Job ID = 14171828 SRX = SRX9986160 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: 00:02:56 13300114 reads; of these: 13300114 (100.00%) were unpaired; of these: 3847808 (28.93%) aligned 0 times 7605110 (57.18%) aligned exactly 1 time 1847196 (13.89%) aligned >1 times 71.07% overall alignment rate Time searching: 00:02:56 Overall time: 00:02:56 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] 1721751 / 9452306 = 0.1822 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 13:08:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9986160/SRX9986160.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9986160/SRX9986160.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9986160/SRX9986160.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9986160/SRX9986160.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 13:08:47: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:08:47: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:08:53: 1000000 INFO @ Sat, 11 Dec 2021 13:09:00: 2000000 INFO @ Sat, 11 Dec 2021 13:09:07: 3000000 INFO @ Sat, 11 Dec 2021 13:09:13: 4000000 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 13:09:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9986160/SRX9986160.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9986160/SRX9986160.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9986160/SRX9986160.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9986160/SRX9986160.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 13:09:17: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:09:17: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:09:20: 5000000 INFO @ Sat, 11 Dec 2021 13:09:24: 1000000 INFO @ Sat, 11 Dec 2021 13:09:27: 6000000 INFO @ Sat, 11 Dec 2021 13:09:32: 2000000 INFO @ Sat, 11 Dec 2021 13:09:35: 7000000 INFO @ Sat, 11 Dec 2021 13:09:39: 3000000 INFO @ Sat, 11 Dec 2021 13:09:40: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:09:40: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:09:40: #1 total tags in treatment: 7730555 INFO @ Sat, 11 Dec 2021 13:09:40: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:09:40: #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 13:09:41: #1 tags after filtering in treatment: 7730419 INFO @ Sat, 11 Dec 2021 13:09:41: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 13:09:41: #1 finished! INFO @ Sat, 11 Dec 2021 13:09:41: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:09:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:09:42: #2 number of paired peaks: 768 WARNING @ Sat, 11 Dec 2021 13:09:42: Fewer paired peaks (768) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 768 pairs to build model! INFO @ Sat, 11 Dec 2021 13:09:42: start model_add_line... INFO @ Sat, 11 Dec 2021 13:09:42: start X-correlation... INFO @ Sat, 11 Dec 2021 13:09:42: end of X-cor INFO @ Sat, 11 Dec 2021 13:09:42: #2 finished! INFO @ Sat, 11 Dec 2021 13:09:42: #2 predicted fragment length is 219 bps INFO @ Sat, 11 Dec 2021 13:09:42: #2 alternative fragment length(s) may be 2,219,240 bps INFO @ Sat, 11 Dec 2021 13:09:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9986160/SRX9986160.05_model.r INFO @ Sat, 11 Dec 2021 13:09:42: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:09:42: #3 Pre-compute pvalue-qvalue table... 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 13:09:46: 4000000 INFO @ Sat, 11 Dec 2021 13:09:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9986160/SRX9986160.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9986160/SRX9986160.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9986160/SRX9986160.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9986160/SRX9986160.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 13:09:47: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:09:47: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:09:54: 5000000 INFO @ Sat, 11 Dec 2021 13:09:54: 1000000 INFO @ Sat, 11 Dec 2021 13:10:00: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:10:01: 6000000 INFO @ Sat, 11 Dec 2021 13:10:02: 2000000 INFO @ Sat, 11 Dec 2021 13:10:08: 7000000 INFO @ Sat, 11 Dec 2021 13:10:09: 3000000 INFO @ Sat, 11 Dec 2021 13:10:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9986160/SRX9986160.05_peaks.xls INFO @ Sat, 11 Dec 2021 13:10:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9986160/SRX9986160.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:10:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9986160/SRX9986160.05_summits.bed INFO @ Sat, 11 Dec 2021 13:10:11: Done! pass1 - making usageList (122 chroms): 2 millis pass2 - checking and writing primary data (1854 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:10:14: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:10:14: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:10:14: #1 total tags in treatment: 7730555 INFO @ Sat, 11 Dec 2021 13:10:14: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:10:14: #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 13:10:15: #1 tags after filtering in treatment: 7730419 INFO @ Sat, 11 Dec 2021 13:10:15: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 13:10:15: #1 finished! INFO @ Sat, 11 Dec 2021 13:10:15: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:10:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:10:15: #2 number of paired peaks: 768 WARNING @ Sat, 11 Dec 2021 13:10:15: Fewer paired peaks (768) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 768 pairs to build model! INFO @ Sat, 11 Dec 2021 13:10:15: start model_add_line... INFO @ Sat, 11 Dec 2021 13:10:15: start X-correlation... INFO @ Sat, 11 Dec 2021 13:10:15: end of X-cor INFO @ Sat, 11 Dec 2021 13:10:15: #2 finished! INFO @ Sat, 11 Dec 2021 13:10:15: #2 predicted fragment length is 219 bps INFO @ Sat, 11 Dec 2021 13:10:15: #2 alternative fragment length(s) may be 2,219,240 bps INFO @ Sat, 11 Dec 2021 13:10:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9986160/SRX9986160.10_model.r INFO @ Sat, 11 Dec 2021 13:10:15: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:10:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:10:16: 4000000 INFO @ Sat, 11 Dec 2021 13:10:22: 5000000 INFO @ Sat, 11 Dec 2021 13:10:29: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 13:10:34: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:10:36: 7000000 INFO @ Sat, 11 Dec 2021 13:10:41: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:10:41: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:10:41: #1 total tags in treatment: 7730555 INFO @ Sat, 11 Dec 2021 13:10:41: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:10:41: #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 13:10:42: #1 tags after filtering in treatment: 7730419 INFO @ Sat, 11 Dec 2021 13:10:42: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 13:10:42: #1 finished! INFO @ Sat, 11 Dec 2021 13:10:42: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:10:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:10:43: #2 number of paired peaks: 768 WARNING @ Sat, 11 Dec 2021 13:10:43: Fewer paired peaks (768) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 768 pairs to build model! INFO @ Sat, 11 Dec 2021 13:10:43: start model_add_line... INFO @ Sat, 11 Dec 2021 13:10:43: start X-correlation... INFO @ Sat, 11 Dec 2021 13:10:43: end of X-cor INFO @ Sat, 11 Dec 2021 13:10:43: #2 finished! INFO @ Sat, 11 Dec 2021 13:10:43: #2 predicted fragment length is 219 bps INFO @ Sat, 11 Dec 2021 13:10:43: #2 alternative fragment length(s) may be 2,219,240 bps INFO @ Sat, 11 Dec 2021 13:10:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9986160/SRX9986160.20_model.r INFO @ Sat, 11 Dec 2021 13:10:43: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:10:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:10:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9986160/SRX9986160.10_peaks.xls INFO @ Sat, 11 Dec 2021 13:10:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9986160/SRX9986160.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:10:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9986160/SRX9986160.10_summits.bed INFO @ Sat, 11 Dec 2021 13:10:44: Done! pass1 - making usageList (73 chroms): 5 millis pass2 - checking and writing primary data (533 records, 4 fields): 7 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 13:11:01: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:11:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9986160/SRX9986160.20_peaks.xls INFO @ Sat, 11 Dec 2021 13:11:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9986160/SRX9986160.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:11:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9986160/SRX9986160.20_summits.bed INFO @ Sat, 11 Dec 2021 13:11:12: Done! pass1 - making usageList (47 chroms): 1 millis pass2 - checking and writing primary data (117 records, 4 fields): 4 millis CompletedMACS2peakCalling