Job ID = 16439673 SRX = SRX13572048 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: 00:02:59 14311616 reads; of these: 14311616 (100.00%) were unpaired; of these: 712005 (4.98%) aligned 0 times 11584540 (80.95%) aligned exactly 1 time 2015071 (14.08%) aligned >1 times 95.02% overall alignment rate Time searching: 00:02:59 Overall time: 00:02:59 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] 801273 / 13599611 = 0.0589 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 15:59:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX13572048/SRX13572048.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX13572048/SRX13572048.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX13572048/SRX13572048.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX13572048/SRX13572048.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 15:59:59: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:59:59: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:00:05: 1000000 INFO @ Tue, 02 Aug 2022 16:00:11: 2000000 INFO @ Tue, 02 Aug 2022 16:00:17: 3000000 INFO @ Tue, 02 Aug 2022 16:00:22: 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 16:00:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX13572048/SRX13572048.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX13572048/SRX13572048.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX13572048/SRX13572048.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX13572048/SRX13572048.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 16:00:27: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:00:27: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:00:28: 5000000 INFO @ Tue, 02 Aug 2022 16:00:33: 1000000 INFO @ Tue, 02 Aug 2022 16:00:34: 6000000 INFO @ Tue, 02 Aug 2022 16:00:39: 2000000 INFO @ Tue, 02 Aug 2022 16:00:40: 7000000 INFO @ Tue, 02 Aug 2022 16:00:45: 8000000 INFO @ Tue, 02 Aug 2022 16:00:45: 3000000 INFO @ Tue, 02 Aug 2022 16:00:51: 9000000 INFO @ Tue, 02 Aug 2022 16:00:51: 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 16:00:57: 10000000 INFO @ Tue, 02 Aug 2022 16:00:57: 5000000 INFO @ Tue, 02 Aug 2022 16:00:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX13572048/SRX13572048.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX13572048/SRX13572048.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX13572048/SRX13572048.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX13572048/SRX13572048.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 16:00:57: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:00:57: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:01:03: 1000000 INFO @ Tue, 02 Aug 2022 16:01:03: 11000000 INFO @ Tue, 02 Aug 2022 16:01:03: 6000000 INFO @ Tue, 02 Aug 2022 16:01:08: 2000000 INFO @ Tue, 02 Aug 2022 16:01:08: 12000000 INFO @ Tue, 02 Aug 2022 16:01:09: 7000000 INFO @ Tue, 02 Aug 2022 16:01:13: #1 tag size is determined as 49 bps INFO @ Tue, 02 Aug 2022 16:01:13: #1 tag size = 49 INFO @ Tue, 02 Aug 2022 16:01:13: #1 total tags in treatment: 12798338 INFO @ Tue, 02 Aug 2022 16:01:13: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:01:13: #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 16:01:14: #1 tags after filtering in treatment: 12798305 INFO @ Tue, 02 Aug 2022 16:01:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 16:01:14: #1 finished! INFO @ Tue, 02 Aug 2022 16:01:14: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:01:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:01:14: 3000000 INFO @ Tue, 02 Aug 2022 16:01:15: #2 number of paired peaks: 163 WARNING @ Tue, 02 Aug 2022 16:01:15: Fewer paired peaks (163) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 163 pairs to build model! INFO @ Tue, 02 Aug 2022 16:01:15: start model_add_line... INFO @ Tue, 02 Aug 2022 16:01:15: start X-correlation... INFO @ Tue, 02 Aug 2022 16:01:15: end of X-cor INFO @ Tue, 02 Aug 2022 16:01:15: #2 finished! INFO @ Tue, 02 Aug 2022 16:01:15: #2 predicted fragment length is 117 bps INFO @ Tue, 02 Aug 2022 16:01:15: #2 alternative fragment length(s) may be 89,99,117,137 bps INFO @ Tue, 02 Aug 2022 16:01:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX13572048/SRX13572048.05_model.r INFO @ Tue, 02 Aug 2022 16:01:15: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:01:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:01:15: 8000000 INFO @ Tue, 02 Aug 2022 16:01:19: 4000000 INFO @ Tue, 02 Aug 2022 16:01:21: 9000000 INFO @ Tue, 02 Aug 2022 16:01:25: 5000000 INFO @ Tue, 02 Aug 2022 16:01:27: 10000000 INFO @ Tue, 02 Aug 2022 16:01:30: 6000000 INFO @ Tue, 02 Aug 2022 16:01:33: 11000000 INFO @ Tue, 02 Aug 2022 16:01:35: 7000000 INFO @ Tue, 02 Aug 2022 16:01:39: 12000000 INFO @ Tue, 02 Aug 2022 16:01:40: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:01:41: 8000000 INFO @ Tue, 02 Aug 2022 16:01:44: #1 tag size is determined as 49 bps INFO @ Tue, 02 Aug 2022 16:01:44: #1 tag size = 49 INFO @ Tue, 02 Aug 2022 16:01:44: #1 total tags in treatment: 12798338 INFO @ Tue, 02 Aug 2022 16:01:44: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:01:44: #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 16:01:45: #1 tags after filtering in treatment: 12798305 INFO @ Tue, 02 Aug 2022 16:01:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 16:01:45: #1 finished! INFO @ Tue, 02 Aug 2022 16:01:45: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:01:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:01:45: #2 number of paired peaks: 163 WARNING @ Tue, 02 Aug 2022 16:01:45: Fewer paired peaks (163) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 163 pairs to build model! INFO @ Tue, 02 Aug 2022 16:01:45: start model_add_line... INFO @ Tue, 02 Aug 2022 16:01:45: start X-correlation... INFO @ Tue, 02 Aug 2022 16:01:45: end of X-cor INFO @ Tue, 02 Aug 2022 16:01:45: #2 finished! INFO @ Tue, 02 Aug 2022 16:01:45: #2 predicted fragment length is 117 bps INFO @ Tue, 02 Aug 2022 16:01:45: #2 alternative fragment length(s) may be 89,99,117,137 bps INFO @ Tue, 02 Aug 2022 16:01:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX13572048/SRX13572048.10_model.r INFO @ Tue, 02 Aug 2022 16:01:46: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:01:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:01:46: 9000000 INFO @ Tue, 02 Aug 2022 16:01:51: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 16:01:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX13572048/SRX13572048.05_peaks.xls INFO @ Tue, 02 Aug 2022 16:01:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX13572048/SRX13572048.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:01:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX13572048/SRX13572048.05_summits.bed INFO @ Tue, 02 Aug 2022 16:01:53: Done! pass1 - making usageList (388 chroms): 1 millis pass2 - checking and writing primary data (1510 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 16:01:57: 11000000 INFO @ Tue, 02 Aug 2022 16:02:02: 12000000 INFO @ Tue, 02 Aug 2022 16:02:06: #1 tag size is determined as 49 bps INFO @ Tue, 02 Aug 2022 16:02:06: #1 tag size = 49 INFO @ Tue, 02 Aug 2022 16:02:06: #1 total tags in treatment: 12798338 INFO @ Tue, 02 Aug 2022 16:02:06: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:02:06: #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 16:02:06: #1 tags after filtering in treatment: 12798305 INFO @ Tue, 02 Aug 2022 16:02:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 16:02:06: #1 finished! INFO @ Tue, 02 Aug 2022 16:02:06: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:02:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:02:07: #2 number of paired peaks: 163 WARNING @ Tue, 02 Aug 2022 16:02:07: Fewer paired peaks (163) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 163 pairs to build model! INFO @ Tue, 02 Aug 2022 16:02:07: start model_add_line... INFO @ Tue, 02 Aug 2022 16:02:07: start X-correlation... INFO @ Tue, 02 Aug 2022 16:02:07: end of X-cor INFO @ Tue, 02 Aug 2022 16:02:07: #2 finished! INFO @ Tue, 02 Aug 2022 16:02:07: #2 predicted fragment length is 117 bps INFO @ Tue, 02 Aug 2022 16:02:07: #2 alternative fragment length(s) may be 89,99,117,137 bps INFO @ Tue, 02 Aug 2022 16:02:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX13572048/SRX13572048.20_model.r INFO @ Tue, 02 Aug 2022 16:02:07: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:02:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:02:09: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 16:02:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX13572048/SRX13572048.10_peaks.xls INFO @ Tue, 02 Aug 2022 16:02:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX13572048/SRX13572048.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:02:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX13572048/SRX13572048.10_summits.bed INFO @ Tue, 02 Aug 2022 16:02:22: Done! pass1 - making usageList (260 chroms): 1 millis pass2 - checking and writing primary data (767 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 16:02:32: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:02:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX13572048/SRX13572048.20_peaks.xls INFO @ Tue, 02 Aug 2022 16:02:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX13572048/SRX13572048.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:02:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX13572048/SRX13572048.20_summits.bed INFO @ Tue, 02 Aug 2022 16:02:45: Done! pass1 - making usageList (91 chroms): 1 millis pass2 - checking and writing primary data (308 records, 4 fields): 25 millis CompletedMACS2peakCalling