Job ID = 6458741 SRX = SRX5431044 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:34:37 prefetch.2.10.7: 1) Downloading 'SRR8632343'... 2020-06-21T12:34:37 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:37:41 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:37:41 prefetch.2.10.7: 1) 'SRR8632343' was downloaded successfully Read 29042910 spots for SRR8632343/SRR8632343.sra Written 29042910 spots for SRR8632343/SRR8632343.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:13 29042910 reads; of these: 29042910 (100.00%) were unpaired; of these: 2541808 (8.75%) aligned 0 times 18523351 (63.78%) aligned exactly 1 time 7977751 (27.47%) aligned >1 times 91.25% overall alignment rate Time searching: 00:08:14 Overall time: 00:08:14 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] 4413307 / 26501102 = 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 21:53:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5431044/SRX5431044.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5431044/SRX5431044.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5431044/SRX5431044.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5431044/SRX5431044.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 21:53:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:53:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:53:15: 1000000 INFO @ Sun, 21 Jun 2020 21:53:21: 2000000 INFO @ Sun, 21 Jun 2020 21:53:26: 3000000 INFO @ Sun, 21 Jun 2020 21:53:31: 4000000 INFO @ Sun, 21 Jun 2020 21:53:36: 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 21:53:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5431044/SRX5431044.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5431044/SRX5431044.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5431044/SRX5431044.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5431044/SRX5431044.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 21:53:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:53:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:53:42: 6000000 INFO @ Sun, 21 Jun 2020 21:53:46: 1000000 INFO @ Sun, 21 Jun 2020 21:53:48: 7000000 INFO @ Sun, 21 Jun 2020 21:53:51: 2000000 INFO @ Sun, 21 Jun 2020 21:53:53: 8000000 INFO @ Sun, 21 Jun 2020 21:53:57: 3000000 INFO @ Sun, 21 Jun 2020 21:53:59: 9000000 INFO @ Sun, 21 Jun 2020 21:54:02: 4000000 INFO @ Sun, 21 Jun 2020 21:54:05: 10000000 INFO @ Sun, 21 Jun 2020 21:54:08: 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 21:54:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5431044/SRX5431044.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5431044/SRX5431044.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5431044/SRX5431044.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5431044/SRX5431044.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 21:54:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:54:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:54:10: 11000000 INFO @ Sun, 21 Jun 2020 21:54:14: 6000000 INFO @ Sun, 21 Jun 2020 21:54:16: 12000000 INFO @ Sun, 21 Jun 2020 21:54:17: 1000000 INFO @ Sun, 21 Jun 2020 21:54:19: 7000000 INFO @ Sun, 21 Jun 2020 21:54:22: 13000000 INFO @ Sun, 21 Jun 2020 21:54:23: 2000000 INFO @ Sun, 21 Jun 2020 21:54:25: 8000000 INFO @ Sun, 21 Jun 2020 21:54:28: 14000000 INFO @ Sun, 21 Jun 2020 21:54:30: 3000000 INFO @ Sun, 21 Jun 2020 21:54:31: 9000000 INFO @ Sun, 21 Jun 2020 21:54:34: 15000000 INFO @ Sun, 21 Jun 2020 21:54:36: 4000000 INFO @ Sun, 21 Jun 2020 21:54:37: 10000000 INFO @ Sun, 21 Jun 2020 21:54:40: 16000000 INFO @ Sun, 21 Jun 2020 21:54:43: 5000000 INFO @ Sun, 21 Jun 2020 21:54:43: 11000000 INFO @ Sun, 21 Jun 2020 21:54:46: 17000000 INFO @ Sun, 21 Jun 2020 21:54:49: 12000000 INFO @ Sun, 21 Jun 2020 21:54:49: 6000000 INFO @ Sun, 21 Jun 2020 21:54:52: 18000000 INFO @ Sun, 21 Jun 2020 21:54:55: 13000000 INFO @ Sun, 21 Jun 2020 21:54:56: 7000000 INFO @ Sun, 21 Jun 2020 21:54:58: 19000000 INFO @ Sun, 21 Jun 2020 21:55:01: 14000000 INFO @ Sun, 21 Jun 2020 21:55:03: 8000000 INFO @ Sun, 21 Jun 2020 21:55:04: 20000000 INFO @ Sun, 21 Jun 2020 21:55:07: 15000000 INFO @ Sun, 21 Jun 2020 21:55:09: 9000000 INFO @ Sun, 21 Jun 2020 21:55:10: 21000000 INFO @ Sun, 21 Jun 2020 21:55:13: 16000000 INFO @ Sun, 21 Jun 2020 21:55:16: 10000000 INFO @ Sun, 21 Jun 2020 21:55:17: 22000000 INFO @ Sun, 21 Jun 2020 21:55:17: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:55:17: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:55:17: #1 total tags in treatment: 22087795 INFO @ Sun, 21 Jun 2020 21:55:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:55:17: #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 21:55:18: #1 tags after filtering in treatment: 22087795 INFO @ Sun, 21 Jun 2020 21:55:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:55:18: #1 finished! INFO @ Sun, 21 Jun 2020 21:55:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:55:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:55:19: 17000000 INFO @ Sun, 21 Jun 2020 21:55:20: #2 number of paired peaks: 605 WARNING @ Sun, 21 Jun 2020 21:55:20: Fewer paired peaks (605) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 605 pairs to build model! INFO @ Sun, 21 Jun 2020 21:55:20: start model_add_line... INFO @ Sun, 21 Jun 2020 21:55:20: start X-correlation... INFO @ Sun, 21 Jun 2020 21:55:20: end of X-cor INFO @ Sun, 21 Jun 2020 21:55:20: #2 finished! INFO @ Sun, 21 Jun 2020 21:55:20: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 21:55:20: #2 alternative fragment length(s) may be 2,30 bps INFO @ Sun, 21 Jun 2020 21:55:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5431044/SRX5431044.05_model.r WARNING @ Sun, 21 Jun 2020 21:55:20: #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 21:55:20: #2 You may need to consider one of the other alternative d(s): 2,30 WARNING @ Sun, 21 Jun 2020 21:55:20: #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 21:55:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:55:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:55:22: 11000000 INFO @ Sun, 21 Jun 2020 21:55:25: 18000000 INFO @ Sun, 21 Jun 2020 21:55:29: 12000000 INFO @ Sun, 21 Jun 2020 21:55:31: 19000000 INFO @ Sun, 21 Jun 2020 21:55:35: 13000000 INFO @ Sun, 21 Jun 2020 21:55:38: 20000000 INFO @ Sun, 21 Jun 2020 21:55:42: 14000000 INFO @ Sun, 21 Jun 2020 21:55:44: 21000000 INFO @ Sun, 21 Jun 2020 21:55:48: 15000000 INFO @ Sun, 21 Jun 2020 21:55:50: 22000000 INFO @ Sun, 21 Jun 2020 21:55:51: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:55:51: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:55:51: #1 total tags in treatment: 22087795 INFO @ Sun, 21 Jun 2020 21:55:51: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:55:51: #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 21:55:52: #1 tags after filtering in treatment: 22087795 INFO @ Sun, 21 Jun 2020 21:55:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:55:52: #1 finished! INFO @ Sun, 21 Jun 2020 21:55:52: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:55:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:55:53: #2 number of paired peaks: 605 WARNING @ Sun, 21 Jun 2020 21:55:53: Fewer paired peaks (605) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 605 pairs to build model! INFO @ Sun, 21 Jun 2020 21:55:53: start model_add_line... INFO @ Sun, 21 Jun 2020 21:55:53: start X-correlation... INFO @ Sun, 21 Jun 2020 21:55:53: end of X-cor INFO @ Sun, 21 Jun 2020 21:55:53: #2 finished! INFO @ Sun, 21 Jun 2020 21:55:53: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 21:55:53: #2 alternative fragment length(s) may be 2,30 bps INFO @ Sun, 21 Jun 2020 21:55:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5431044/SRX5431044.10_model.r WARNING @ Sun, 21 Jun 2020 21:55:53: #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 21:55:53: #2 You may need to consider one of the other alternative d(s): 2,30 WARNING @ Sun, 21 Jun 2020 21:55:53: #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 21:55:53: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:55:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:55:54: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:56:01: 17000000 INFO @ Sun, 21 Jun 2020 21:56:01: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:56:07: 18000000 INFO @ Sun, 21 Jun 2020 21:56:13: 19000000 INFO @ Sun, 21 Jun 2020 21:56:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5431044/SRX5431044.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:56:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5431044/SRX5431044.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:56:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5431044/SRX5431044.05_summits.bed INFO @ Sun, 21 Jun 2020 21:56:19: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:56:20: 20000000 INFO @ Sun, 21 Jun 2020 21:56:26: 21000000 INFO @ Sun, 21 Jun 2020 21:56:32: 22000000 INFO @ Sun, 21 Jun 2020 21:56:33: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:56:33: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:56:33: #1 total tags in treatment: 22087795 INFO @ Sun, 21 Jun 2020 21:56:33: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:56:33: #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 21:56:33: #1 tags after filtering in treatment: 22087795 INFO @ Sun, 21 Jun 2020 21:56:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:56:33: #1 finished! INFO @ Sun, 21 Jun 2020 21:56:33: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:56:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:56:34: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:56:35: #2 number of paired peaks: 605 WARNING @ Sun, 21 Jun 2020 21:56:35: Fewer paired peaks (605) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 605 pairs to build model! INFO @ Sun, 21 Jun 2020 21:56:35: start model_add_line... INFO @ Sun, 21 Jun 2020 21:56:35: start X-correlation... INFO @ Sun, 21 Jun 2020 21:56:35: end of X-cor INFO @ Sun, 21 Jun 2020 21:56:35: #2 finished! INFO @ Sun, 21 Jun 2020 21:56:35: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 21:56:35: #2 alternative fragment length(s) may be 2,30 bps INFO @ Sun, 21 Jun 2020 21:56:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5431044/SRX5431044.20_model.r WARNING @ Sun, 21 Jun 2020 21:56:35: #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 21:56:35: #2 You may need to consider one of the other alternative d(s): 2,30 WARNING @ Sun, 21 Jun 2020 21:56:35: #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 21:56:35: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:56:35: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:56:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5431044/SRX5431044.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:56:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5431044/SRX5431044.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:56:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5431044/SRX5431044.10_summits.bed INFO @ Sun, 21 Jun 2020 21:56:52: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:57:14: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:57:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5431044/SRX5431044.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:57:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5431044/SRX5431044.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:57:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5431044/SRX5431044.20_summits.bed INFO @ Sun, 21 Jun 2020 21:57:31: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling