Job ID = 6529459 SRX = SRX287605 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: 00:04:03 18523762 reads; of these: 18523762 (100.00%) were unpaired; of these: 1239779 (6.69%) aligned 0 times 15912349 (85.90%) aligned exactly 1 time 1371634 (7.40%) aligned >1 times 93.31% overall alignment rate Time searching: 00:04:03 Overall time: 00:04:03 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] 6204563 / 17283983 = 0.3590 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 02:13:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287605/SRX287605.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287605/SRX287605.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287605/SRX287605.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287605/SRX287605.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 02:13:37: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:13:37: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:13:44: 1000000 INFO @ Tue, 30 Jun 2020 02:13:52: 2000000 INFO @ Tue, 30 Jun 2020 02:14:00: 3000000 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 02:14:07: 4000000 INFO @ Tue, 30 Jun 2020 02:14:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287605/SRX287605.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287605/SRX287605.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287605/SRX287605.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287605/SRX287605.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 02:14:08: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:14:08: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:14:16: 5000000 INFO @ Tue, 30 Jun 2020 02:14:16: 1000000 INFO @ Tue, 30 Jun 2020 02:14:24: 6000000 INFO @ Tue, 30 Jun 2020 02:14:25: 2000000 INFO @ Tue, 30 Jun 2020 02:14:32: 7000000 INFO @ Tue, 30 Jun 2020 02:14:33: 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 02:14:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287605/SRX287605.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287605/SRX287605.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287605/SRX287605.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287605/SRX287605.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 02:14:37: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:14:37: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:14:39: 8000000 INFO @ Tue, 30 Jun 2020 02:14:41: 4000000 INFO @ Tue, 30 Jun 2020 02:14:45: 1000000 INFO @ Tue, 30 Jun 2020 02:14:46: 9000000 INFO @ Tue, 30 Jun 2020 02:14:49: 5000000 INFO @ Tue, 30 Jun 2020 02:14:52: 2000000 INFO @ Tue, 30 Jun 2020 02:14:54: 10000000 INFO @ Tue, 30 Jun 2020 02:14:57: 6000000 INFO @ Tue, 30 Jun 2020 02:14:59: 3000000 INFO @ Tue, 30 Jun 2020 02:15:01: 11000000 INFO @ Tue, 30 Jun 2020 02:15:02: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:15:02: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:15:02: #1 total tags in treatment: 11079420 INFO @ Tue, 30 Jun 2020 02:15:02: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:15:02: #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 02:15:02: #1 tags after filtering in treatment: 11079319 INFO @ Tue, 30 Jun 2020 02:15:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:15:02: #1 finished! INFO @ Tue, 30 Jun 2020 02:15:02: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:15:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:15:03: #2 number of paired peaks: 275 WARNING @ Tue, 30 Jun 2020 02:15:03: Fewer paired peaks (275) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 275 pairs to build model! INFO @ Tue, 30 Jun 2020 02:15:03: start model_add_line... INFO @ Tue, 30 Jun 2020 02:15:03: start X-correlation... INFO @ Tue, 30 Jun 2020 02:15:03: end of X-cor INFO @ Tue, 30 Jun 2020 02:15:03: #2 finished! INFO @ Tue, 30 Jun 2020 02:15:03: #2 predicted fragment length is 172 bps INFO @ Tue, 30 Jun 2020 02:15:03: #2 alternative fragment length(s) may be 2,71,163,172 bps INFO @ Tue, 30 Jun 2020 02:15:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287605/SRX287605.05_model.r INFO @ Tue, 30 Jun 2020 02:15:03: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:15:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:15:04: 7000000 INFO @ Tue, 30 Jun 2020 02:15:06: 4000000 INFO @ Tue, 30 Jun 2020 02:15:12: 8000000 INFO @ Tue, 30 Jun 2020 02:15:13: 5000000 INFO @ Tue, 30 Jun 2020 02:15:20: 6000000 INFO @ Tue, 30 Jun 2020 02:15:21: 9000000 INFO @ Tue, 30 Jun 2020 02:15:27: 7000000 INFO @ Tue, 30 Jun 2020 02:15:28: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:15:30: 10000000 INFO @ Tue, 30 Jun 2020 02:15:34: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:15:38: 11000000 INFO @ Tue, 30 Jun 2020 02:15:39: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:15:39: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:15:39: #1 total tags in treatment: 11079420 INFO @ Tue, 30 Jun 2020 02:15:39: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:15:39: #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 02:15:40: #1 tags after filtering in treatment: 11079319 INFO @ Tue, 30 Jun 2020 02:15:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:15:40: #1 finished! INFO @ Tue, 30 Jun 2020 02:15:40: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:15:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:15:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287605/SRX287605.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:15:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287605/SRX287605.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:15:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287605/SRX287605.05_summits.bed INFO @ Tue, 30 Jun 2020 02:15:40: Done! INFO @ Tue, 30 Jun 2020 02:15:40: #2 number of paired peaks: 275 WARNING @ Tue, 30 Jun 2020 02:15:40: Fewer paired peaks (275) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 275 pairs to build model! INFO @ Tue, 30 Jun 2020 02:15:40: start model_add_line... INFO @ Tue, 30 Jun 2020 02:15:40: start X-correlation... INFO @ Tue, 30 Jun 2020 02:15:40: end of X-cor INFO @ Tue, 30 Jun 2020 02:15:40: #2 finished! INFO @ Tue, 30 Jun 2020 02:15:40: #2 predicted fragment length is 172 bps INFO @ Tue, 30 Jun 2020 02:15:40: #2 alternative fragment length(s) may be 2,71,163,172 bps INFO @ Tue, 30 Jun 2020 02:15:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287605/SRX287605.10_model.r pass1 - making usageList (63 chroms): 1 millis INFO @ Tue, 30 Jun 2020 02:15:40: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:15:40: #3 Pre-compute pvalue-qvalue table... pass2 - checking and writing primary data (789 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:15:40: 9000000 INFO @ Tue, 30 Jun 2020 02:15:47: 10000000 INFO @ Tue, 30 Jun 2020 02:15:53: 11000000 INFO @ Tue, 30 Jun 2020 02:15:53: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:15:53: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:15:53: #1 total tags in treatment: 11079420 INFO @ Tue, 30 Jun 2020 02:15:53: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:15:53: #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 02:15:54: #1 tags after filtering in treatment: 11079319 INFO @ Tue, 30 Jun 2020 02:15:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:15:54: #1 finished! INFO @ Tue, 30 Jun 2020 02:15:54: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:15:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:15:54: #2 number of paired peaks: 275 WARNING @ Tue, 30 Jun 2020 02:15:54: Fewer paired peaks (275) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 275 pairs to build model! INFO @ Tue, 30 Jun 2020 02:15:54: start model_add_line... INFO @ Tue, 30 Jun 2020 02:15:54: start X-correlation... INFO @ Tue, 30 Jun 2020 02:15:54: end of X-cor INFO @ Tue, 30 Jun 2020 02:15:54: #2 finished! INFO @ Tue, 30 Jun 2020 02:15:54: #2 predicted fragment length is 172 bps INFO @ Tue, 30 Jun 2020 02:15:54: #2 alternative fragment length(s) may be 2,71,163,172 bps INFO @ Tue, 30 Jun 2020 02:15:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287605/SRX287605.20_model.r INFO @ Tue, 30 Jun 2020 02:15:54: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:15:54: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:16:05: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:16:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287605/SRX287605.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:16:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287605/SRX287605.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:16:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287605/SRX287605.10_summits.bed INFO @ Tue, 30 Jun 2020 02:16:17: Done! pass1 - making usageList (44 chroms): 0 millis pass2 - checking and writing primary data (135 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:16:18: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:16:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287605/SRX287605.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:16:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287605/SRX287605.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:16:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287605/SRX287605.20_summits.bed INFO @ Tue, 30 Jun 2020 02:16:30: Done! pass1 - making usageList (31 chroms): 0 millis pass2 - checking and writing primary data (66 records, 4 fields): 2 millis CompletedMACS2peakCalling