Job ID = 6455532 SRX = SRX287862 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:06:40 prefetch.2.10.7: 1) Downloading 'SRR870051'... 2020-06-21T10:06:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:10:40 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:10:40 prefetch.2.10.7: 1) 'SRR870051' was downloaded successfully Read 17667108 spots for SRR870051/SRR870051.sra Written 17667108 spots for SRR870051/SRR870051.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: 00:05:21 17667108 reads; of these: 17667108 (100.00%) were unpaired; of these: 989120 (5.60%) aligned 0 times 11539810 (65.32%) aligned exactly 1 time 5138178 (29.08%) aligned >1 times 94.40% overall alignment rate Time searching: 00:05:21 Overall time: 00:05:21 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] 2390534 / 16677988 = 0.1433 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 19:21:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287862/SRX287862.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287862/SRX287862.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287862/SRX287862.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287862/SRX287862.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 19:21:14: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:21:14: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:21:21: 1000000 INFO @ Sun, 21 Jun 2020 19:21:28: 2000000 INFO @ Sun, 21 Jun 2020 19:21:35: 3000000 INFO @ Sun, 21 Jun 2020 19:21:42: 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 19:21:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287862/SRX287862.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287862/SRX287862.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287862/SRX287862.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287862/SRX287862.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 19:21:44: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:21:44: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:21:49: 5000000 INFO @ Sun, 21 Jun 2020 19:21:51: 1000000 INFO @ Sun, 21 Jun 2020 19:21:57: 6000000 INFO @ Sun, 21 Jun 2020 19:21:58: 2000000 INFO @ Sun, 21 Jun 2020 19:22:05: 7000000 INFO @ Sun, 21 Jun 2020 19:22:05: 3000000 INFO @ Sun, 21 Jun 2020 19:22:12: 4000000 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 19:22:13: 8000000 INFO @ Sun, 21 Jun 2020 19:22:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287862/SRX287862.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287862/SRX287862.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287862/SRX287862.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287862/SRX287862.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 19:22:14: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:22:14: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:22:19: 5000000 INFO @ Sun, 21 Jun 2020 19:22:21: 9000000 INFO @ Sun, 21 Jun 2020 19:22:22: 1000000 INFO @ Sun, 21 Jun 2020 19:22:26: 6000000 INFO @ Sun, 21 Jun 2020 19:22:29: 10000000 INFO @ Sun, 21 Jun 2020 19:22:30: 2000000 INFO @ Sun, 21 Jun 2020 19:22:33: 7000000 INFO @ Sun, 21 Jun 2020 19:22:37: 11000000 INFO @ Sun, 21 Jun 2020 19:22:38: 3000000 INFO @ Sun, 21 Jun 2020 19:22:40: 8000000 INFO @ Sun, 21 Jun 2020 19:22:45: 12000000 INFO @ Sun, 21 Jun 2020 19:22:46: 4000000 INFO @ Sun, 21 Jun 2020 19:22:47: 9000000 INFO @ Sun, 21 Jun 2020 19:22:53: 13000000 INFO @ Sun, 21 Jun 2020 19:22:53: 5000000 INFO @ Sun, 21 Jun 2020 19:22:54: 10000000 INFO @ Sun, 21 Jun 2020 19:23:01: 14000000 INFO @ Sun, 21 Jun 2020 19:23:01: 6000000 INFO @ Sun, 21 Jun 2020 19:23:02: 11000000 INFO @ Sun, 21 Jun 2020 19:23:03: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:23:03: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:23:03: #1 total tags in treatment: 14287454 INFO @ Sun, 21 Jun 2020 19:23:03: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:23:03: #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 19:23:04: #1 tags after filtering in treatment: 14287454 INFO @ Sun, 21 Jun 2020 19:23:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:23:04: #1 finished! INFO @ Sun, 21 Jun 2020 19:23:04: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:23:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:23:05: #2 number of paired peaks: 433 WARNING @ Sun, 21 Jun 2020 19:23:05: Fewer paired peaks (433) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 433 pairs to build model! INFO @ Sun, 21 Jun 2020 19:23:05: start model_add_line... INFO @ Sun, 21 Jun 2020 19:23:05: start X-correlation... INFO @ Sun, 21 Jun 2020 19:23:05: end of X-cor INFO @ Sun, 21 Jun 2020 19:23:05: #2 finished! INFO @ Sun, 21 Jun 2020 19:23:05: #2 predicted fragment length is 44 bps INFO @ Sun, 21 Jun 2020 19:23:05: #2 alternative fragment length(s) may be 4,44 bps INFO @ Sun, 21 Jun 2020 19:23:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287862/SRX287862.05_model.r WARNING @ Sun, 21 Jun 2020 19:23:05: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:23:05: #2 You may need to consider one of the other alternative d(s): 4,44 WARNING @ Sun, 21 Jun 2020 19:23:05: #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 19:23:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:23:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:23:09: 12000000 INFO @ Sun, 21 Jun 2020 19:23:09: 7000000 INFO @ Sun, 21 Jun 2020 19:23:16: 13000000 INFO @ Sun, 21 Jun 2020 19:23:17: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:23:23: 14000000 INFO @ Sun, 21 Jun 2020 19:23:25: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:23:25: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:23:25: #1 total tags in treatment: 14287454 INFO @ Sun, 21 Jun 2020 19:23:25: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:23:25: #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 19:23:25: 9000000 INFO @ Sun, 21 Jun 2020 19:23:26: #1 tags after filtering in treatment: 14287454 INFO @ Sun, 21 Jun 2020 19:23:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:23:26: #1 finished! INFO @ Sun, 21 Jun 2020 19:23:26: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:23:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:23:27: #2 number of paired peaks: 433 WARNING @ Sun, 21 Jun 2020 19:23:27: Fewer paired peaks (433) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 433 pairs to build model! INFO @ Sun, 21 Jun 2020 19:23:27: start model_add_line... INFO @ Sun, 21 Jun 2020 19:23:27: start X-correlation... INFO @ Sun, 21 Jun 2020 19:23:27: end of X-cor INFO @ Sun, 21 Jun 2020 19:23:27: #2 finished! INFO @ Sun, 21 Jun 2020 19:23:27: #2 predicted fragment length is 44 bps INFO @ Sun, 21 Jun 2020 19:23:27: #2 alternative fragment length(s) may be 4,44 bps INFO @ Sun, 21 Jun 2020 19:23:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287862/SRX287862.10_model.r WARNING @ Sun, 21 Jun 2020 19:23:27: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:23:27: #2 You may need to consider one of the other alternative d(s): 4,44 WARNING @ Sun, 21 Jun 2020 19:23:27: #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 19:23:27: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:23:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:23:31: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:23:33: 10000000 INFO @ Sun, 21 Jun 2020 19:23:40: 11000000 INFO @ Sun, 21 Jun 2020 19:23:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287862/SRX287862.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:23:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287862/SRX287862.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:23:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287862/SRX287862.05_summits.bed INFO @ Sun, 21 Jun 2020 19:23:44: Done! pass1 - making usageList (620 chroms): 1 millis pass2 - checking and writing primary data (2353 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:23:48: 12000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:23:54: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:23:55: 13000000 INFO @ Sun, 21 Jun 2020 19:24:03: 14000000 INFO @ Sun, 21 Jun 2020 19:24:05: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:24:05: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:24:05: #1 total tags in treatment: 14287454 INFO @ Sun, 21 Jun 2020 19:24:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:24:05: #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 19:24:05: #1 tags after filtering in treatment: 14287454 INFO @ Sun, 21 Jun 2020 19:24:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:24:05: #1 finished! INFO @ Sun, 21 Jun 2020 19:24:05: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:24:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:24:06: #2 number of paired peaks: 433 WARNING @ Sun, 21 Jun 2020 19:24:06: Fewer paired peaks (433) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 433 pairs to build model! INFO @ Sun, 21 Jun 2020 19:24:06: start model_add_line... INFO @ Sun, 21 Jun 2020 19:24:06: start X-correlation... INFO @ Sun, 21 Jun 2020 19:24:06: end of X-cor INFO @ Sun, 21 Jun 2020 19:24:06: #2 finished! INFO @ Sun, 21 Jun 2020 19:24:06: #2 predicted fragment length is 44 bps INFO @ Sun, 21 Jun 2020 19:24:06: #2 alternative fragment length(s) may be 4,44 bps INFO @ Sun, 21 Jun 2020 19:24:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287862/SRX287862.20_model.r WARNING @ Sun, 21 Jun 2020 19:24:06: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:24:06: #2 You may need to consider one of the other alternative d(s): 4,44 WARNING @ Sun, 21 Jun 2020 19:24:06: #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 19:24:06: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:24:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:24:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287862/SRX287862.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:24:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287862/SRX287862.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:24:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287862/SRX287862.10_summits.bed INFO @ Sun, 21 Jun 2020 19:24:07: Done! pass1 - making usageList (515 chroms): 1 millis pass2 - checking and writing primary data (1829 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:24:34: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:24:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287862/SRX287862.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:24:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287862/SRX287862.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:24:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287862/SRX287862.20_summits.bed INFO @ Sun, 21 Jun 2020 19:24:47: Done! pass1 - making usageList (309 chroms): 0 millis pass2 - checking and writing primary data (645 records, 4 fields): 9 millis CompletedMACS2peakCalling