Job ID = 6455510 SRX = SRX287844 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:04:55 prefetch.2.10.7: 1) Downloading 'SRR870033'... 2020-06-21T10:04:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:08:34 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:08:35 prefetch.2.10.7: 'SRR870033' is valid 2020-06-21T10:08:35 prefetch.2.10.7: 1) 'SRR870033' was downloaded successfully Read 15807247 spots for SRR870033/SRR870033.sra Written 15807247 spots for SRR870033/SRR870033.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: 00:04:14 15807247 reads; of these: 15807247 (100.00%) were unpaired; of these: 1170737 (7.41%) aligned 0 times 11156204 (70.58%) aligned exactly 1 time 3480306 (22.02%) aligned >1 times 92.59% overall alignment rate Time searching: 00:04:14 Overall time: 00:04:14 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] 2933569 / 14636510 = 0.2004 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 19:17:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287844/SRX287844.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287844/SRX287844.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287844/SRX287844.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287844/SRX287844.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 19:17:32: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:17:32: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:17:39: 1000000 INFO @ Sun, 21 Jun 2020 19:17:47: 2000000 INFO @ Sun, 21 Jun 2020 19:17:54: 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 @ Sun, 21 Jun 2020 19:18:01: 4000000 INFO @ Sun, 21 Jun 2020 19:18:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287844/SRX287844.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287844/SRX287844.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287844/SRX287844.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287844/SRX287844.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 19:18:02: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:18:02: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:18:09: 5000000 INFO @ Sun, 21 Jun 2020 19:18:10: 1000000 INFO @ Sun, 21 Jun 2020 19:18:17: 6000000 INFO @ Sun, 21 Jun 2020 19:18:18: 2000000 INFO @ Sun, 21 Jun 2020 19:18:25: 7000000 INFO @ Sun, 21 Jun 2020 19:18:26: 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 @ Sun, 21 Jun 2020 19:18:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287844/SRX287844.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287844/SRX287844.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287844/SRX287844.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287844/SRX287844.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 19:18:32: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:18:32: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:18:33: 8000000 INFO @ Sun, 21 Jun 2020 19:18:34: 4000000 INFO @ Sun, 21 Jun 2020 19:18:40: 1000000 INFO @ Sun, 21 Jun 2020 19:18:41: 9000000 INFO @ Sun, 21 Jun 2020 19:18:42: 5000000 INFO @ Sun, 21 Jun 2020 19:18:47: 2000000 INFO @ Sun, 21 Jun 2020 19:18:50: 10000000 INFO @ Sun, 21 Jun 2020 19:18:50: 6000000 INFO @ Sun, 21 Jun 2020 19:18:55: 3000000 INFO @ Sun, 21 Jun 2020 19:18:58: 11000000 INFO @ Sun, 21 Jun 2020 19:18:58: 7000000 INFO @ Sun, 21 Jun 2020 19:19:03: 4000000 INFO @ Sun, 21 Jun 2020 19:19:04: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:19:04: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:19:04: #1 total tags in treatment: 11702941 INFO @ Sun, 21 Jun 2020 19:19:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:19:04: #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 19:19:04: #1 tags after filtering in treatment: 11702931 INFO @ Sun, 21 Jun 2020 19:19:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:19:04: #1 finished! INFO @ Sun, 21 Jun 2020 19:19:04: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:19:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:19:05: #2 number of paired peaks: 625 WARNING @ Sun, 21 Jun 2020 19:19:05: Fewer paired peaks (625) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 625 pairs to build model! INFO @ Sun, 21 Jun 2020 19:19:05: start model_add_line... INFO @ Sun, 21 Jun 2020 19:19:05: start X-correlation... INFO @ Sun, 21 Jun 2020 19:19:05: end of X-cor INFO @ Sun, 21 Jun 2020 19:19:05: #2 finished! INFO @ Sun, 21 Jun 2020 19:19:05: #2 predicted fragment length is 156 bps INFO @ Sun, 21 Jun 2020 19:19:05: #2 alternative fragment length(s) may be 156 bps INFO @ Sun, 21 Jun 2020 19:19:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287844/SRX287844.05_model.r INFO @ Sun, 21 Jun 2020 19:19:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:19:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:19:06: 8000000 INFO @ Sun, 21 Jun 2020 19:19:10: 5000000 INFO @ Sun, 21 Jun 2020 19:19:14: 9000000 INFO @ Sun, 21 Jun 2020 19:19:18: 6000000 INFO @ Sun, 21 Jun 2020 19:19:23: 10000000 INFO @ Sun, 21 Jun 2020 19:19:25: 7000000 INFO @ Sun, 21 Jun 2020 19:19:29: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:19:31: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:19:33: 8000000 INFO @ Sun, 21 Jun 2020 19:19:38: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:19:38: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:19:38: #1 total tags in treatment: 11702941 INFO @ Sun, 21 Jun 2020 19:19:38: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:19:38: #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 19:19:38: #1 tags after filtering in treatment: 11702931 INFO @ Sun, 21 Jun 2020 19:19:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:19:38: #1 finished! INFO @ Sun, 21 Jun 2020 19:19:38: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:19:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:19:39: #2 number of paired peaks: 625 WARNING @ Sun, 21 Jun 2020 19:19:39: Fewer paired peaks (625) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 625 pairs to build model! INFO @ Sun, 21 Jun 2020 19:19:39: start model_add_line... INFO @ Sun, 21 Jun 2020 19:19:39: start X-correlation... INFO @ Sun, 21 Jun 2020 19:19:39: end of X-cor INFO @ Sun, 21 Jun 2020 19:19:39: #2 finished! INFO @ Sun, 21 Jun 2020 19:19:39: #2 predicted fragment length is 156 bps INFO @ Sun, 21 Jun 2020 19:19:39: #2 alternative fragment length(s) may be 156 bps INFO @ Sun, 21 Jun 2020 19:19:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287844/SRX287844.10_model.r INFO @ Sun, 21 Jun 2020 19:19:39: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:19:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:19:40: 9000000 INFO @ Sun, 21 Jun 2020 19:19:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287844/SRX287844.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:19:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287844/SRX287844.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:19:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287844/SRX287844.05_summits.bed INFO @ Sun, 21 Jun 2020 19:19:41: Done! pass1 - making usageList (690 chroms): 2 millis pass2 - checking and writing primary data (4606 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:19:47: 10000000 INFO @ Sun, 21 Jun 2020 19:19:53: 11000000 INFO @ Sun, 21 Jun 2020 19:19:58: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:19:58: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:19:58: #1 total tags in treatment: 11702941 INFO @ Sun, 21 Jun 2020 19:19:58: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:19:58: #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 19:19:58: #1 tags after filtering in treatment: 11702931 INFO @ Sun, 21 Jun 2020 19:19:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:19:58: #1 finished! INFO @ Sun, 21 Jun 2020 19:19:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:19:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:19:59: #2 number of paired peaks: 625 WARNING @ Sun, 21 Jun 2020 19:19:59: Fewer paired peaks (625) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 625 pairs to build model! INFO @ Sun, 21 Jun 2020 19:19:59: start model_add_line... INFO @ Sun, 21 Jun 2020 19:19:59: start X-correlation... INFO @ Sun, 21 Jun 2020 19:19:59: end of X-cor INFO @ Sun, 21 Jun 2020 19:19:59: #2 finished! INFO @ Sun, 21 Jun 2020 19:19:59: #2 predicted fragment length is 156 bps INFO @ Sun, 21 Jun 2020 19:19:59: #2 alternative fragment length(s) may be 156 bps INFO @ Sun, 21 Jun 2020 19:19:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287844/SRX287844.20_model.r INFO @ Sun, 21 Jun 2020 19:19:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:19:59: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:20:04: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:20:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287844/SRX287844.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:20:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287844/SRX287844.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:20:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287844/SRX287844.10_summits.bed INFO @ Sun, 21 Jun 2020 19:20:17: Done! pass1 - making usageList (586 chroms): 1 millis pass2 - checking and writing primary data (2673 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:20:26: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:20:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287844/SRX287844.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:20:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287844/SRX287844.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:20:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287844/SRX287844.20_summits.bed INFO @ Sun, 21 Jun 2020 19:20:39: Done! pass1 - making usageList (360 chroms): 1 millis pass2 - checking and writing primary data (1069 records, 4 fields): 12 millis CompletedMACS2peakCalling