Job ID = 6455173 SRX = SRX2804231 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:49:25 prefetch.2.10.7: 1) Downloading 'SRR5534659'... 2020-06-21T09:49:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:52:35 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:52:35 prefetch.2.10.7: 1) 'SRR5534659' was downloaded successfully 2020-06-21T09:52:35 prefetch.2.10.7: 'SRR5534659' has 0 unresolved dependencies Read 34261541 spots for SRR5534659/SRR5534659.sra Written 34261541 spots for SRR5534659/SRR5534659.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: 00:08:33 34261541 reads; of these: 34261541 (100.00%) were unpaired; of these: 6601512 (19.27%) aligned 0 times 18087925 (52.79%) aligned exactly 1 time 9572104 (27.94%) aligned >1 times 80.73% overall alignment rate Time searching: 00:08:33 Overall time: 00:08:33 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] 6372450 / 27660029 = 0.2304 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 19:07:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2804231/SRX2804231.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2804231/SRX2804231.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2804231/SRX2804231.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2804231/SRX2804231.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 19:07:53: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:07:53: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:07:59: 1000000 INFO @ Sun, 21 Jun 2020 19:08:04: 2000000 INFO @ Sun, 21 Jun 2020 19:08:10: 3000000 INFO @ Sun, 21 Jun 2020 19:08:15: 4000000 INFO @ Sun, 21 Jun 2020 19:08:20: 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 19:08:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2804231/SRX2804231.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2804231/SRX2804231.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2804231/SRX2804231.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2804231/SRX2804231.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 19:08:23: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:08:23: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:08:26: 6000000 INFO @ Sun, 21 Jun 2020 19:08:31: 1000000 INFO @ Sun, 21 Jun 2020 19:08:32: 7000000 INFO @ Sun, 21 Jun 2020 19:08:38: 2000000 INFO @ Sun, 21 Jun 2020 19:08:39: 8000000 INFO @ Sun, 21 Jun 2020 19:08:44: 3000000 INFO @ Sun, 21 Jun 2020 19:08:45: 9000000 INFO @ Sun, 21 Jun 2020 19:08:51: 4000000 INFO @ Sun, 21 Jun 2020 19:08:51: 10000000 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 19:08:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2804231/SRX2804231.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2804231/SRX2804231.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2804231/SRX2804231.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2804231/SRX2804231.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 19:08:53: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:08:53: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:08:58: 11000000 INFO @ Sun, 21 Jun 2020 19:08:58: 5000000 INFO @ Sun, 21 Jun 2020 19:09:00: 1000000 INFO @ Sun, 21 Jun 2020 19:09:04: 12000000 INFO @ Sun, 21 Jun 2020 19:09:05: 6000000 INFO @ Sun, 21 Jun 2020 19:09:07: 2000000 INFO @ Sun, 21 Jun 2020 19:09:11: 13000000 INFO @ Sun, 21 Jun 2020 19:09:12: 7000000 INFO @ Sun, 21 Jun 2020 19:09:14: 3000000 INFO @ Sun, 21 Jun 2020 19:09:17: 14000000 INFO @ Sun, 21 Jun 2020 19:09:19: 8000000 INFO @ Sun, 21 Jun 2020 19:09:21: 4000000 INFO @ Sun, 21 Jun 2020 19:09:24: 15000000 INFO @ Sun, 21 Jun 2020 19:09:26: 9000000 INFO @ Sun, 21 Jun 2020 19:09:28: 5000000 INFO @ Sun, 21 Jun 2020 19:09:30: 16000000 INFO @ Sun, 21 Jun 2020 19:09:34: 10000000 INFO @ Sun, 21 Jun 2020 19:09:35: 6000000 INFO @ Sun, 21 Jun 2020 19:09:37: 17000000 INFO @ Sun, 21 Jun 2020 19:09:41: 11000000 INFO @ Sun, 21 Jun 2020 19:09:42: 7000000 INFO @ Sun, 21 Jun 2020 19:09:43: 18000000 INFO @ Sun, 21 Jun 2020 19:09:48: 12000000 INFO @ Sun, 21 Jun 2020 19:09:49: 8000000 INFO @ Sun, 21 Jun 2020 19:09:50: 19000000 INFO @ Sun, 21 Jun 2020 19:09:55: 13000000 INFO @ Sun, 21 Jun 2020 19:09:56: 9000000 INFO @ Sun, 21 Jun 2020 19:09:56: 20000000 INFO @ Sun, 21 Jun 2020 19:10:02: 14000000 INFO @ Sun, 21 Jun 2020 19:10:03: 21000000 INFO @ Sun, 21 Jun 2020 19:10:03: 10000000 INFO @ Sun, 21 Jun 2020 19:10:05: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:10:05: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:10:05: #1 total tags in treatment: 21287579 INFO @ Sun, 21 Jun 2020 19:10:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:10:05: #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 19:10:05: #1 tags after filtering in treatment: 21287579 INFO @ Sun, 21 Jun 2020 19:10:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:10:05: #1 finished! INFO @ Sun, 21 Jun 2020 19:10:05: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:10:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:10:07: #2 number of paired peaks: 692 WARNING @ Sun, 21 Jun 2020 19:10:07: Fewer paired peaks (692) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 692 pairs to build model! INFO @ Sun, 21 Jun 2020 19:10:07: start model_add_line... INFO @ Sun, 21 Jun 2020 19:10:07: start X-correlation... INFO @ Sun, 21 Jun 2020 19:10:07: end of X-cor INFO @ Sun, 21 Jun 2020 19:10:07: #2 finished! INFO @ Sun, 21 Jun 2020 19:10:07: #2 predicted fragment length is 46 bps INFO @ Sun, 21 Jun 2020 19:10:07: #2 alternative fragment length(s) may be 2,46 bps INFO @ Sun, 21 Jun 2020 19:10:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2804231/SRX2804231.05_model.r WARNING @ Sun, 21 Jun 2020 19:10:07: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:10:07: #2 You may need to consider one of the other alternative d(s): 2,46 WARNING @ Sun, 21 Jun 2020 19:10:07: #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 19:10:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:10:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:10:09: 15000000 INFO @ Sun, 21 Jun 2020 19:10:10: 11000000 INFO @ Sun, 21 Jun 2020 19:10:16: 16000000 INFO @ Sun, 21 Jun 2020 19:10:17: 12000000 INFO @ Sun, 21 Jun 2020 19:10:23: 17000000 INFO @ Sun, 21 Jun 2020 19:10:24: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:10:30: 18000000 INFO @ Sun, 21 Jun 2020 19:10:31: 14000000 INFO @ Sun, 21 Jun 2020 19:10:37: 19000000 INFO @ Sun, 21 Jun 2020 19:10:38: 15000000 INFO @ Sun, 21 Jun 2020 19:10:44: 20000000 INFO @ Sun, 21 Jun 2020 19:10:45: 16000000 INFO @ Sun, 21 Jun 2020 19:10:45: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:10:51: 21000000 INFO @ Sun, 21 Jun 2020 19:10:52: 17000000 INFO @ Sun, 21 Jun 2020 19:10:53: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:10:53: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:10:53: #1 total tags in treatment: 21287579 INFO @ Sun, 21 Jun 2020 19:10:53: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:10:53: #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 19:10:54: #1 tags after filtering in treatment: 21287579 INFO @ Sun, 21 Jun 2020 19:10:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:10:54: #1 finished! INFO @ Sun, 21 Jun 2020 19:10:54: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:10:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:10:55: #2 number of paired peaks: 692 WARNING @ Sun, 21 Jun 2020 19:10:55: Fewer paired peaks (692) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 692 pairs to build model! INFO @ Sun, 21 Jun 2020 19:10:55: start model_add_line... INFO @ Sun, 21 Jun 2020 19:10:55: start X-correlation... INFO @ Sun, 21 Jun 2020 19:10:55: end of X-cor INFO @ Sun, 21 Jun 2020 19:10:55: #2 finished! INFO @ Sun, 21 Jun 2020 19:10:55: #2 predicted fragment length is 46 bps INFO @ Sun, 21 Jun 2020 19:10:55: #2 alternative fragment length(s) may be 2,46 bps INFO @ Sun, 21 Jun 2020 19:10:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2804231/SRX2804231.10_model.r WARNING @ Sun, 21 Jun 2020 19:10:55: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:10:55: #2 You may need to consider one of the other alternative d(s): 2,46 WARNING @ Sun, 21 Jun 2020 19:10:55: #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 19:10:55: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:10:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:10:58: 18000000 INFO @ Sun, 21 Jun 2020 19:11:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2804231/SRX2804231.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:11:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2804231/SRX2804231.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:11:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2804231/SRX2804231.05_summits.bed INFO @ Sun, 21 Jun 2020 19:11:04: Done! pass1 - making usageList (748 chroms): 1 millis pass2 - checking and writing primary data (5126 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:11:05: 19000000 INFO @ Sun, 21 Jun 2020 19:11:11: 20000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:11:17: 21000000 INFO @ Sun, 21 Jun 2020 19:11:19: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:11:19: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:11:19: #1 total tags in treatment: 21287579 INFO @ Sun, 21 Jun 2020 19:11:19: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:11:19: #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 19:11:20: #1 tags after filtering in treatment: 21287579 INFO @ Sun, 21 Jun 2020 19:11:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:11:20: #1 finished! INFO @ Sun, 21 Jun 2020 19:11:20: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:11:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:11:21: #2 number of paired peaks: 692 WARNING @ Sun, 21 Jun 2020 19:11:21: Fewer paired peaks (692) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 692 pairs to build model! INFO @ Sun, 21 Jun 2020 19:11:21: start model_add_line... INFO @ Sun, 21 Jun 2020 19:11:21: start X-correlation... INFO @ Sun, 21 Jun 2020 19:11:21: end of X-cor INFO @ Sun, 21 Jun 2020 19:11:21: #2 finished! INFO @ Sun, 21 Jun 2020 19:11:21: #2 predicted fragment length is 46 bps INFO @ Sun, 21 Jun 2020 19:11:21: #2 alternative fragment length(s) may be 2,46 bps INFO @ Sun, 21 Jun 2020 19:11:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2804231/SRX2804231.20_model.r WARNING @ Sun, 21 Jun 2020 19:11:21: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:11:21: #2 You may need to consider one of the other alternative d(s): 2,46 WARNING @ Sun, 21 Jun 2020 19:11:21: #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 19:11:21: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:11:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:11:33: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:11:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2804231/SRX2804231.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:11:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2804231/SRX2804231.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:11:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2804231/SRX2804231.10_summits.bed INFO @ Sun, 21 Jun 2020 19:11:51: Done! pass1 - making usageList (620 chroms): 1 millis pass2 - checking and writing primary data (2864 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:12:00: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:12:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2804231/SRX2804231.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:12:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2804231/SRX2804231.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:12:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2804231/SRX2804231.20_summits.bed INFO @ Sun, 21 Jun 2020 19:12:18: Done! pass1 - making usageList (443 chroms): 1 millis pass2 - checking and writing primary data (1404 records, 4 fields): 13 millis CompletedMACS2peakCalling