Job ID = 6529482 SRX = SRX287757 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:10 22133183 reads; of these: 22133183 (100.00%) were unpaired; of these: 1385346 (6.26%) aligned 0 times 13961431 (63.08%) aligned exactly 1 time 6786406 (30.66%) aligned >1 times 93.74% overall alignment rate Time searching: 00:07:11 Overall time: 00:07:11 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] 4724212 / 20747837 = 0.2277 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 @ Tue, 30 Jun 2020 02:21:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287757/SRX287757.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287757/SRX287757.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287757/SRX287757.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287757/SRX287757.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 @ Tue, 30 Jun 2020 02:21:26: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:21:26: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:21:32: 1000000 INFO @ Tue, 30 Jun 2020 02:21:39: 2000000 INFO @ Tue, 30 Jun 2020 02:21:46: 3000000 INFO @ Tue, 30 Jun 2020 02:21:53: 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 @ Tue, 30 Jun 2020 02:21:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287757/SRX287757.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287757/SRX287757.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287757/SRX287757.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287757/SRX287757.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 @ Tue, 30 Jun 2020 02:21:56: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:21:56: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:22:01: 5000000 INFO @ Tue, 30 Jun 2020 02:22:04: 1000000 INFO @ Tue, 30 Jun 2020 02:22:09: 6000000 INFO @ Tue, 30 Jun 2020 02:22:12: 2000000 INFO @ Tue, 30 Jun 2020 02:22:17: 7000000 INFO @ Tue, 30 Jun 2020 02:22:19: 3000000 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 @ Tue, 30 Jun 2020 02:22:24: 8000000 INFO @ Tue, 30 Jun 2020 02:22:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287757/SRX287757.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287757/SRX287757.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287757/SRX287757.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287757/SRX287757.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 @ Tue, 30 Jun 2020 02:22:26: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:22:26: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:22:27: 4000000 INFO @ Tue, 30 Jun 2020 02:22:32: 9000000 INFO @ Tue, 30 Jun 2020 02:22:34: 1000000 INFO @ Tue, 30 Jun 2020 02:22:35: 5000000 INFO @ Tue, 30 Jun 2020 02:22:40: 10000000 INFO @ Tue, 30 Jun 2020 02:22:42: 2000000 INFO @ Tue, 30 Jun 2020 02:22:43: 6000000 INFO @ Tue, 30 Jun 2020 02:22:49: 11000000 INFO @ Tue, 30 Jun 2020 02:22:51: 3000000 INFO @ Tue, 30 Jun 2020 02:22:52: 7000000 INFO @ Tue, 30 Jun 2020 02:22:57: 12000000 INFO @ Tue, 30 Jun 2020 02:22:59: 4000000 INFO @ Tue, 30 Jun 2020 02:23:00: 8000000 INFO @ Tue, 30 Jun 2020 02:23:06: 13000000 INFO @ Tue, 30 Jun 2020 02:23:07: 5000000 INFO @ Tue, 30 Jun 2020 02:23:08: 9000000 INFO @ Tue, 30 Jun 2020 02:23:14: 14000000 INFO @ Tue, 30 Jun 2020 02:23:16: 6000000 INFO @ Tue, 30 Jun 2020 02:23:16: 10000000 INFO @ Tue, 30 Jun 2020 02:23:22: 15000000 INFO @ Tue, 30 Jun 2020 02:23:24: 11000000 INFO @ Tue, 30 Jun 2020 02:23:24: 7000000 INFO @ Tue, 30 Jun 2020 02:23:31: 16000000 INFO @ Tue, 30 Jun 2020 02:23:31: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:23:31: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:23:31: #1 total tags in treatment: 16023625 INFO @ Tue, 30 Jun 2020 02:23:31: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:23:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:23:32: #1 tags after filtering in treatment: 16023625 INFO @ Tue, 30 Jun 2020 02:23:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:23:32: #1 finished! INFO @ Tue, 30 Jun 2020 02:23:32: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:23:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:23:32: 12000000 INFO @ Tue, 30 Jun 2020 02:23:32: 8000000 INFO @ Tue, 30 Jun 2020 02:23:33: #2 number of paired peaks: 737 WARNING @ Tue, 30 Jun 2020 02:23:33: Fewer paired peaks (737) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 737 pairs to build model! INFO @ Tue, 30 Jun 2020 02:23:33: start model_add_line... INFO @ Tue, 30 Jun 2020 02:23:33: start X-correlation... INFO @ Tue, 30 Jun 2020 02:23:33: end of X-cor INFO @ Tue, 30 Jun 2020 02:23:33: #2 finished! INFO @ Tue, 30 Jun 2020 02:23:33: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 02:23:33: #2 alternative fragment length(s) may be 2,29 bps INFO @ Tue, 30 Jun 2020 02:23:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287757/SRX287757.05_model.r WARNING @ Tue, 30 Jun 2020 02:23:33: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:23:33: #2 You may need to consider one of the other alternative d(s): 2,29 WARNING @ Tue, 30 Jun 2020 02:23:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:23:33: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:23:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:23:40: 9000000 INFO @ Tue, 30 Jun 2020 02:23:40: 13000000 INFO @ Tue, 30 Jun 2020 02:23:47: 10000000 INFO @ Tue, 30 Jun 2020 02:23:48: 14000000 INFO @ Tue, 30 Jun 2020 02:23:56: 11000000 INFO @ Tue, 30 Jun 2020 02:23:56: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:23:59: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:24:03: 12000000 INFO @ Tue, 30 Jun 2020 02:24:04: 16000000 INFO @ Tue, 30 Jun 2020 02:24:05: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:24:05: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:24:05: #1 total tags in treatment: 16023625 INFO @ Tue, 30 Jun 2020 02:24:05: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:24:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:24:05: #1 tags after filtering in treatment: 16023625 INFO @ Tue, 30 Jun 2020 02:24:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:24:05: #1 finished! INFO @ Tue, 30 Jun 2020 02:24:05: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:24:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:24:07: #2 number of paired peaks: 737 WARNING @ Tue, 30 Jun 2020 02:24:07: Fewer paired peaks (737) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 737 pairs to build model! INFO @ Tue, 30 Jun 2020 02:24:07: start model_add_line... INFO @ Tue, 30 Jun 2020 02:24:07: start X-correlation... INFO @ Tue, 30 Jun 2020 02:24:07: end of X-cor INFO @ Tue, 30 Jun 2020 02:24:07: #2 finished! INFO @ Tue, 30 Jun 2020 02:24:07: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 02:24:07: #2 alternative fragment length(s) may be 2,29 bps INFO @ Tue, 30 Jun 2020 02:24:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287757/SRX287757.10_model.r WARNING @ Tue, 30 Jun 2020 02:24:07: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:24:07: #2 You may need to consider one of the other alternative d(s): 2,29 WARNING @ Tue, 30 Jun 2020 02:24:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:24:07: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:24:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:24:11: 13000000 INFO @ Tue, 30 Jun 2020 02:24:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287757/SRX287757.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:24:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287757/SRX287757.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:24:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287757/SRX287757.05_summits.bed INFO @ Tue, 30 Jun 2020 02:24:12: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:24:18: 14000000 INFO @ Tue, 30 Jun 2020 02:24:25: 15000000 INFO @ Tue, 30 Jun 2020 02:24:32: 16000000 INFO @ Tue, 30 Jun 2020 02:24:32: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:24:32: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:24:32: #1 total tags in treatment: 16023625 INFO @ Tue, 30 Jun 2020 02:24:32: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:24:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:24:33: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:24:33: #1 tags after filtering in treatment: 16023625 INFO @ Tue, 30 Jun 2020 02:24:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:24:33: #1 finished! INFO @ Tue, 30 Jun 2020 02:24:33: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:24:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:24:34: #2 number of paired peaks: 737 WARNING @ Tue, 30 Jun 2020 02:24:34: Fewer paired peaks (737) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 737 pairs to build model! INFO @ Tue, 30 Jun 2020 02:24:34: start model_add_line... INFO @ Tue, 30 Jun 2020 02:24:34: start X-correlation... INFO @ Tue, 30 Jun 2020 02:24:34: end of X-cor INFO @ Tue, 30 Jun 2020 02:24:34: #2 finished! INFO @ Tue, 30 Jun 2020 02:24:34: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 02:24:34: #2 alternative fragment length(s) may be 2,29 bps INFO @ Tue, 30 Jun 2020 02:24:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287757/SRX287757.20_model.r WARNING @ Tue, 30 Jun 2020 02:24:34: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:24:34: #2 You may need to consider one of the other alternative d(s): 2,29 WARNING @ Tue, 30 Jun 2020 02:24:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:24:34: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:24:34: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:24:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287757/SRX287757.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:24:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287757/SRX287757.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:24:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287757/SRX287757.10_summits.bed INFO @ Tue, 30 Jun 2020 02:24:45: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:25:00: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:25:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287757/SRX287757.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:25:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287757/SRX287757.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:25:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287757/SRX287757.20_summits.bed INFO @ Tue, 30 Jun 2020 02:25:13: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling