Job ID = 14171662 SRX = SRX9986105 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: 00:15:40 20164486 reads; of these: 20164486 (100.00%) were unpaired; of these: 3181851 (15.78%) aligned 0 times 7098312 (35.20%) aligned exactly 1 time 9884323 (49.02%) aligned >1 times 84.22% overall alignment rate Time searching: 00:15:40 Overall time: 00:15:40 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] 10704869 / 16982635 = 0.6303 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 12:40:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9986105/SRX9986105.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9986105/SRX9986105.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9986105/SRX9986105.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9986105/SRX9986105.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 @ Sat, 11 Dec 2021 12:40:19: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:40:19: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:40:29: 1000000 INFO @ Sat, 11 Dec 2021 12:40:38: 2000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 12:40:48: 3000000 INFO @ Sat, 11 Dec 2021 12:40:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9986105/SRX9986105.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9986105/SRX9986105.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9986105/SRX9986105.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9986105/SRX9986105.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 @ Sat, 11 Dec 2021 12:40:49: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:40:49: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:40:59: 4000000 INFO @ Sat, 11 Dec 2021 12:41:00: 1000000 INFO @ Sat, 11 Dec 2021 12:41:09: 5000000 INFO @ Sat, 11 Dec 2021 12:41:10: 2000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 12:41:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9986105/SRX9986105.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9986105/SRX9986105.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9986105/SRX9986105.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9986105/SRX9986105.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 @ Sat, 11 Dec 2021 12:41:19: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:41:19: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:41:20: 6000000 INFO @ Sat, 11 Dec 2021 12:41:20: 3000000 INFO @ Sat, 11 Dec 2021 12:41:23: #1 tag size is determined as 58 bps INFO @ Sat, 11 Dec 2021 12:41:23: #1 tag size = 58 INFO @ Sat, 11 Dec 2021 12:41:23: #1 total tags in treatment: 6277766 INFO @ Sat, 11 Dec 2021 12:41:23: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:41:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 12:41:24: #1 tags after filtering in treatment: 6277619 INFO @ Sat, 11 Dec 2021 12:41:24: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 12:41:24: #1 finished! INFO @ Sat, 11 Dec 2021 12:41:24: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:41:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:41:24: #2 number of paired peaks: 703 WARNING @ Sat, 11 Dec 2021 12:41:24: Fewer paired peaks (703) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 703 pairs to build model! INFO @ Sat, 11 Dec 2021 12:41:24: start model_add_line... INFO @ Sat, 11 Dec 2021 12:41:24: start X-correlation... INFO @ Sat, 11 Dec 2021 12:41:24: end of X-cor INFO @ Sat, 11 Dec 2021 12:41:24: #2 finished! INFO @ Sat, 11 Dec 2021 12:41:24: #2 predicted fragment length is 213 bps INFO @ Sat, 11 Dec 2021 12:41:24: #2 alternative fragment length(s) may be 213 bps INFO @ Sat, 11 Dec 2021 12:41:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9986105/SRX9986105.05_model.r INFO @ Sat, 11 Dec 2021 12:41:24: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:41:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:41:30: 1000000 INFO @ Sat, 11 Dec 2021 12:41:31: 4000000 INFO @ Sat, 11 Dec 2021 12:41:41: 2000000 INFO @ Sat, 11 Dec 2021 12:41:41: 5000000 INFO @ Sat, 11 Dec 2021 12:41:46: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:41:51: 3000000 INFO @ Sat, 11 Dec 2021 12:41:53: 6000000 INFO @ Sat, 11 Dec 2021 12:41:56: #1 tag size is determined as 58 bps INFO @ Sat, 11 Dec 2021 12:41:56: #1 tag size = 58 INFO @ Sat, 11 Dec 2021 12:41:56: #1 total tags in treatment: 6277766 INFO @ Sat, 11 Dec 2021 12:41:56: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:41:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 12:41:56: #1 tags after filtering in treatment: 6277619 INFO @ Sat, 11 Dec 2021 12:41:56: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 12:41:56: #1 finished! INFO @ Sat, 11 Dec 2021 12:41:56: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:41:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:41:57: #2 number of paired peaks: 703 WARNING @ Sat, 11 Dec 2021 12:41:57: Fewer paired peaks (703) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 703 pairs to build model! INFO @ Sat, 11 Dec 2021 12:41:57: start model_add_line... INFO @ Sat, 11 Dec 2021 12:41:57: start X-correlation... INFO @ Sat, 11 Dec 2021 12:41:57: end of X-cor INFO @ Sat, 11 Dec 2021 12:41:57: #2 finished! INFO @ Sat, 11 Dec 2021 12:41:57: #2 predicted fragment length is 213 bps INFO @ Sat, 11 Dec 2021 12:41:57: #2 alternative fragment length(s) may be 213 bps INFO @ Sat, 11 Dec 2021 12:41:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9986105/SRX9986105.10_model.r INFO @ Sat, 11 Dec 2021 12:41:57: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:41:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:41:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9986105/SRX9986105.05_peaks.xls INFO @ Sat, 11 Dec 2021 12:41:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9986105/SRX9986105.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:41:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9986105/SRX9986105.05_summits.bed INFO @ Sat, 11 Dec 2021 12:41:58: Done! pass1 - making usageList (512 chroms): 4 millis pass2 - checking and writing primary data (10878 records, 4 fields): 36 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 12:42:01: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 12:42:11: 5000000 INFO @ Sat, 11 Dec 2021 12:42:18: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:42:21: 6000000 INFO @ Sat, 11 Dec 2021 12:42:24: #1 tag size is determined as 58 bps INFO @ Sat, 11 Dec 2021 12:42:24: #1 tag size = 58 INFO @ Sat, 11 Dec 2021 12:42:24: #1 total tags in treatment: 6277766 INFO @ Sat, 11 Dec 2021 12:42:24: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:42:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 12:42:25: #1 tags after filtering in treatment: 6277619 INFO @ Sat, 11 Dec 2021 12:42:25: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 12:42:25: #1 finished! INFO @ Sat, 11 Dec 2021 12:42:25: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:42:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:42:25: #2 number of paired peaks: 703 WARNING @ Sat, 11 Dec 2021 12:42:25: Fewer paired peaks (703) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 703 pairs to build model! INFO @ Sat, 11 Dec 2021 12:42:25: start model_add_line... INFO @ Sat, 11 Dec 2021 12:42:25: start X-correlation... INFO @ Sat, 11 Dec 2021 12:42:25: end of X-cor INFO @ Sat, 11 Dec 2021 12:42:25: #2 finished! INFO @ Sat, 11 Dec 2021 12:42:25: #2 predicted fragment length is 213 bps INFO @ Sat, 11 Dec 2021 12:42:25: #2 alternative fragment length(s) may be 213 bps INFO @ Sat, 11 Dec 2021 12:42:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9986105/SRX9986105.20_model.r INFO @ Sat, 11 Dec 2021 12:42:25: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:42:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:42:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9986105/SRX9986105.10_peaks.xls INFO @ Sat, 11 Dec 2021 12:42:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9986105/SRX9986105.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:42:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9986105/SRX9986105.10_summits.bed INFO @ Sat, 11 Dec 2021 12:42:29: Done! pass1 - making usageList (319 chroms): 2 millis pass2 - checking and writing primary data (4066 records, 4 fields): 20 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 12:42:46: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:42:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9986105/SRX9986105.20_peaks.xls INFO @ Sat, 11 Dec 2021 12:42:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9986105/SRX9986105.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:42:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9986105/SRX9986105.20_summits.bed INFO @ Sat, 11 Dec 2021 12:42:57: Done! pass1 - making usageList (124 chroms): 2 millis pass2 - checking and writing primary data (653 records, 4 fields): 9 millis CompletedMACS2peakCalling