Job ID = 6529195 SRX = SRX040612 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: 00:03:07 15981209 reads; of these: 15981209 (100.00%) were unpaired; of these: 659462 (4.13%) aligned 0 times 13468527 (84.28%) aligned exactly 1 time 1853220 (11.60%) aligned >1 times 95.87% overall alignment rate Time searching: 00:03:07 Overall time: 00:03:07 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] 4636316 / 15321747 = 0.3026 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 01:44:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX040612/SRX040612.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX040612/SRX040612.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX040612/SRX040612.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX040612/SRX040612.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 01:44:15: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:44:15: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:44:20: 1000000 INFO @ Tue, 30 Jun 2020 01:44:26: 2000000 INFO @ Tue, 30 Jun 2020 01:44:31: 3000000 INFO @ Tue, 30 Jun 2020 01:44:36: 4000000 INFO @ Tue, 30 Jun 2020 01:44:41: 5000000 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 01:44:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX040612/SRX040612.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX040612/SRX040612.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX040612/SRX040612.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX040612/SRX040612.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 01:44:45: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:44:45: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:44:47: 6000000 INFO @ Tue, 30 Jun 2020 01:44:51: 1000000 INFO @ Tue, 30 Jun 2020 01:44:52: 7000000 INFO @ Tue, 30 Jun 2020 01:44:56: 2000000 INFO @ Tue, 30 Jun 2020 01:44:58: 8000000 INFO @ Tue, 30 Jun 2020 01:45:02: 3000000 INFO @ Tue, 30 Jun 2020 01:45:04: 9000000 INFO @ Tue, 30 Jun 2020 01:45:08: 4000000 INFO @ Tue, 30 Jun 2020 01:45:09: 10000000 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 01:45:13: 5000000 INFO @ Tue, 30 Jun 2020 01:45:13: #1 tag size is determined as 40 bps INFO @ Tue, 30 Jun 2020 01:45:13: #1 tag size = 40 INFO @ Tue, 30 Jun 2020 01:45:13: #1 total tags in treatment: 10685431 INFO @ Tue, 30 Jun 2020 01:45:13: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:45:13: #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 01:45:14: #1 tags after filtering in treatment: 10685361 INFO @ Tue, 30 Jun 2020 01:45:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:45:14: #1 finished! INFO @ Tue, 30 Jun 2020 01:45:14: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:45:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:45:14: #2 number of paired peaks: 289 WARNING @ Tue, 30 Jun 2020 01:45:14: Fewer paired peaks (289) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 289 pairs to build model! INFO @ Tue, 30 Jun 2020 01:45:14: start model_add_line... INFO @ Tue, 30 Jun 2020 01:45:14: start X-correlation... INFO @ Tue, 30 Jun 2020 01:45:14: end of X-cor INFO @ Tue, 30 Jun 2020 01:45:14: #2 finished! INFO @ Tue, 30 Jun 2020 01:45:14: #2 predicted fragment length is 145 bps INFO @ Tue, 30 Jun 2020 01:45:14: #2 alternative fragment length(s) may be 145 bps INFO @ Tue, 30 Jun 2020 01:45:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX040612/SRX040612.05_model.r INFO @ Tue, 30 Jun 2020 01:45:14: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:45:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:45:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX040612/SRX040612.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX040612/SRX040612.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX040612/SRX040612.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX040612/SRX040612.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 01:45:15: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:45:15: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:45:19: 6000000 INFO @ Tue, 30 Jun 2020 01:45:22: 1000000 INFO @ Tue, 30 Jun 2020 01:45:26: 7000000 INFO @ Tue, 30 Jun 2020 01:45:29: 2000000 INFO @ Tue, 30 Jun 2020 01:45:32: 8000000 INFO @ Tue, 30 Jun 2020 01:45:35: 3000000 INFO @ Tue, 30 Jun 2020 01:45:38: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:45:39: 9000000 INFO @ Tue, 30 Jun 2020 01:45:42: 4000000 INFO @ Tue, 30 Jun 2020 01:45:45: 10000000 INFO @ Tue, 30 Jun 2020 01:45:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX040612/SRX040612.05_peaks.xls INFO @ Tue, 30 Jun 2020 01:45:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX040612/SRX040612.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:45:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX040612/SRX040612.05_summits.bed INFO @ Tue, 30 Jun 2020 01:45:48: Done! pass1 - making usageList (159 chroms): 1 millis pass2 - checking and writing primary data (6690 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:45:49: 5000000 INFO @ Tue, 30 Jun 2020 01:45:50: #1 tag size is determined as 40 bps INFO @ Tue, 30 Jun 2020 01:45:50: #1 tag size = 40 INFO @ Tue, 30 Jun 2020 01:45:50: #1 total tags in treatment: 10685431 INFO @ Tue, 30 Jun 2020 01:45:50: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:45:50: #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 01:45:50: #1 tags after filtering in treatment: 10685361 INFO @ Tue, 30 Jun 2020 01:45:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:45:50: #1 finished! INFO @ Tue, 30 Jun 2020 01:45:50: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:45:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:45:51: #2 number of paired peaks: 289 WARNING @ Tue, 30 Jun 2020 01:45:51: Fewer paired peaks (289) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 289 pairs to build model! INFO @ Tue, 30 Jun 2020 01:45:51: start model_add_line... INFO @ Tue, 30 Jun 2020 01:45:51: start X-correlation... INFO @ Tue, 30 Jun 2020 01:45:51: end of X-cor INFO @ Tue, 30 Jun 2020 01:45:51: #2 finished! INFO @ Tue, 30 Jun 2020 01:45:51: #2 predicted fragment length is 145 bps INFO @ Tue, 30 Jun 2020 01:45:51: #2 alternative fragment length(s) may be 145 bps INFO @ Tue, 30 Jun 2020 01:45:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX040612/SRX040612.10_model.r INFO @ Tue, 30 Jun 2020 01:45:51: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:45:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:45:56: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 01:46:02: 7000000 INFO @ Tue, 30 Jun 2020 01:46:09: 8000000 INFO @ Tue, 30 Jun 2020 01:46:15: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:46:15: 9000000 INFO @ Tue, 30 Jun 2020 01:46:22: 10000000 BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 01:46:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX040612/SRX040612.10_peaks.xls INFO @ Tue, 30 Jun 2020 01:46:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX040612/SRX040612.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:46:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX040612/SRX040612.10_summits.bed INFO @ Tue, 30 Jun 2020 01:46:26: Done! pass1 - making usageList (98 chroms): 1 millis pass2 - checking and writing primary data (2165 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:46:26: #1 tag size is determined as 40 bps INFO @ Tue, 30 Jun 2020 01:46:26: #1 tag size = 40 INFO @ Tue, 30 Jun 2020 01:46:26: #1 total tags in treatment: 10685431 INFO @ Tue, 30 Jun 2020 01:46:26: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:46:26: #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 01:46:27: #1 tags after filtering in treatment: 10685361 INFO @ Tue, 30 Jun 2020 01:46:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:46:27: #1 finished! INFO @ Tue, 30 Jun 2020 01:46:27: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:46:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:46:27: #2 number of paired peaks: 289 WARNING @ Tue, 30 Jun 2020 01:46:27: Fewer paired peaks (289) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 289 pairs to build model! INFO @ Tue, 30 Jun 2020 01:46:27: start model_add_line... INFO @ Tue, 30 Jun 2020 01:46:27: start X-correlation... INFO @ Tue, 30 Jun 2020 01:46:27: end of X-cor INFO @ Tue, 30 Jun 2020 01:46:27: #2 finished! INFO @ Tue, 30 Jun 2020 01:46:27: #2 predicted fragment length is 145 bps INFO @ Tue, 30 Jun 2020 01:46:27: #2 alternative fragment length(s) may be 145 bps INFO @ Tue, 30 Jun 2020 01:46:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX040612/SRX040612.20_model.r INFO @ Tue, 30 Jun 2020 01:46:27: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:46:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:46:50: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:47:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX040612/SRX040612.20_peaks.xls INFO @ Tue, 30 Jun 2020 01:47:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX040612/SRX040612.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:47:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX040612/SRX040612.20_summits.bed INFO @ Tue, 30 Jun 2020 01:47:01: Done! pass1 - making usageList (74 chroms): 1 millis pass2 - checking and writing primary data (281 records, 4 fields): 4 millis CompletedMACS2peakCalling