Job ID = 6459255 SRX = SRX6468498 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T13:02:04 prefetch.2.10.7: 1) Downloading 'SRR9710584'... 2020-06-21T13:02:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:06:45 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:06:45 prefetch.2.10.7: 1) 'SRR9710584' was downloaded successfully Read 26759923 spots for SRR9710584/SRR9710584.sra Written 26759923 spots for SRR9710584/SRR9710584.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: 00:07:00 26759923 reads; of these: 26759923 (100.00%) were unpaired; of these: 3388788 (12.66%) aligned 0 times 15627559 (58.40%) aligned exactly 1 time 7743576 (28.94%) aligned >1 times 87.34% overall alignment rate Time searching: 00:07:00 Overall time: 00:07:00 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] 7656576 / 23371135 = 0.3276 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 22:20:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6468498/SRX6468498.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6468498/SRX6468498.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6468498/SRX6468498.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6468498/SRX6468498.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 22:20:24: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:20:24: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:20:30: 1000000 INFO @ Sun, 21 Jun 2020 22:20:37: 2000000 INFO @ Sun, 21 Jun 2020 22:20:43: 3000000 INFO @ Sun, 21 Jun 2020 22:20:50: 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 22:20:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6468498/SRX6468498.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6468498/SRX6468498.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6468498/SRX6468498.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6468498/SRX6468498.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 22:20:54: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:20:54: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:20:57: 5000000 INFO @ Sun, 21 Jun 2020 22:21:01: 1000000 INFO @ Sun, 21 Jun 2020 22:21:05: 6000000 INFO @ Sun, 21 Jun 2020 22:21:08: 2000000 INFO @ Sun, 21 Jun 2020 22:21:12: 7000000 INFO @ Sun, 21 Jun 2020 22:21:16: 3000000 INFO @ Sun, 21 Jun 2020 22:21:19: 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 22:21:23: 4000000 INFO @ Sun, 21 Jun 2020 22:21:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6468498/SRX6468498.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6468498/SRX6468498.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6468498/SRX6468498.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6468498/SRX6468498.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 22:21:24: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:21:24: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:21:26: 9000000 INFO @ Sun, 21 Jun 2020 22:21:30: 5000000 INFO @ Sun, 21 Jun 2020 22:21:31: 1000000 INFO @ Sun, 21 Jun 2020 22:21:33: 10000000 INFO @ Sun, 21 Jun 2020 22:21:37: 2000000 INFO @ Sun, 21 Jun 2020 22:21:38: 6000000 INFO @ Sun, 21 Jun 2020 22:21:40: 11000000 INFO @ Sun, 21 Jun 2020 22:21:44: 3000000 INFO @ Sun, 21 Jun 2020 22:21:45: 7000000 INFO @ Sun, 21 Jun 2020 22:21:48: 12000000 INFO @ Sun, 21 Jun 2020 22:21:51: 4000000 INFO @ Sun, 21 Jun 2020 22:21:52: 8000000 INFO @ Sun, 21 Jun 2020 22:21:55: 13000000 INFO @ Sun, 21 Jun 2020 22:21:58: 5000000 INFO @ Sun, 21 Jun 2020 22:22:00: 9000000 INFO @ Sun, 21 Jun 2020 22:22:02: 14000000 INFO @ Sun, 21 Jun 2020 22:22:04: 6000000 INFO @ Sun, 21 Jun 2020 22:22:07: 10000000 INFO @ Sun, 21 Jun 2020 22:22:10: 15000000 INFO @ Sun, 21 Jun 2020 22:22:11: 7000000 INFO @ Sun, 21 Jun 2020 22:22:14: 11000000 INFO @ Sun, 21 Jun 2020 22:22:15: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:22:15: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:22:15: #1 total tags in treatment: 15714559 INFO @ Sun, 21 Jun 2020 22:22:15: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:22:15: #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 22:22:15: #1 tags after filtering in treatment: 15714559 INFO @ Sun, 21 Jun 2020 22:22:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:22:15: #1 finished! INFO @ Sun, 21 Jun 2020 22:22:15: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:22:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:22:16: #2 number of paired peaks: 240 WARNING @ Sun, 21 Jun 2020 22:22:16: Fewer paired peaks (240) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 240 pairs to build model! INFO @ Sun, 21 Jun 2020 22:22:16: start model_add_line... INFO @ Sun, 21 Jun 2020 22:22:16: start X-correlation... INFO @ Sun, 21 Jun 2020 22:22:17: end of X-cor INFO @ Sun, 21 Jun 2020 22:22:17: #2 finished! INFO @ Sun, 21 Jun 2020 22:22:17: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 22:22:17: #2 alternative fragment length(s) may be 1,33,554 bps INFO @ Sun, 21 Jun 2020 22:22:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6468498/SRX6468498.05_model.r WARNING @ Sun, 21 Jun 2020 22:22:17: #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 22:22:17: #2 You may need to consider one of the other alternative d(s): 1,33,554 WARNING @ Sun, 21 Jun 2020 22:22:17: #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 22:22:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:22:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:22:18: 8000000 INFO @ Sun, 21 Jun 2020 22:22:21: 12000000 INFO @ Sun, 21 Jun 2020 22:22:24: 9000000 INFO @ Sun, 21 Jun 2020 22:22:29: 13000000 INFO @ Sun, 21 Jun 2020 22:22:31: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:22:36: 14000000 INFO @ Sun, 21 Jun 2020 22:22:38: 11000000 INFO @ Sun, 21 Jun 2020 22:22:43: 15000000 INFO @ Sun, 21 Jun 2020 22:22:45: 12000000 INFO @ Sun, 21 Jun 2020 22:22:45: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:22:48: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:22:48: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:22:48: #1 total tags in treatment: 15714559 INFO @ Sun, 21 Jun 2020 22:22:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:22:48: #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 22:22:49: #1 tags after filtering in treatment: 15714559 INFO @ Sun, 21 Jun 2020 22:22:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:22:49: #1 finished! INFO @ Sun, 21 Jun 2020 22:22:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:22:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:22:50: #2 number of paired peaks: 240 WARNING @ Sun, 21 Jun 2020 22:22:50: Fewer paired peaks (240) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 240 pairs to build model! INFO @ Sun, 21 Jun 2020 22:22:50: start model_add_line... INFO @ Sun, 21 Jun 2020 22:22:50: start X-correlation... INFO @ Sun, 21 Jun 2020 22:22:50: end of X-cor INFO @ Sun, 21 Jun 2020 22:22:50: #2 finished! INFO @ Sun, 21 Jun 2020 22:22:50: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 22:22:50: #2 alternative fragment length(s) may be 1,33,554 bps INFO @ Sun, 21 Jun 2020 22:22:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6468498/SRX6468498.10_model.r WARNING @ Sun, 21 Jun 2020 22:22:50: #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 22:22:50: #2 You may need to consider one of the other alternative d(s): 1,33,554 WARNING @ Sun, 21 Jun 2020 22:22:50: #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 22:22:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:22:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:22:51: 13000000 INFO @ Sun, 21 Jun 2020 22:22:57: 14000000 INFO @ Sun, 21 Jun 2020 22:22:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6468498/SRX6468498.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:22:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6468498/SRX6468498.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:22:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6468498/SRX6468498.05_summits.bed INFO @ Sun, 21 Jun 2020 22:22:58: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:23:03: 15000000 INFO @ Sun, 21 Jun 2020 22:23:07: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:23:07: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:23:07: #1 total tags in treatment: 15714559 INFO @ Sun, 21 Jun 2020 22:23:07: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:23:07: #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 22:23:08: #1 tags after filtering in treatment: 15714559 INFO @ Sun, 21 Jun 2020 22:23:08: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:23:08: #1 finished! INFO @ Sun, 21 Jun 2020 22:23:08: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:23:08: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:23:09: #2 number of paired peaks: 240 WARNING @ Sun, 21 Jun 2020 22:23:09: Fewer paired peaks (240) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 240 pairs to build model! INFO @ Sun, 21 Jun 2020 22:23:09: start model_add_line... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:23:09: start X-correlation... INFO @ Sun, 21 Jun 2020 22:23:09: end of X-cor INFO @ Sun, 21 Jun 2020 22:23:09: #2 finished! INFO @ Sun, 21 Jun 2020 22:23:09: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 22:23:09: #2 alternative fragment length(s) may be 1,33,554 bps INFO @ Sun, 21 Jun 2020 22:23:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6468498/SRX6468498.20_model.r WARNING @ Sun, 21 Jun 2020 22:23:09: #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 22:23:09: #2 You may need to consider one of the other alternative d(s): 1,33,554 WARNING @ Sun, 21 Jun 2020 22:23:09: #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 22:23:09: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:23:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:23:18: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:23:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6468498/SRX6468498.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:23:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6468498/SRX6468498.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:23:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6468498/SRX6468498.10_summits.bed INFO @ Sun, 21 Jun 2020 22:23:31: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:23:37: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:23:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6468498/SRX6468498.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:23:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6468498/SRX6468498.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:23:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6468498/SRX6468498.20_summits.bed INFO @ Sun, 21 Jun 2020 22:23:50: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling