Job ID = 6454970 SRX = SRX2618513 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:27:29 prefetch.2.10.7: 1) Downloading 'SRR5319067'... 2020-06-21T09:27:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:33:54 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:33:54 prefetch.2.10.7: 1) 'SRR5319067' was downloaded successfully 2020-06-21T09:33:54 prefetch.2.10.7: 'SRR5319067' has 0 unresolved dependencies Read 46509756 spots for SRR5319067/SRR5319067.sra Written 46509756 spots for SRR5319067/SRR5319067.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: 00:09:12 46509756 reads; of these: 46509756 (100.00%) were unpaired; of these: 17448993 (37.52%) aligned 0 times 25416487 (54.65%) aligned exactly 1 time 3644276 (7.84%) aligned >1 times 62.48% overall alignment rate Time searching: 00:09:12 Overall time: 00:09:12 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] 3519703 / 29060763 = 0.1211 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 18:51:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618513/SRX2618513.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618513/SRX2618513.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618513/SRX2618513.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618513/SRX2618513.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 18:51:49: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:51:49: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:51:53: 1000000 INFO @ Sun, 21 Jun 2020 18:51:58: 2000000 INFO @ Sun, 21 Jun 2020 18:52:03: 3000000 INFO @ Sun, 21 Jun 2020 18:52:08: 4000000 INFO @ Sun, 21 Jun 2020 18:52:13: 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 18:52:17: 6000000 INFO @ Sun, 21 Jun 2020 18:52:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618513/SRX2618513.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618513/SRX2618513.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618513/SRX2618513.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618513/SRX2618513.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 18:52:19: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:52:19: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:52:22: 7000000 INFO @ Sun, 21 Jun 2020 18:52:24: 1000000 INFO @ Sun, 21 Jun 2020 18:52:27: 8000000 INFO @ Sun, 21 Jun 2020 18:52:29: 2000000 INFO @ Sun, 21 Jun 2020 18:52:32: 9000000 INFO @ Sun, 21 Jun 2020 18:52:34: 3000000 INFO @ Sun, 21 Jun 2020 18:52:37: 10000000 INFO @ Sun, 21 Jun 2020 18:52:39: 4000000 INFO @ Sun, 21 Jun 2020 18:52:42: 11000000 INFO @ Sun, 21 Jun 2020 18:52:43: 5000000 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 18:52:47: 12000000 INFO @ Sun, 21 Jun 2020 18:52:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618513/SRX2618513.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618513/SRX2618513.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618513/SRX2618513.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618513/SRX2618513.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 18:52:48: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:52:48: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:52:48: 6000000 INFO @ Sun, 21 Jun 2020 18:52:52: 13000000 INFO @ Sun, 21 Jun 2020 18:52:53: 7000000 INFO @ Sun, 21 Jun 2020 18:52:53: 1000000 INFO @ Sun, 21 Jun 2020 18:52:57: 14000000 INFO @ Sun, 21 Jun 2020 18:52:58: 8000000 INFO @ Sun, 21 Jun 2020 18:52:58: 2000000 INFO @ Sun, 21 Jun 2020 18:53:02: 15000000 INFO @ Sun, 21 Jun 2020 18:53:03: 9000000 INFO @ Sun, 21 Jun 2020 18:53:04: 3000000 INFO @ Sun, 21 Jun 2020 18:53:07: 16000000 INFO @ Sun, 21 Jun 2020 18:53:08: 10000000 INFO @ Sun, 21 Jun 2020 18:53:09: 4000000 INFO @ Sun, 21 Jun 2020 18:53:12: 17000000 INFO @ Sun, 21 Jun 2020 18:53:13: 11000000 INFO @ Sun, 21 Jun 2020 18:53:14: 5000000 INFO @ Sun, 21 Jun 2020 18:53:17: 18000000 INFO @ Sun, 21 Jun 2020 18:53:18: 12000000 INFO @ Sun, 21 Jun 2020 18:53:19: 6000000 INFO @ Sun, 21 Jun 2020 18:53:22: 19000000 INFO @ Sun, 21 Jun 2020 18:53:23: 13000000 INFO @ Sun, 21 Jun 2020 18:53:23: 7000000 INFO @ Sun, 21 Jun 2020 18:53:27: 20000000 INFO @ Sun, 21 Jun 2020 18:53:28: 14000000 INFO @ Sun, 21 Jun 2020 18:53:28: 8000000 INFO @ Sun, 21 Jun 2020 18:53:32: 21000000 INFO @ Sun, 21 Jun 2020 18:53:33: 15000000 INFO @ Sun, 21 Jun 2020 18:53:33: 9000000 INFO @ Sun, 21 Jun 2020 18:53:37: 22000000 INFO @ Sun, 21 Jun 2020 18:53:38: 16000000 INFO @ Sun, 21 Jun 2020 18:53:38: 10000000 INFO @ Sun, 21 Jun 2020 18:53:42: 23000000 INFO @ Sun, 21 Jun 2020 18:53:43: 17000000 INFO @ Sun, 21 Jun 2020 18:53:43: 11000000 INFO @ Sun, 21 Jun 2020 18:53:47: 24000000 INFO @ Sun, 21 Jun 2020 18:53:48: 18000000 INFO @ Sun, 21 Jun 2020 18:53:48: 12000000 INFO @ Sun, 21 Jun 2020 18:53:52: 25000000 INFO @ Sun, 21 Jun 2020 18:53:52: 19000000 INFO @ Sun, 21 Jun 2020 18:53:53: 13000000 INFO @ Sun, 21 Jun 2020 18:53:55: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:53:55: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:53:55: #1 total tags in treatment: 25541060 INFO @ Sun, 21 Jun 2020 18:53:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:53:55: #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 18:53:55: #1 tags after filtering in treatment: 25541054 INFO @ Sun, 21 Jun 2020 18:53:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:53:55: #1 finished! INFO @ Sun, 21 Jun 2020 18:53:55: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:53:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:53:57: #2 number of paired peaks: 129 WARNING @ Sun, 21 Jun 2020 18:53:57: Fewer paired peaks (129) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 129 pairs to build model! INFO @ Sun, 21 Jun 2020 18:53:57: start model_add_line... INFO @ Sun, 21 Jun 2020 18:53:57: start X-correlation... INFO @ Sun, 21 Jun 2020 18:53:57: end of X-cor INFO @ Sun, 21 Jun 2020 18:53:57: #2 finished! INFO @ Sun, 21 Jun 2020 18:53:57: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 18:53:57: #2 alternative fragment length(s) may be 1,46,594 bps INFO @ Sun, 21 Jun 2020 18:53:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618513/SRX2618513.05_model.r WARNING @ Sun, 21 Jun 2020 18:53:57: #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 18:53:57: #2 You may need to consider one of the other alternative d(s): 1,46,594 WARNING @ Sun, 21 Jun 2020 18:53:57: #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 18:53:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:53:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:53:57: 20000000 INFO @ Sun, 21 Jun 2020 18:53:58: 14000000 INFO @ Sun, 21 Jun 2020 18:54:02: 21000000 INFO @ Sun, 21 Jun 2020 18:54:03: 15000000 INFO @ Sun, 21 Jun 2020 18:54:07: 22000000 INFO @ Sun, 21 Jun 2020 18:54:07: 16000000 INFO @ Sun, 21 Jun 2020 18:54:12: 23000000 INFO @ Sun, 21 Jun 2020 18:54:12: 17000000 INFO @ Sun, 21 Jun 2020 18:54:17: 24000000 INFO @ Sun, 21 Jun 2020 18:54:17: 18000000 INFO @ Sun, 21 Jun 2020 18:54:21: 25000000 INFO @ Sun, 21 Jun 2020 18:54:22: 19000000 INFO @ Sun, 21 Jun 2020 18:54:24: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:54:24: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:54:24: #1 total tags in treatment: 25541060 INFO @ Sun, 21 Jun 2020 18:54:24: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:54:24: #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 18:54:25: #1 tags after filtering in treatment: 25541054 INFO @ Sun, 21 Jun 2020 18:54:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:54:25: #1 finished! INFO @ Sun, 21 Jun 2020 18:54:25: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:54:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:54:26: 20000000 INFO @ Sun, 21 Jun 2020 18:54:27: #2 number of paired peaks: 129 WARNING @ Sun, 21 Jun 2020 18:54:27: Fewer paired peaks (129) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 129 pairs to build model! INFO @ Sun, 21 Jun 2020 18:54:27: start model_add_line... INFO @ Sun, 21 Jun 2020 18:54:27: start X-correlation... INFO @ Sun, 21 Jun 2020 18:54:27: end of X-cor INFO @ Sun, 21 Jun 2020 18:54:27: #2 finished! INFO @ Sun, 21 Jun 2020 18:54:27: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 18:54:27: #2 alternative fragment length(s) may be 1,46,594 bps INFO @ Sun, 21 Jun 2020 18:54:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618513/SRX2618513.10_model.r WARNING @ Sun, 21 Jun 2020 18:54:27: #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 18:54:27: #2 You may need to consider one of the other alternative d(s): 1,46,594 WARNING @ Sun, 21 Jun 2020 18:54:27: #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 18:54:27: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:54:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:54:31: 21000000 INFO @ Sun, 21 Jun 2020 18:54:36: 22000000 INFO @ Sun, 21 Jun 2020 18:54:38: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:54:41: 23000000 INFO @ Sun, 21 Jun 2020 18:54:45: 24000000 INFO @ Sun, 21 Jun 2020 18:54:50: 25000000 INFO @ Sun, 21 Jun 2020 18:54:53: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:54:53: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:54:53: #1 total tags in treatment: 25541060 INFO @ Sun, 21 Jun 2020 18:54:53: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:54:53: #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 18:54:53: #1 tags after filtering in treatment: 25541054 INFO @ Sun, 21 Jun 2020 18:54:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:54:53: #1 finished! INFO @ Sun, 21 Jun 2020 18:54:53: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:54:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:54:55: #2 number of paired peaks: 129 WARNING @ Sun, 21 Jun 2020 18:54:55: Fewer paired peaks (129) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 129 pairs to build model! INFO @ Sun, 21 Jun 2020 18:54:55: start model_add_line... INFO @ Sun, 21 Jun 2020 18:54:55: start X-correlation... INFO @ Sun, 21 Jun 2020 18:54:55: end of X-cor INFO @ Sun, 21 Jun 2020 18:54:55: #2 finished! INFO @ Sun, 21 Jun 2020 18:54:55: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 18:54:55: #2 alternative fragment length(s) may be 1,46,594 bps INFO @ Sun, 21 Jun 2020 18:54:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618513/SRX2618513.20_model.r WARNING @ Sun, 21 Jun 2020 18:54:55: #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 18:54:55: #2 You may need to consider one of the other alternative d(s): 1,46,594 WARNING @ Sun, 21 Jun 2020 18:54:55: #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 18:54:55: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:54:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:54:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618513/SRX2618513.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:54:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618513/SRX2618513.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:54:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618513/SRX2618513.05_summits.bed INFO @ Sun, 21 Jun 2020 18:54:57: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:55:07: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:55:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618513/SRX2618513.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:55:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618513/SRX2618513.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:55:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618513/SRX2618513.10_summits.bed INFO @ Sun, 21 Jun 2020 18:55:26: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:55:34: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:55:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618513/SRX2618513.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:55:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618513/SRX2618513.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:55:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618513/SRX2618513.20_summits.bed INFO @ Sun, 21 Jun 2020 18:55:52: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling