Job ID = 6456857 SRX = SRX3989971 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:05:24 prefetch.2.10.7: 1) Downloading 'SRR7059012'... 2020-06-21T11:05:24 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:07:26 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:07:27 prefetch.2.10.7: 'SRR7059012' is valid 2020-06-21T11:07:27 prefetch.2.10.7: 1) 'SRR7059012' was downloaded successfully 2020-06-21T11:07:27 prefetch.2.10.7: 'SRR7059012' has 0 unresolved dependencies Read 15654495 spots for SRR7059012/SRR7059012.sra Written 15654495 spots for SRR7059012/SRR7059012.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: 00:04:10 15654495 reads; of these: 15654495 (100.00%) were unpaired; of these: 1531308 (9.78%) aligned 0 times 11618320 (74.22%) aligned exactly 1 time 2504867 (16.00%) aligned >1 times 90.22% overall alignment rate Time searching: 00:04:10 Overall time: 00:04:10 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] 3036797 / 14123187 = 0.2150 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 20:17:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3989971/SRX3989971.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3989971/SRX3989971.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3989971/SRX3989971.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3989971/SRX3989971.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 20:17:04: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:17:04: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:17:10: 1000000 INFO @ Sun, 21 Jun 2020 20:17:17: 2000000 INFO @ Sun, 21 Jun 2020 20:17:24: 3000000 INFO @ Sun, 21 Jun 2020 20:17:31: 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 20:17:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3989971/SRX3989971.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3989971/SRX3989971.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3989971/SRX3989971.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3989971/SRX3989971.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 20:17:34: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:17:34: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:17:38: 5000000 INFO @ Sun, 21 Jun 2020 20:17:41: 1000000 INFO @ Sun, 21 Jun 2020 20:17:45: 6000000 INFO @ Sun, 21 Jun 2020 20:17:48: 2000000 INFO @ Sun, 21 Jun 2020 20:17:52: 7000000 INFO @ Sun, 21 Jun 2020 20:17:56: 3000000 INFO @ Sun, 21 Jun 2020 20:17:59: 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 20:18:03: 4000000 INFO @ Sun, 21 Jun 2020 20:18:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3989971/SRX3989971.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3989971/SRX3989971.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3989971/SRX3989971.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3989971/SRX3989971.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 20:18:04: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:18:04: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:18:06: 9000000 INFO @ Sun, 21 Jun 2020 20:18:11: 5000000 INFO @ Sun, 21 Jun 2020 20:18:12: 1000000 INFO @ Sun, 21 Jun 2020 20:18:14: 10000000 INFO @ Sun, 21 Jun 2020 20:18:19: 6000000 INFO @ Sun, 21 Jun 2020 20:18:20: 2000000 INFO @ Sun, 21 Jun 2020 20:18:23: 11000000 INFO @ Sun, 21 Jun 2020 20:18:23: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 20:18:23: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 20:18:23: #1 total tags in treatment: 11086390 INFO @ Sun, 21 Jun 2020 20:18:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:18:23: #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 20:18:24: #1 tags after filtering in treatment: 11086385 INFO @ Sun, 21 Jun 2020 20:18:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:18:24: #1 finished! INFO @ Sun, 21 Jun 2020 20:18:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:18:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:18:25: #2 number of paired peaks: 161 WARNING @ Sun, 21 Jun 2020 20:18:25: Fewer paired peaks (161) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 161 pairs to build model! INFO @ Sun, 21 Jun 2020 20:18:25: start model_add_line... INFO @ Sun, 21 Jun 2020 20:18:25: start X-correlation... INFO @ Sun, 21 Jun 2020 20:18:25: end of X-cor INFO @ Sun, 21 Jun 2020 20:18:25: #2 finished! INFO @ Sun, 21 Jun 2020 20:18:25: #2 predicted fragment length is 4 bps INFO @ Sun, 21 Jun 2020 20:18:25: #2 alternative fragment length(s) may be 4,8,26,471,485,591 bps INFO @ Sun, 21 Jun 2020 20:18:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3989971/SRX3989971.05_model.r WARNING @ Sun, 21 Jun 2020 20:18:25: #2 Since the d (4) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:18:25: #2 You may need to consider one of the other alternative d(s): 4,8,26,471,485,591 WARNING @ Sun, 21 Jun 2020 20:18:25: #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 20:18:25: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:18:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:18:28: 7000000 INFO @ Sun, 21 Jun 2020 20:18:28: 3000000 INFO @ Sun, 21 Jun 2020 20:18:36: 4000000 INFO @ Sun, 21 Jun 2020 20:18:36: 8000000 INFO @ Sun, 21 Jun 2020 20:18:44: 5000000 INFO @ Sun, 21 Jun 2020 20:18:44: 9000000 INFO @ Sun, 21 Jun 2020 20:18:49: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:18:52: 6000000 INFO @ Sun, 21 Jun 2020 20:18:53: 10000000 INFO @ Sun, 21 Jun 2020 20:18:59: 7000000 INFO @ Sun, 21 Jun 2020 20:19:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3989971/SRX3989971.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:19:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3989971/SRX3989971.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:19:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3989971/SRX3989971.05_summits.bed INFO @ Sun, 21 Jun 2020 20:19:01: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:19:02: 11000000 INFO @ Sun, 21 Jun 2020 20:19:02: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 20:19:02: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 20:19:02: #1 total tags in treatment: 11086390 INFO @ Sun, 21 Jun 2020 20:19:02: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:19:02: #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 20:19:03: #1 tags after filtering in treatment: 11086385 INFO @ Sun, 21 Jun 2020 20:19:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:19:03: #1 finished! INFO @ Sun, 21 Jun 2020 20:19:03: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:19:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:19:04: #2 number of paired peaks: 161 WARNING @ Sun, 21 Jun 2020 20:19:04: Fewer paired peaks (161) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 161 pairs to build model! INFO @ Sun, 21 Jun 2020 20:19:04: start model_add_line... INFO @ Sun, 21 Jun 2020 20:19:04: start X-correlation... INFO @ Sun, 21 Jun 2020 20:19:04: end of X-cor INFO @ Sun, 21 Jun 2020 20:19:04: #2 finished! INFO @ Sun, 21 Jun 2020 20:19:04: #2 predicted fragment length is 4 bps INFO @ Sun, 21 Jun 2020 20:19:04: #2 alternative fragment length(s) may be 4,8,26,471,485,591 bps INFO @ Sun, 21 Jun 2020 20:19:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3989971/SRX3989971.10_model.r WARNING @ Sun, 21 Jun 2020 20:19:04: #2 Since the d (4) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:19:04: #2 You may need to consider one of the other alternative d(s): 4,8,26,471,485,591 WARNING @ Sun, 21 Jun 2020 20:19:04: #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 20:19:04: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:19:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:19:07: 8000000 INFO @ Sun, 21 Jun 2020 20:19:14: 9000000 INFO @ Sun, 21 Jun 2020 20:19:20: 10000000 INFO @ Sun, 21 Jun 2020 20:19:27: 11000000 INFO @ Sun, 21 Jun 2020 20:19:28: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 20:19:28: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 20:19:28: #1 total tags in treatment: 11086390 INFO @ Sun, 21 Jun 2020 20:19:28: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:19:28: #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 20:19:28: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:19:28: #1 tags after filtering in treatment: 11086385 INFO @ Sun, 21 Jun 2020 20:19:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:19:28: #1 finished! INFO @ Sun, 21 Jun 2020 20:19:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:19:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:19:29: #2 number of paired peaks: 161 WARNING @ Sun, 21 Jun 2020 20:19:29: Fewer paired peaks (161) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 161 pairs to build model! INFO @ Sun, 21 Jun 2020 20:19:29: start model_add_line... INFO @ Sun, 21 Jun 2020 20:19:29: start X-correlation... INFO @ Sun, 21 Jun 2020 20:19:29: end of X-cor INFO @ Sun, 21 Jun 2020 20:19:29: #2 finished! INFO @ Sun, 21 Jun 2020 20:19:29: #2 predicted fragment length is 4 bps INFO @ Sun, 21 Jun 2020 20:19:29: #2 alternative fragment length(s) may be 4,8,26,471,485,591 bps INFO @ Sun, 21 Jun 2020 20:19:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3989971/SRX3989971.20_model.r WARNING @ Sun, 21 Jun 2020 20:19:29: #2 Since the d (4) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:19:29: #2 You may need to consider one of the other alternative d(s): 4,8,26,471,485,591 WARNING @ Sun, 21 Jun 2020 20:19:29: #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 20:19:29: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:19:29: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:19:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3989971/SRX3989971.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:19:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3989971/SRX3989971.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:19:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3989971/SRX3989971.10_summits.bed INFO @ Sun, 21 Jun 2020 20:19:40: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:19:54: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:20:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3989971/SRX3989971.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:20:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3989971/SRX3989971.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:20:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3989971/SRX3989971.20_summits.bed INFO @ Sun, 21 Jun 2020 20:20:05: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling