Job ID = 6455666 SRX = SRX287971 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:12:06 prefetch.2.10.7: 1) Downloading 'SRR870160'... 2020-06-21T10:12:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:14:10 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:14:11 prefetch.2.10.7: 'SRR870160' is valid 2020-06-21T10:14:11 prefetch.2.10.7: 1) 'SRR870160' was downloaded successfully Read 13809114 spots for SRR870160/SRR870160.sra Written 13809114 spots for SRR870160/SRR870160.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: 00:04:07 13809114 reads; of these: 13809114 (100.00%) were unpaired; of these: 756601 (5.48%) aligned 0 times 9039913 (65.46%) aligned exactly 1 time 4012600 (29.06%) aligned >1 times 94.52% overall alignment rate Time searching: 00:04:07 Overall time: 00:04:07 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 8 files... [bam_rmdupse_core] 2216468 / 13052513 = 0.1698 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 19:22:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287971/SRX287971.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287971/SRX287971.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287971/SRX287971.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287971/SRX287971.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 19:22:27: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:22:27: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:22:33: 1000000 INFO @ Sun, 21 Jun 2020 19:22:40: 2000000 INFO @ Sun, 21 Jun 2020 19:22:46: 3000000 INFO @ Sun, 21 Jun 2020 19:22:52: 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 19:22:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287971/SRX287971.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287971/SRX287971.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287971/SRX287971.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287971/SRX287971.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 19:22:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:22:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:22:59: 5000000 INFO @ Sun, 21 Jun 2020 19:23:04: 1000000 INFO @ Sun, 21 Jun 2020 19:23:07: 6000000 INFO @ Sun, 21 Jun 2020 19:23:11: 2000000 INFO @ Sun, 21 Jun 2020 19:23:14: 7000000 INFO @ Sun, 21 Jun 2020 19:23:19: 3000000 INFO @ Sun, 21 Jun 2020 19:23:21: 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 19:23:26: 4000000 INFO @ Sun, 21 Jun 2020 19:23:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287971/SRX287971.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287971/SRX287971.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287971/SRX287971.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287971/SRX287971.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 19:23:27: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:23:27: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:23:29: 9000000 INFO @ Sun, 21 Jun 2020 19:23:34: 5000000 INFO @ Sun, 21 Jun 2020 19:23:34: 1000000 INFO @ Sun, 21 Jun 2020 19:23:37: 10000000 INFO @ Sun, 21 Jun 2020 19:23:41: 6000000 INFO @ Sun, 21 Jun 2020 19:23:42: 2000000 INFO @ Sun, 21 Jun 2020 19:23:43: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:23:43: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:23:43: #1 total tags in treatment: 10836045 INFO @ Sun, 21 Jun 2020 19:23:43: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:23:43: #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 19:23:44: #1 tags after filtering in treatment: 10836045 INFO @ Sun, 21 Jun 2020 19:23:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:23:44: #1 finished! INFO @ Sun, 21 Jun 2020 19:23:44: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:23:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:23:44: #2 number of paired peaks: 711 WARNING @ Sun, 21 Jun 2020 19:23:44: Fewer paired peaks (711) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 711 pairs to build model! INFO @ Sun, 21 Jun 2020 19:23:44: start model_add_line... INFO @ Sun, 21 Jun 2020 19:23:44: start X-correlation... INFO @ Sun, 21 Jun 2020 19:23:44: end of X-cor INFO @ Sun, 21 Jun 2020 19:23:44: #2 finished! INFO @ Sun, 21 Jun 2020 19:23:44: #2 predicted fragment length is 46 bps INFO @ Sun, 21 Jun 2020 19:23:44: #2 alternative fragment length(s) may be 4,46 bps INFO @ Sun, 21 Jun 2020 19:23:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287971/SRX287971.05_model.r WARNING @ Sun, 21 Jun 2020 19:23:44: #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 19:23:44: #2 You may need to consider one of the other alternative d(s): 4,46 WARNING @ Sun, 21 Jun 2020 19:23:44: #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 19:23:44: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:23:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:23:49: 7000000 INFO @ Sun, 21 Jun 2020 19:23:49: 3000000 INFO @ Sun, 21 Jun 2020 19:23:56: 8000000 INFO @ Sun, 21 Jun 2020 19:23:56: 4000000 INFO @ Sun, 21 Jun 2020 19:24:03: 5000000 INFO @ Sun, 21 Jun 2020 19:24:04: 9000000 INFO @ Sun, 21 Jun 2020 19:24:06: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:24:11: 6000000 INFO @ Sun, 21 Jun 2020 19:24:11: 10000000 INFO @ Sun, 21 Jun 2020 19:24:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287971/SRX287971.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:24:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287971/SRX287971.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:24:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287971/SRX287971.05_summits.bed INFO @ Sun, 21 Jun 2020 19:24:16: Done! pass1 - making usageList (579 chroms): 1 millis pass2 - checking and writing primary data (2210 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:24:17: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:24:17: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:24:17: #1 total tags in treatment: 10836045 INFO @ Sun, 21 Jun 2020 19:24:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:24:17: #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 19:24:18: #1 tags after filtering in treatment: 10836045 INFO @ Sun, 21 Jun 2020 19:24:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:24:18: #1 finished! INFO @ Sun, 21 Jun 2020 19:24:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:24:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:24:18: 7000000 INFO @ Sun, 21 Jun 2020 19:24:18: #2 number of paired peaks: 711 WARNING @ Sun, 21 Jun 2020 19:24:18: Fewer paired peaks (711) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 711 pairs to build model! INFO @ Sun, 21 Jun 2020 19:24:18: start model_add_line... INFO @ Sun, 21 Jun 2020 19:24:19: start X-correlation... INFO @ Sun, 21 Jun 2020 19:24:19: end of X-cor INFO @ Sun, 21 Jun 2020 19:24:19: #2 finished! INFO @ Sun, 21 Jun 2020 19:24:19: #2 predicted fragment length is 46 bps INFO @ Sun, 21 Jun 2020 19:24:19: #2 alternative fragment length(s) may be 4,46 bps INFO @ Sun, 21 Jun 2020 19:24:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287971/SRX287971.10_model.r WARNING @ Sun, 21 Jun 2020 19:24:19: #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 19:24:19: #2 You may need to consider one of the other alternative d(s): 4,46 WARNING @ Sun, 21 Jun 2020 19:24:19: #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 19:24:19: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:24:19: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:24:25: 8000000 INFO @ Sun, 21 Jun 2020 19:24:32: 9000000 INFO @ Sun, 21 Jun 2020 19:24:39: 10000000 INFO @ Sun, 21 Jun 2020 19:24:40: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:24:45: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:24:45: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:24:45: #1 total tags in treatment: 10836045 INFO @ Sun, 21 Jun 2020 19:24:45: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:24:45: #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 19:24:46: #1 tags after filtering in treatment: 10836045 INFO @ Sun, 21 Jun 2020 19:24:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:24:46: #1 finished! INFO @ Sun, 21 Jun 2020 19:24:46: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:24:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:24:47: #2 number of paired peaks: 711 WARNING @ Sun, 21 Jun 2020 19:24:47: Fewer paired peaks (711) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 711 pairs to build model! INFO @ Sun, 21 Jun 2020 19:24:47: start model_add_line... INFO @ Sun, 21 Jun 2020 19:24:47: start X-correlation... INFO @ Sun, 21 Jun 2020 19:24:47: end of X-cor INFO @ Sun, 21 Jun 2020 19:24:47: #2 finished! INFO @ Sun, 21 Jun 2020 19:24:47: #2 predicted fragment length is 46 bps INFO @ Sun, 21 Jun 2020 19:24:47: #2 alternative fragment length(s) may be 4,46 bps INFO @ Sun, 21 Jun 2020 19:24:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287971/SRX287971.20_model.r WARNING @ Sun, 21 Jun 2020 19:24:47: #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 19:24:47: #2 You may need to consider one of the other alternative d(s): 4,46 WARNING @ Sun, 21 Jun 2020 19:24:47: #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 19:24:47: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:24:47: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:24:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287971/SRX287971.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:24:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287971/SRX287971.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:24:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287971/SRX287971.10_summits.bed INFO @ Sun, 21 Jun 2020 19:24:50: Done! pass1 - making usageList (492 chroms): 1 millis pass2 - checking and writing primary data (1816 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:25:08: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:25:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287971/SRX287971.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:25:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287971/SRX287971.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:25:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287971/SRX287971.20_summits.bed INFO @ Sun, 21 Jun 2020 19:25:18: Done! pass1 - making usageList (325 chroms): 1 millis pass2 - checking and writing primary data (703 records, 4 fields): 11 millis CompletedMACS2peakCalling