Job ID = 6453007 SRX = SRX097620 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:57:59 prefetch.2.10.7: 1) Downloading 'SRR345571'... 2020-06-21T07:57:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:07:07 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:07:07 prefetch.2.10.7: 1) 'SRR345571' was downloaded successfully Read 38502055 spots for SRR345571/SRR345571.sra Written 38502055 spots for SRR345571/SRR345571.sra 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: 00:07:06 38502055 reads; of these: 38502055 (100.00%) were unpaired; of these: 9711110 (25.22%) aligned 0 times 22191209 (57.64%) aligned exactly 1 time 6599736 (17.14%) aligned >1 times 74.78% overall alignment rate Time searching: 00:07:06 Overall time: 00:07:06 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] 11977248 / 28790945 = 0.4160 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 @ Sun, 21 Jun 2020 17:21:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX097620/SRX097620.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX097620/SRX097620.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX097620/SRX097620.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX097620/SRX097620.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 @ Sun, 21 Jun 2020 17:21:28: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:21:28: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:21:34: 1000000 INFO @ Sun, 21 Jun 2020 17:21:40: 2000000 INFO @ Sun, 21 Jun 2020 17:21:46: 3000000 INFO @ Sun, 21 Jun 2020 17:21:52: 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 @ Sun, 21 Jun 2020 17:21:58: 5000000 INFO @ Sun, 21 Jun 2020 17:21:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX097620/SRX097620.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX097620/SRX097620.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX097620/SRX097620.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX097620/SRX097620.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 @ Sun, 21 Jun 2020 17:21:59: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:21:59: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:22:04: 6000000 INFO @ Sun, 21 Jun 2020 17:22:05: 1000000 INFO @ Sun, 21 Jun 2020 17:22:10: 7000000 INFO @ Sun, 21 Jun 2020 17:22:11: 2000000 INFO @ Sun, 21 Jun 2020 17:22:16: 8000000 INFO @ Sun, 21 Jun 2020 17:22:17: 3000000 INFO @ Sun, 21 Jun 2020 17:22:22: 9000000 INFO @ Sun, 21 Jun 2020 17:22:23: 4000000 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 @ Sun, 21 Jun 2020 17:22:28: 10000000 INFO @ Sun, 21 Jun 2020 17:22:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX097620/SRX097620.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX097620/SRX097620.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX097620/SRX097620.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX097620/SRX097620.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 @ Sun, 21 Jun 2020 17:22:28: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:22:28: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:22:29: 5000000 INFO @ Sun, 21 Jun 2020 17:22:34: 1000000 INFO @ Sun, 21 Jun 2020 17:22:35: 11000000 INFO @ Sun, 21 Jun 2020 17:22:35: 6000000 INFO @ Sun, 21 Jun 2020 17:22:40: 2000000 INFO @ Sun, 21 Jun 2020 17:22:41: 12000000 INFO @ Sun, 21 Jun 2020 17:22:42: 7000000 INFO @ Sun, 21 Jun 2020 17:22:46: 3000000 INFO @ Sun, 21 Jun 2020 17:22:48: 13000000 INFO @ Sun, 21 Jun 2020 17:22:49: 8000000 INFO @ Sun, 21 Jun 2020 17:22:52: 4000000 INFO @ Sun, 21 Jun 2020 17:22:54: 14000000 INFO @ Sun, 21 Jun 2020 17:22:55: 9000000 INFO @ Sun, 21 Jun 2020 17:22:57: 5000000 INFO @ Sun, 21 Jun 2020 17:23:01: 15000000 INFO @ Sun, 21 Jun 2020 17:23:02: 10000000 INFO @ Sun, 21 Jun 2020 17:23:03: 6000000 INFO @ Sun, 21 Jun 2020 17:23:08: 16000000 INFO @ Sun, 21 Jun 2020 17:23:09: 11000000 INFO @ Sun, 21 Jun 2020 17:23:09: 7000000 INFO @ Sun, 21 Jun 2020 17:23:14: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:23:14: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:23:14: #1 total tags in treatment: 16813697 INFO @ Sun, 21 Jun 2020 17:23:14: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:23:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 17:23:14: #1 tags after filtering in treatment: 16813643 INFO @ Sun, 21 Jun 2020 17:23:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:23:14: #1 finished! INFO @ Sun, 21 Jun 2020 17:23:14: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:23:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:23:15: 8000000 INFO @ Sun, 21 Jun 2020 17:23:15: 12000000 INFO @ Sun, 21 Jun 2020 17:23:15: #2 number of paired peaks: 875 WARNING @ Sun, 21 Jun 2020 17:23:15: Fewer paired peaks (875) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 875 pairs to build model! INFO @ Sun, 21 Jun 2020 17:23:15: start model_add_line... INFO @ Sun, 21 Jun 2020 17:23:15: start X-correlation... INFO @ Sun, 21 Jun 2020 17:23:15: end of X-cor INFO @ Sun, 21 Jun 2020 17:23:15: #2 finished! INFO @ Sun, 21 Jun 2020 17:23:15: #2 predicted fragment length is 96 bps INFO @ Sun, 21 Jun 2020 17:23:15: #2 alternative fragment length(s) may be 96 bps INFO @ Sun, 21 Jun 2020 17:23:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX097620/SRX097620.05_model.r INFO @ Sun, 21 Jun 2020 17:23:15: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:23:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:23:21: 9000000 INFO @ Sun, 21 Jun 2020 17:23:22: 13000000 INFO @ Sun, 21 Jun 2020 17:23:26: 10000000 INFO @ Sun, 21 Jun 2020 17:23:28: 14000000 INFO @ Sun, 21 Jun 2020 17:23:32: 11000000 INFO @ Sun, 21 Jun 2020 17:23:35: 15000000 INFO @ Sun, 21 Jun 2020 17:23:38: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:23:42: 16000000 INFO @ Sun, 21 Jun 2020 17:23:44: 13000000 INFO @ Sun, 21 Jun 2020 17:23:47: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:23:47: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:23:47: #1 total tags in treatment: 16813697 INFO @ Sun, 21 Jun 2020 17:23:47: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:23:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 17:23:47: #1 tags after filtering in treatment: 16813643 INFO @ Sun, 21 Jun 2020 17:23:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:23:47: #1 finished! INFO @ Sun, 21 Jun 2020 17:23:47: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:23:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:23:49: #2 number of paired peaks: 875 WARNING @ Sun, 21 Jun 2020 17:23:49: Fewer paired peaks (875) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 875 pairs to build model! INFO @ Sun, 21 Jun 2020 17:23:49: start model_add_line... INFO @ Sun, 21 Jun 2020 17:23:49: start X-correlation... INFO @ Sun, 21 Jun 2020 17:23:49: end of X-cor INFO @ Sun, 21 Jun 2020 17:23:49: #2 finished! INFO @ Sun, 21 Jun 2020 17:23:49: #2 predicted fragment length is 96 bps INFO @ Sun, 21 Jun 2020 17:23:49: #2 alternative fragment length(s) may be 96 bps INFO @ Sun, 21 Jun 2020 17:23:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX097620/SRX097620.10_model.r INFO @ Sun, 21 Jun 2020 17:23:49: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:23:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:23:49: 14000000 INFO @ Sun, 21 Jun 2020 17:23:52: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:23:55: 15000000 INFO @ Sun, 21 Jun 2020 17:24:00: 16000000 INFO @ Sun, 21 Jun 2020 17:24:04: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:24:04: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:24:04: #1 total tags in treatment: 16813697 INFO @ Sun, 21 Jun 2020 17:24:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:24:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 17:24:05: #1 tags after filtering in treatment: 16813643 INFO @ Sun, 21 Jun 2020 17:24:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:24:05: #1 finished! INFO @ Sun, 21 Jun 2020 17:24:05: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:24:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:24:06: #2 number of paired peaks: 875 WARNING @ Sun, 21 Jun 2020 17:24:06: Fewer paired peaks (875) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 875 pairs to build model! INFO @ Sun, 21 Jun 2020 17:24:06: start model_add_line... INFO @ Sun, 21 Jun 2020 17:24:06: start X-correlation... INFO @ Sun, 21 Jun 2020 17:24:06: end of X-cor INFO @ Sun, 21 Jun 2020 17:24:06: #2 finished! INFO @ Sun, 21 Jun 2020 17:24:06: #2 predicted fragment length is 96 bps INFO @ Sun, 21 Jun 2020 17:24:06: #2 alternative fragment length(s) may be 96 bps INFO @ Sun, 21 Jun 2020 17:24:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX097620/SRX097620.20_model.r INFO @ Sun, 21 Jun 2020 17:24:06: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:24:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:24:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX097620/SRX097620.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:24:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX097620/SRX097620.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:24:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX097620/SRX097620.05_summits.bed INFO @ Sun, 21 Jun 2020 17:24:08: Done! pass1 - making usageList (445 chroms): 1 millis pass2 - checking and writing primary data (7471 records, 4 fields): 19 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:24:23: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:24:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX097620/SRX097620.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:24:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX097620/SRX097620.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:24:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX097620/SRX097620.10_summits.bed INFO @ Sun, 21 Jun 2020 17:24:40: Done! pass1 - making usageList (337 chroms): 2 millis pass2 - checking and writing primary data (4388 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:24:41: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:24:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX097620/SRX097620.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:24:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX097620/SRX097620.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:24:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX097620/SRX097620.20_summits.bed INFO @ Sun, 21 Jun 2020 17:24:58: Done! pass1 - making usageList (209 chroms): 1 millis pass2 - checking and writing primary data (2052 records, 4 fields): 9 millis CompletedMACS2peakCalling