Job ID = 6453346 SRX = SRX111815 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:20:02 prefetch.2.10.7: 1) Downloading 'SRR390279'... 2020-06-21T08:20:02 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:21:53 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:21:54 prefetch.2.10.7: 'SRR390279' is valid 2020-06-21T08:21:54 prefetch.2.10.7: 1) 'SRR390279' was downloaded successfully Read 15830139 spots for SRR390279/SRR390279.sra Written 15830139 spots for SRR390279/SRR390279.sra 2020-06-21T08:22:51 prefetch.2.10.7: 1) Downloading 'SRR390280'... 2020-06-21T08:22:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:25:08 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:25:08 prefetch.2.10.7: 1) 'SRR390280' was downloaded successfully Read 18878990 spots for SRR390280/SRR390280.sra Written 18878990 spots for SRR390280/SRR390280.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: 00:00:01 Multiseed full-index search: 00:06:29 34709129 reads; of these: 34709129 (100.00%) were unpaired; of these: 13872058 (39.97%) aligned 0 times 15393058 (44.35%) aligned exactly 1 time 5444013 (15.68%) aligned >1 times 60.03% overall alignment rate Time searching: 00:06:30 Overall time: 00:06:30 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] 6169619 / 20837071 = 0.2961 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 17:37:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX111815/SRX111815.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX111815/SRX111815.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX111815/SRX111815.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX111815/SRX111815.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 17:37:46: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:37:46: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:37:51: 1000000 INFO @ Sun, 21 Jun 2020 17:37:57: 2000000 INFO @ Sun, 21 Jun 2020 17:38:02: 3000000 INFO @ Sun, 21 Jun 2020 17:38:07: 4000000 INFO @ Sun, 21 Jun 2020 17:38:13: 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 17:38:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX111815/SRX111815.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX111815/SRX111815.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX111815/SRX111815.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX111815/SRX111815.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 17:38:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:38:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:38:18: 6000000 INFO @ Sun, 21 Jun 2020 17:38:22: 1000000 INFO @ Sun, 21 Jun 2020 17:38:24: 7000000 INFO @ Sun, 21 Jun 2020 17:38:28: 2000000 INFO @ Sun, 21 Jun 2020 17:38:30: 8000000 INFO @ Sun, 21 Jun 2020 17:38:33: 3000000 INFO @ Sun, 21 Jun 2020 17:38:36: 9000000 INFO @ Sun, 21 Jun 2020 17:38:39: 4000000 INFO @ Sun, 21 Jun 2020 17:38:41: 10000000 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 17:38:45: 5000000 INFO @ Sun, 21 Jun 2020 17:38:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX111815/SRX111815.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX111815/SRX111815.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX111815/SRX111815.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX111815/SRX111815.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 17:38:46: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:38:46: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:38:47: 11000000 INFO @ Sun, 21 Jun 2020 17:38:51: 6000000 INFO @ Sun, 21 Jun 2020 17:38:52: 1000000 INFO @ Sun, 21 Jun 2020 17:38:54: 12000000 INFO @ Sun, 21 Jun 2020 17:38:57: 7000000 INFO @ Sun, 21 Jun 2020 17:38:58: 2000000 INFO @ Sun, 21 Jun 2020 17:39:00: 13000000 INFO @ Sun, 21 Jun 2020 17:39:03: 8000000 INFO @ Sun, 21 Jun 2020 17:39:05: 3000000 INFO @ Sun, 21 Jun 2020 17:39:06: 14000000 INFO @ Sun, 21 Jun 2020 17:39:10: 9000000 INFO @ Sun, 21 Jun 2020 17:39:10: #1 tag size is determined as 44 bps INFO @ Sun, 21 Jun 2020 17:39:10: #1 tag size = 44 INFO @ Sun, 21 Jun 2020 17:39:10: #1 total tags in treatment: 14667452 INFO @ Sun, 21 Jun 2020 17:39:10: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:39:10: #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 17:39:11: #1 tags after filtering in treatment: 14667450 INFO @ Sun, 21 Jun 2020 17:39:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:39:11: #1 finished! INFO @ Sun, 21 Jun 2020 17:39:11: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:39:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:39:12: #2 number of paired peaks: 339 WARNING @ Sun, 21 Jun 2020 17:39:12: Fewer paired peaks (339) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 339 pairs to build model! INFO @ Sun, 21 Jun 2020 17:39:12: start model_add_line... INFO @ Sun, 21 Jun 2020 17:39:12: 4000000 INFO @ Sun, 21 Jun 2020 17:39:12: start X-correlation... INFO @ Sun, 21 Jun 2020 17:39:12: end of X-cor INFO @ Sun, 21 Jun 2020 17:39:12: #2 finished! INFO @ Sun, 21 Jun 2020 17:39:12: #2 predicted fragment length is 4 bps INFO @ Sun, 21 Jun 2020 17:39:12: #2 alternative fragment length(s) may be 4,49,91,136,362,410,454,502,541,591 bps INFO @ Sun, 21 Jun 2020 17:39:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX111815/SRX111815.05_model.r WARNING @ Sun, 21 Jun 2020 17:39:12: #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 17:39:12: #2 You may need to consider one of the other alternative d(s): 4,49,91,136,362,410,454,502,541,591 WARNING @ Sun, 21 Jun 2020 17:39:12: #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 17:39:12: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:39:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:39:16: 10000000 INFO @ Sun, 21 Jun 2020 17:39:19: 5000000 INFO @ Sun, 21 Jun 2020 17:39:22: 11000000 INFO @ Sun, 21 Jun 2020 17:39:26: 6000000 INFO @ Sun, 21 Jun 2020 17:39:29: 12000000 INFO @ Sun, 21 Jun 2020 17:39:33: 7000000 INFO @ Sun, 21 Jun 2020 17:39:35: 13000000 INFO @ Sun, 21 Jun 2020 17:39:39: 8000000 INFO @ Sun, 21 Jun 2020 17:39:40: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:39:41: 14000000 INFO @ Sun, 21 Jun 2020 17:39:45: #1 tag size is determined as 44 bps INFO @ Sun, 21 Jun 2020 17:39:45: #1 tag size = 44 INFO @ Sun, 21 Jun 2020 17:39:45: #1 total tags in treatment: 14667452 INFO @ Sun, 21 Jun 2020 17:39:45: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:39:45: #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 17:39:46: #1 tags after filtering in treatment: 14667450 INFO @ Sun, 21 Jun 2020 17:39:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:39:46: #1 finished! INFO @ Sun, 21 Jun 2020 17:39:46: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:39:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:39:46: 9000000 INFO @ Sun, 21 Jun 2020 17:39:47: #2 number of paired peaks: 339 WARNING @ Sun, 21 Jun 2020 17:39:47: Fewer paired peaks (339) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 339 pairs to build model! INFO @ Sun, 21 Jun 2020 17:39:47: start model_add_line... INFO @ Sun, 21 Jun 2020 17:39:47: start X-correlation... INFO @ Sun, 21 Jun 2020 17:39:47: end of X-cor INFO @ Sun, 21 Jun 2020 17:39:47: #2 finished! INFO @ Sun, 21 Jun 2020 17:39:47: #2 predicted fragment length is 4 bps INFO @ Sun, 21 Jun 2020 17:39:47: #2 alternative fragment length(s) may be 4,49,91,136,362,410,454,502,541,591 bps INFO @ Sun, 21 Jun 2020 17:39:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX111815/SRX111815.10_model.r WARNING @ Sun, 21 Jun 2020 17:39:47: #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 17:39:47: #2 You may need to consider one of the other alternative d(s): 4,49,91,136,362,410,454,502,541,591 WARNING @ Sun, 21 Jun 2020 17:39:47: #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 17:39:47: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:39:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:39:53: 10000000 INFO @ Sun, 21 Jun 2020 17:39:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX111815/SRX111815.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:39:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX111815/SRX111815.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:39:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX111815/SRX111815.05_summits.bed INFO @ Sun, 21 Jun 2020 17:39:54: 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 17:39:59: 11000000 INFO @ Sun, 21 Jun 2020 17:40:06: 12000000 INFO @ Sun, 21 Jun 2020 17:40:13: 13000000 INFO @ Sun, 21 Jun 2020 17:40:16: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:40:19: 14000000 INFO @ Sun, 21 Jun 2020 17:40:24: #1 tag size is determined as 44 bps INFO @ Sun, 21 Jun 2020 17:40:24: #1 tag size = 44 INFO @ Sun, 21 Jun 2020 17:40:24: #1 total tags in treatment: 14667452 INFO @ Sun, 21 Jun 2020 17:40:24: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:40:24: #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 17:40:24: #1 tags after filtering in treatment: 14667450 INFO @ Sun, 21 Jun 2020 17:40:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:40:24: #1 finished! INFO @ Sun, 21 Jun 2020 17:40:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:40:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:40:25: #2 number of paired peaks: 339 WARNING @ Sun, 21 Jun 2020 17:40:25: Fewer paired peaks (339) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 339 pairs to build model! INFO @ Sun, 21 Jun 2020 17:40:25: start model_add_line... INFO @ Sun, 21 Jun 2020 17:40:25: start X-correlation... INFO @ Sun, 21 Jun 2020 17:40:25: end of X-cor INFO @ Sun, 21 Jun 2020 17:40:25: #2 finished! INFO @ Sun, 21 Jun 2020 17:40:25: #2 predicted fragment length is 4 bps INFO @ Sun, 21 Jun 2020 17:40:25: #2 alternative fragment length(s) may be 4,49,91,136,362,410,454,502,541,591 bps INFO @ Sun, 21 Jun 2020 17:40:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX111815/SRX111815.20_model.r WARNING @ Sun, 21 Jun 2020 17:40:25: #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 17:40:25: #2 You may need to consider one of the other alternative d(s): 4,49,91,136,362,410,454,502,541,591 WARNING @ Sun, 21 Jun 2020 17:40:25: #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 17:40:25: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:40:25: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:40:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX111815/SRX111815.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:40:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX111815/SRX111815.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:40:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX111815/SRX111815.10_summits.bed INFO @ Sun, 21 Jun 2020 17:40:30: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:40:55: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:41:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX111815/SRX111815.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:41:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX111815/SRX111815.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:41:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX111815/SRX111815.20_summits.bed INFO @ Sun, 21 Jun 2020 17:41:09: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling