Job ID = 16439292 SRX = SRX15206470 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: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:01:41 5961611 reads; of these: 5961611 (100.00%) were unpaired; of these: 178715 (3.00%) aligned 0 times 3413656 (57.26%) aligned exactly 1 time 2369240 (39.74%) aligned >1 times 97.00% overall alignment rate Time searching: 00:01:41 Overall time: 00:01:41 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_rmdupse_core] 432687 / 5782896 = 0.0748 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 14:54:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15206470/SRX15206470.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15206470/SRX15206470.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15206470/SRX15206470.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15206470/SRX15206470.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, 02 Aug 2022 14:54:14: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:54:14: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:54:20: 1000000 INFO @ Tue, 02 Aug 2022 14:54:25: 2000000 INFO @ Tue, 02 Aug 2022 14:54:31: 3000000 INFO @ Tue, 02 Aug 2022 14:54:36: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 14:54:42: 5000000 INFO @ Tue, 02 Aug 2022 14:54:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15206470/SRX15206470.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15206470/SRX15206470.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15206470/SRX15206470.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15206470/SRX15206470.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, 02 Aug 2022 14:54:44: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:54:44: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:54:44: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 14:54:44: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 14:54:44: #1 total tags in treatment: 5350209 INFO @ Tue, 02 Aug 2022 14:54:44: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:54:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 14:54:44: #1 tags after filtering in treatment: 5350097 INFO @ Tue, 02 Aug 2022 14:54:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:54:44: #1 finished! INFO @ Tue, 02 Aug 2022 14:54:44: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:54:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:54:45: #2 number of paired peaks: 894 WARNING @ Tue, 02 Aug 2022 14:54:45: Fewer paired peaks (894) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 894 pairs to build model! INFO @ Tue, 02 Aug 2022 14:54:45: start model_add_line... INFO @ Tue, 02 Aug 2022 14:54:45: start X-correlation... INFO @ Tue, 02 Aug 2022 14:54:45: end of X-cor INFO @ Tue, 02 Aug 2022 14:54:45: #2 finished! INFO @ Tue, 02 Aug 2022 14:54:45: #2 predicted fragment length is 185 bps INFO @ Tue, 02 Aug 2022 14:54:45: #2 alternative fragment length(s) may be 185 bps INFO @ Tue, 02 Aug 2022 14:54:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15206470/SRX15206470.05_model.r INFO @ Tue, 02 Aug 2022 14:54:45: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:54:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:54:50: 1000000 INFO @ Tue, 02 Aug 2022 14:54:56: 2000000 INFO @ Tue, 02 Aug 2022 14:54:57: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:55:02: 3000000 INFO @ Tue, 02 Aug 2022 14:55:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15206470/SRX15206470.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:55:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15206470/SRX15206470.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:55:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15206470/SRX15206470.05_summits.bed INFO @ Tue, 02 Aug 2022 14:55:03: Done! pass1 - making usageList (470 chroms): 2 millis pass2 - checking and writing primary data (1555 records, 4 fields): 44 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:55:08: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 14:55:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15206470/SRX15206470.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15206470/SRX15206470.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15206470/SRX15206470.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15206470/SRX15206470.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, 02 Aug 2022 14:55:14: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:55:14: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:55:14: 5000000 INFO @ Tue, 02 Aug 2022 14:55:17: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 14:55:17: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 14:55:17: #1 total tags in treatment: 5350209 INFO @ Tue, 02 Aug 2022 14:55:17: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:55:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 14:55:17: #1 tags after filtering in treatment: 5350097 INFO @ Tue, 02 Aug 2022 14:55:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:55:17: #1 finished! INFO @ Tue, 02 Aug 2022 14:55:17: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:55:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:55:17: #2 number of paired peaks: 894 WARNING @ Tue, 02 Aug 2022 14:55:17: Fewer paired peaks (894) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 894 pairs to build model! INFO @ Tue, 02 Aug 2022 14:55:17: start model_add_line... INFO @ Tue, 02 Aug 2022 14:55:17: start X-correlation... INFO @ Tue, 02 Aug 2022 14:55:17: end of X-cor INFO @ Tue, 02 Aug 2022 14:55:17: #2 finished! INFO @ Tue, 02 Aug 2022 14:55:17: #2 predicted fragment length is 185 bps INFO @ Tue, 02 Aug 2022 14:55:17: #2 alternative fragment length(s) may be 185 bps INFO @ Tue, 02 Aug 2022 14:55:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15206470/SRX15206470.10_model.r INFO @ Tue, 02 Aug 2022 14:55:17: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:55:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:55:20: 1000000 INFO @ Tue, 02 Aug 2022 14:55:27: 2000000 INFO @ Tue, 02 Aug 2022 14:55:30: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:55:33: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:55:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15206470/SRX15206470.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:55:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15206470/SRX15206470.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:55:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15206470/SRX15206470.10_summits.bed INFO @ Tue, 02 Aug 2022 14:55:36: Done! pass1 - making usageList (244 chroms): 1 millis pass2 - checking and writing primary data (582 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:55:40: 4000000 INFO @ Tue, 02 Aug 2022 14:55:46: 5000000 INFO @ Tue, 02 Aug 2022 14:55:48: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 14:55:48: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 14:55:48: #1 total tags in treatment: 5350209 INFO @ Tue, 02 Aug 2022 14:55:48: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:55:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:55:49: #1 tags after filtering in treatment: 5350097 INFO @ Tue, 02 Aug 2022 14:55:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:55:49: #1 finished! INFO @ Tue, 02 Aug 2022 14:55:49: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:55:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:55:49: #2 number of paired peaks: 894 WARNING @ Tue, 02 Aug 2022 14:55:49: Fewer paired peaks (894) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 894 pairs to build model! INFO @ Tue, 02 Aug 2022 14:55:49: start model_add_line... INFO @ Tue, 02 Aug 2022 14:55:50: start X-correlation... INFO @ Tue, 02 Aug 2022 14:55:50: end of X-cor INFO @ Tue, 02 Aug 2022 14:55:50: #2 finished! INFO @ Tue, 02 Aug 2022 14:55:50: #2 predicted fragment length is 185 bps INFO @ Tue, 02 Aug 2022 14:55:50: #2 alternative fragment length(s) may be 185 bps INFO @ Tue, 02 Aug 2022 14:55:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15206470/SRX15206470.20_model.r INFO @ Tue, 02 Aug 2022 14:55:50: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:55:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:56:02: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:56:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15206470/SRX15206470.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:56:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15206470/SRX15206470.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:56:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15206470/SRX15206470.20_summits.bed INFO @ Tue, 02 Aug 2022 14:56:08: Done! pass1 - making usageList (108 chroms): 1 millis pass2 - checking and writing primary data (201 records, 4 fields): 21 millis CompletedMACS2peakCalling