2020 22:13:00: 1000000 INFO @ Sun, 21 Jun 2020 22:13:00: 6000000 INFO @ Sun, 21 Jun 2020 22:13:03: 12000000 INFO @ Sun, 21 Jun 2020 22:13:06: 2000000 INFO @ Sun, 21 Jun 2020 22:13:06: 7000000 INFO @ Sun, 21 Jun 2020 22:13:09: 13000000 INFO @ Sun, 21 Jun 2020 22:13:12: 3000000 INFO @ Sun, 21 Jun 2020 22:13:12: 8000000 INFO @ Sun, 21 Jun 2020 22:13:15: 14000000 INFO @ Sun, 21 Jun 2020 22:13:18: 4000000 INFO @ Sun, 21 Jun 2020 22:13:18: 9000000 INFO @ Sun, 21 Jun 2020 22:13:21: 15000000 INFO @ Sun, 21 Jun 2020 22:13:24: 5000000 INFO @ Sun, 21 Jun 2020 22:13:24: 10000000 INFO @ Sun, 21 Jun 2020 22:13:27: 16000000 INFO @ Sun, 21 Jun 2020 22:13:30: 6000000 INFO @ Sun, 21 Jun 2020 22:13:30: 11000000 INFO @ Sun, 21 Jun 2020 22:13:33: 17000000 INFO @ Sun, 21 Jun 2020 22:13:36: 7000000 INFO @ Sun, 21 Jun 2020 22:13:36: 12000000 INFO @ Sun, 21 Jun 2020 22:13:38: 18000000 INFO @ Sun, 21 Jun 2020 22:13:42: 8000000 INFO @ Sun, 21 Jun 2020 22:13:42: 13000000 INFO @ Sun, 21 Jun 2020 22:13:45: 19000000 INFO @ Sun, 21 Jun 2020 22:13:47: 14000000 INFO @ Sun, 21 Jun 2020 22:13:48: 9000000 INFO @ Sun, 21 Jun 2020 22:13:51: 20000000 INFO @ Sun, 21 Jun 2020 22:13:53: 15000000 INFO @ Sun, 21 Jun 2020 22:13:54: 10000000 INFO @ Sun, 21 Jun 2020 22:13:57: 21000000 INFO @ Sun, 21 Jun 2020 22:13:59: 16000000 INFO @ Sun, 21 Jun 2020 22:14:00: 11000000 INFO @ Sun, 21 Jun 2020 22:14:03: 22000000 INFO @ Sun, 21 Jun 2020 22:14:05: 17000000 INFO @ Sun, 21 Jun 2020 22:14:06: 12000000 INFO @ Sun, 21 Jun 2020 22:14:09: 23000000 INFO @ Sun, 21 Jun 2020 22:14:11: 18000000 INFO @ Sun, 21 Jun 2020 22:14:12: 13000000 INFO @ Sun, 21 Jun 2020 22:14:13: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:14:13: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:14:13: #1 total tags in treatment: 23671151 INFO @ Sun, 21 Jun 2020 22:14:13: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:14:13: #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 22:14:14: #1 tags after filtering in treatment: 23671151 INFO @ Sun, 21 Jun 2020 22:14:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:14:14: #1 finished! INFO @ Sun, 21 Jun 2020 22:14:14: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:14:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:14:16: #2 number of paired peaks: 565 WARNING @ Sun, 21 Jun 2020 22:14:16: Fewer paired peaks (565) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 565 pairs to build model! INFO @ Sun, 21 Jun 2020 22:14:16: start model_add_line... INFO @ Sun, 21 Jun 2020 22:14:16: start X-correlation... INFO @ Sun, 21 Jun 2020 22:14:16: end of X-cor INFO @ Sun, 21 Jun 2020 22:14:16: #2 finished! INFO @ Sun, 21 Jun 2020 22:14:16: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 22:14:16: #2 alternative fragment length(s) may be 1 bps INFO @ Sun, 21 Jun 2020 22:14:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5431045/SRX5431045.05_model.r WARNING @ Sun, 21 Jun 2020 22:14:16: #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 22:14:16: #2 You may need to consider one of the other alternative d(s): 1 WARNING @ Sun, 21 Jun 2020 22:14:16: #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 22:14:16: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:14:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:14:17: 19000000 INFO @ Sun, 21 Jun 2020 22:14:18: 14000000 INFO @ Sun, 21 Jun 2020 22:14:22: 20000000 INFO @ Sun, 21 Jun 2020 22:14:23: 15000000 INFO @ Sun, 21 Jun 2020 22:14:28: 21000000 INFO @ Sun, 21 Jun 2020 22:14:29: 16000000 INFO @ Sun, 21 Jun 2020 22:14:33: 22000000 INFO @ Sun, 21 Jun 2020 22:14:35: 17000000 INFO @ Sun, 21 Jun 2020 22:14:39: 23000000 INFO @ Sun, 21 Jun 2020 22:14:41: 18000000 INFO @ Sun, 21 Jun 2020 22:14:43: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:14:43: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:14:43: #1 total tags in treatment: 23671151 INFO @ Sun, 21 Jun 2020 22:14:43: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:14:43: #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 22:14:44: #1 tags after filtering in treatment: 23671151 INFO @ Sun, 21 Jun 2020 22:14:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:14:44: #1 finished! INFO @ Sun, 21 Jun 2020 22:14:44: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:14:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:14:46: #2 number of paired peaks: 565 WARNING @ Sun, 21 Jun 2020 22:14:46: Fewer paired peaks (565) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 565 pairs to build model! INFO @ Sun, 21 Jun 2020 22:14:46: start model_add_line... INFO @ Sun, 21 Jun 2020 22:14:46: start X-correlation... INFO @ Sun, 21 Jun 2020 22:14:46: end of X-cor INFO @ Sun, 21 Jun 2020 22:14:46: #2 finished! INFO @ Sun, 21 Jun 2020 22:14:46: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 22:14:46: #2 alternative fragment length(s) may be 1 bps INFO @ Sun, 21 Jun 2020 22:14:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5431045/SRX5431045.10_model.r WARNING @ Sun, 21 Jun 2020 22:14:46: #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 22:14:46: #2 You may need to consider one of the other alternative d(s): 1 WARNING @ Sun, 21 Jun 2020 22:14:46: #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 22:14:46: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:14:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:14:48: 19000000 INFO @ Sun, 21 Jun 2020 22:14:52: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:14:54: 20000000 INFO @ Sun, 21 Jun 2020 22:15:00: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:15:06: 22000000 INFO @ Sun, 21 Jun 2020 22:15:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5431045/SRX5431045.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:15:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5431045/SRX5431045.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:15:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5431045/SRX5431045.05_summits.bed INFO @ Sun, 21 Jun 2020 22:15:09: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:15:12: 23000000 INFO @ Sun, 21 Jun 2020 22:15:16: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:15:16: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:15:16: #1 total tags in treatment: 23671151 INFO @ Sun, 21 Jun 2020 22:15:16: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:15:16: #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 22:15:17: #1 tags after filtering in treatment: 23671151 INFO @ Sun, 21 Jun 2020 22:15:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:15:17: #1 finished! INFO @ Sun, 21 Jun 2020 22:15:17: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:15:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:15:19: #2 number of paired peaks: 565 WARNING @ Sun, 21 Jun 2020 22:15:19: Fewer paired peaks (565) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 565 pairs to build model! INFO @ Sun, 21 Jun 2020 22:15:19: start model_add_line... INFO @ Sun, 21 Jun 2020 22:15:19: start X-correlation... INFO @ Sun, 21 Jun 2020 22:15:19: end of X-cor INFO @ Sun, 21 Jun 2020 22:15:19: #2 finished! INFO @ Sun, 21 Jun 2020 22:15:19: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 22:15:19: #2 alternative fragment length(s) may be 1 bps INFO @ Sun, 21 Jun 2020 22:15:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5431045/SRX5431045.20_model.r WARNING @ Sun, 21 Jun 2020 22:15:19: #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 22:15:19: #2 You may need to consider one of the other alternative d(s): 1 WARNING @ Sun, 21 Jun 2020 22:15:19: #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 22:15:19: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:15:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:15:22: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:15:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5431045/SRX5431045.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:15:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5431045/SRX5431045.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:15:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5431045/SRX5431045.10_summits.bed INFO @ Sun, 21 Jun 2020 22:15:39: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:15:55: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:16:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5431045/SRX5431045.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:16:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5431045/SRX5431045.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:16:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5431045/SRX5431045.20_summits.bed INFO @ Sun, 21 Jun 2020 22:16:12: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。