Job ID = 6529249 SRX = SRX110796 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:33 14420359 reads; of these: 14420359 (100.00%) were unpaired; of these: 389799 (2.70%) aligned 0 times 6745881 (46.78%) aligned exactly 1 time 7284679 (50.52%) aligned >1 times 97.30% overall alignment rate Time searching: 00:04:34 Overall time: 00:04:34 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] 1129977 / 14030560 = 0.0805 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 02:16:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX110796/SRX110796.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX110796/SRX110796.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX110796/SRX110796.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX110796/SRX110796.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 02:16:04: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:16:04: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:16:10: 1000000 INFO @ Tue, 30 Jun 2020 02:16:16: 2000000 INFO @ Tue, 30 Jun 2020 02:16:22: 3000000 INFO @ Tue, 30 Jun 2020 02:16:28: 4000000 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 02:16:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX110796/SRX110796.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX110796/SRX110796.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX110796/SRX110796.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX110796/SRX110796.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 02:16:34: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:16:34: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:16:35: 5000000 INFO @ Tue, 30 Jun 2020 02:16:40: 1000000 INFO @ Tue, 30 Jun 2020 02:16:41: 6000000 INFO @ Tue, 30 Jun 2020 02:16:46: 2000000 INFO @ Tue, 30 Jun 2020 02:16:47: 7000000 INFO @ Tue, 30 Jun 2020 02:16:52: 3000000 INFO @ Tue, 30 Jun 2020 02:16:53: 8000000 INFO @ Tue, 30 Jun 2020 02:16:58: 4000000 INFO @ Tue, 30 Jun 2020 02:16:59: 9000000 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 02:17:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX110796/SRX110796.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX110796/SRX110796.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX110796/SRX110796.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX110796/SRX110796.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 02:17:04: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:17:04: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:17:04: 5000000 INFO @ Tue, 30 Jun 2020 02:17:05: 10000000 INFO @ Tue, 30 Jun 2020 02:17:10: 1000000 INFO @ Tue, 30 Jun 2020 02:17:10: 6000000 INFO @ Tue, 30 Jun 2020 02:17:12: 11000000 INFO @ Tue, 30 Jun 2020 02:17:16: 2000000 INFO @ Tue, 30 Jun 2020 02:17:17: 7000000 INFO @ Tue, 30 Jun 2020 02:17:18: 12000000 INFO @ Tue, 30 Jun 2020 02:17:22: 3000000 INFO @ Tue, 30 Jun 2020 02:17:23: 8000000 INFO @ Tue, 30 Jun 2020 02:17:24: #1 tag size is determined as 18 bps INFO @ Tue, 30 Jun 2020 02:17:24: #1 tag size = 18 INFO @ Tue, 30 Jun 2020 02:17:24: #1 total tags in treatment: 12900583 INFO @ Tue, 30 Jun 2020 02:17:24: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:17:24: #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 02:17:24: #1 tags after filtering in treatment: 12900583 INFO @ Tue, 30 Jun 2020 02:17:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:17:24: #1 finished! INFO @ Tue, 30 Jun 2020 02:17:24: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:17:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:17:25: #2 number of paired peaks: 215 WARNING @ Tue, 30 Jun 2020 02:17:25: Fewer paired peaks (215) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 215 pairs to build model! INFO @ Tue, 30 Jun 2020 02:17:25: start model_add_line... INFO @ Tue, 30 Jun 2020 02:17:25: start X-correlation... INFO @ Tue, 30 Jun 2020 02:17:25: end of X-cor INFO @ Tue, 30 Jun 2020 02:17:25: #2 finished! INFO @ Tue, 30 Jun 2020 02:17:25: #2 predicted fragment length is 53 bps INFO @ Tue, 30 Jun 2020 02:17:25: #2 alternative fragment length(s) may be 4,53 bps INFO @ Tue, 30 Jun 2020 02:17:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX110796/SRX110796.05_model.r INFO @ Tue, 30 Jun 2020 02:17:25: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:17:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:17:28: 4000000 INFO @ Tue, 30 Jun 2020 02:17:29: 9000000 INFO @ Tue, 30 Jun 2020 02:17:34: 5000000 INFO @ Tue, 30 Jun 2020 02:17:35: 10000000 INFO @ Tue, 30 Jun 2020 02:17:40: 6000000 INFO @ Tue, 30 Jun 2020 02:17:41: 11000000 INFO @ Tue, 30 Jun 2020 02:17:46: 7000000 INFO @ Tue, 30 Jun 2020 02:17:47: 12000000 INFO @ Tue, 30 Jun 2020 02:17:49: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:17:51: 8000000 INFO @ Tue, 30 Jun 2020 02:17:53: #1 tag size is determined as 18 bps INFO @ Tue, 30 Jun 2020 02:17:53: #1 tag size = 18 INFO @ Tue, 30 Jun 2020 02:17:53: #1 total tags in treatment: 12900583 INFO @ Tue, 30 Jun 2020 02:17:53: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:17:53: #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 02:17:54: #1 tags after filtering in treatment: 12900583 INFO @ Tue, 30 Jun 2020 02:17:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:17:54: #1 finished! INFO @ Tue, 30 Jun 2020 02:17:54: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:17:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:17:55: #2 number of paired peaks: 215 WARNING @ Tue, 30 Jun 2020 02:17:55: Fewer paired peaks (215) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 215 pairs to build model! INFO @ Tue, 30 Jun 2020 02:17:55: start model_add_line... INFO @ Tue, 30 Jun 2020 02:17:55: start X-correlation... INFO @ Tue, 30 Jun 2020 02:17:55: end of X-cor INFO @ Tue, 30 Jun 2020 02:17:55: #2 finished! INFO @ Tue, 30 Jun 2020 02:17:55: #2 predicted fragment length is 53 bps INFO @ Tue, 30 Jun 2020 02:17:55: #2 alternative fragment length(s) may be 4,53 bps INFO @ Tue, 30 Jun 2020 02:17:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX110796/SRX110796.10_model.r INFO @ Tue, 30 Jun 2020 02:17:55: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:17:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:17:57: 9000000 INFO @ Tue, 30 Jun 2020 02:18:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX110796/SRX110796.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:18:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX110796/SRX110796.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:18:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX110796/SRX110796.05_summits.bed INFO @ Tue, 30 Jun 2020 02:18:02: Done! pass1 - making usageList (444 chroms): 2 millis pass2 - checking and writing primary data (2031 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:18:03: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:18:10: 11000000 INFO @ Tue, 30 Jun 2020 02:18:15: 12000000 INFO @ Tue, 30 Jun 2020 02:18:18: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:18:21: #1 tag size is determined as 18 bps INFO @ Tue, 30 Jun 2020 02:18:21: #1 tag size = 18 INFO @ Tue, 30 Jun 2020 02:18:21: #1 total tags in treatment: 12900583 INFO @ Tue, 30 Jun 2020 02:18:21: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:18:21: #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 02:18:22: #1 tags after filtering in treatment: 12900583 INFO @ Tue, 30 Jun 2020 02:18:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:18:22: #1 finished! INFO @ Tue, 30 Jun 2020 02:18:22: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:18:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:18:23: #2 number of paired peaks: 215 WARNING @ Tue, 30 Jun 2020 02:18:23: Fewer paired peaks (215) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 215 pairs to build model! INFO @ Tue, 30 Jun 2020 02:18:23: start model_add_line... INFO @ Tue, 30 Jun 2020 02:18:23: start X-correlation... INFO @ Tue, 30 Jun 2020 02:18:23: end of X-cor INFO @ Tue, 30 Jun 2020 02:18:23: #2 finished! INFO @ Tue, 30 Jun 2020 02:18:23: #2 predicted fragment length is 53 bps INFO @ Tue, 30 Jun 2020 02:18:23: #2 alternative fragment length(s) may be 4,53 bps INFO @ Tue, 30 Jun 2020 02:18:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX110796/SRX110796.20_model.r INFO @ Tue, 30 Jun 2020 02:18:23: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:18:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:18:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX110796/SRX110796.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:18:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX110796/SRX110796.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:18:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX110796/SRX110796.10_summits.bed INFO @ Tue, 30 Jun 2020 02:18:30: Done! pass1 - making usageList (320 chroms): 1 millis pass2 - checking and writing primary data (731 records, 4 fields): 19 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:18:46: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:18:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX110796/SRX110796.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:18:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX110796/SRX110796.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:18:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX110796/SRX110796.20_summits.bed INFO @ Tue, 30 Jun 2020 02:18:59: Done! pass1 - making usageList (95 chroms): 1 millis pass2 - checking and writing primary data (217 records, 4 fields): 6 millis CompletedMACS2peakCalling