Job ID = 6453271 SRX = SRX110785 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:19:47 prefetch.2.10.7: 1) Downloading 'SRR388367'... 2020-06-21T08:19:47 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:21:07 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:21:08 prefetch.2.10.7: 'SRR388367' is valid 2020-06-21T08:21:08 prefetch.2.10.7: 1) 'SRR388367' was downloaded successfully Read 16296767 spots for SRR388367/SRR388367.sra Written 16296767 spots for SRR388367/SRR388367.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:03 16296767 reads; of these: 16296767 (100.00%) were unpaired; of these: 933083 (5.73%) aligned 0 times 8189517 (50.25%) aligned exactly 1 time 7174167 (44.02%) aligned >1 times 94.27% overall alignment rate Time searching: 00:05:04 Overall time: 00:05:04 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] 1487808 / 15363684 = 0.0968 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 17:30:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX110785/SRX110785.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX110785/SRX110785.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX110785/SRX110785.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX110785/SRX110785.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 17:30:09: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:30:09: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:30:14: 1000000 INFO @ Sun, 21 Jun 2020 17:30:19: 2000000 INFO @ Sun, 21 Jun 2020 17:30:23: 3000000 INFO @ Sun, 21 Jun 2020 17:30:28: 4000000 INFO @ Sun, 21 Jun 2020 17:30:33: 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 @ Sun, 21 Jun 2020 17:30:37: 6000000 INFO @ Sun, 21 Jun 2020 17:30:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX110785/SRX110785.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX110785/SRX110785.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX110785/SRX110785.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX110785/SRX110785.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 17:30:39: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:30:39: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:30:42: 7000000 INFO @ Sun, 21 Jun 2020 17:30:44: 1000000 INFO @ Sun, 21 Jun 2020 17:30:47: 8000000 INFO @ Sun, 21 Jun 2020 17:30:49: 2000000 INFO @ Sun, 21 Jun 2020 17:30:53: 9000000 INFO @ Sun, 21 Jun 2020 17:30:54: 3000000 INFO @ Sun, 21 Jun 2020 17:30:58: 10000000 INFO @ Sun, 21 Jun 2020 17:31:00: 4000000 INFO @ Sun, 21 Jun 2020 17:31:03: 11000000 INFO @ Sun, 21 Jun 2020 17:31:05: 5000000 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 17:31:08: 12000000 INFO @ Sun, 21 Jun 2020 17:31:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX110785/SRX110785.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX110785/SRX110785.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX110785/SRX110785.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX110785/SRX110785.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 17:31:09: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:31:09: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:31:10: 6000000 INFO @ Sun, 21 Jun 2020 17:31:14: 13000000 INFO @ Sun, 21 Jun 2020 17:31:14: 1000000 INFO @ Sun, 21 Jun 2020 17:31:15: 7000000 INFO @ Sun, 21 Jun 2020 17:31:19: #1 tag size is determined as 18 bps INFO @ Sun, 21 Jun 2020 17:31:19: #1 tag size = 18 INFO @ Sun, 21 Jun 2020 17:31:19: #1 total tags in treatment: 13875876 INFO @ Sun, 21 Jun 2020 17:31:19: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:31:19: #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 17:31:19: #1 tags after filtering in treatment: 13875876 INFO @ Sun, 21 Jun 2020 17:31:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:31:19: #1 finished! INFO @ Sun, 21 Jun 2020 17:31:19: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:31:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:31:20: 2000000 INFO @ Sun, 21 Jun 2020 17:31:20: 8000000 INFO @ Sun, 21 Jun 2020 17:31:20: #2 number of paired peaks: 635 WARNING @ Sun, 21 Jun 2020 17:31:20: Fewer paired peaks (635) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 635 pairs to build model! INFO @ Sun, 21 Jun 2020 17:31:20: start model_add_line... INFO @ Sun, 21 Jun 2020 17:31:20: start X-correlation... INFO @ Sun, 21 Jun 2020 17:31:20: end of X-cor INFO @ Sun, 21 Jun 2020 17:31:20: #2 finished! INFO @ Sun, 21 Jun 2020 17:31:20: #2 predicted fragment length is 58 bps INFO @ Sun, 21 Jun 2020 17:31:20: #2 alternative fragment length(s) may be 4,58 bps INFO @ Sun, 21 Jun 2020 17:31:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX110785/SRX110785.05_model.r INFO @ Sun, 21 Jun 2020 17:31:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:31:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:31:25: 3000000 INFO @ Sun, 21 Jun 2020 17:31:25: 9000000 INFO @ Sun, 21 Jun 2020 17:31:30: 10000000 INFO @ Sun, 21 Jun 2020 17:31:30: 4000000 INFO @ Sun, 21 Jun 2020 17:31:35: 11000000 INFO @ Sun, 21 Jun 2020 17:31:36: 5000000 INFO @ Sun, 21 Jun 2020 17:31:41: 6000000 INFO @ Sun, 21 Jun 2020 17:31:41: 12000000 INFO @ Sun, 21 Jun 2020 17:31:46: 7000000 INFO @ Sun, 21 Jun 2020 17:31:46: 13000000 INFO @ Sun, 21 Jun 2020 17:31:50: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:31:51: #1 tag size is determined as 18 bps INFO @ Sun, 21 Jun 2020 17:31:51: #1 tag size = 18 INFO @ Sun, 21 Jun 2020 17:31:51: #1 total tags in treatment: 13875876 INFO @ Sun, 21 Jun 2020 17:31:51: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:31:51: #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 17:31:51: 8000000 INFO @ Sun, 21 Jun 2020 17:31:52: #1 tags after filtering in treatment: 13875876 INFO @ Sun, 21 Jun 2020 17:31:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:31:52: #1 finished! INFO @ Sun, 21 Jun 2020 17:31:52: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:31:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:31:53: #2 number of paired peaks: 635 WARNING @ Sun, 21 Jun 2020 17:31:53: Fewer paired peaks (635) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 635 pairs to build model! INFO @ Sun, 21 Jun 2020 17:31:53: start model_add_line... INFO @ Sun, 21 Jun 2020 17:31:53: start X-correlation... INFO @ Sun, 21 Jun 2020 17:31:53: end of X-cor INFO @ Sun, 21 Jun 2020 17:31:53: #2 finished! INFO @ Sun, 21 Jun 2020 17:31:53: #2 predicted fragment length is 58 bps INFO @ Sun, 21 Jun 2020 17:31:53: #2 alternative fragment length(s) may be 4,58 bps INFO @ Sun, 21 Jun 2020 17:31:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX110785/SRX110785.10_model.r INFO @ Sun, 21 Jun 2020 17:31:53: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:31:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:31:56: 9000000 INFO @ Sun, 21 Jun 2020 17:32:01: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:32:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX110785/SRX110785.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:32:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX110785/SRX110785.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:32:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX110785/SRX110785.05_summits.bed INFO @ Sun, 21 Jun 2020 17:32:05: Done! pass1 - making usageList (197 chroms): 1 millis pass2 - checking and writing primary data (5083 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:32:06: 11000000 INFO @ Sun, 21 Jun 2020 17:32:11: 12000000 INFO @ Sun, 21 Jun 2020 17:32:16: 13000000 INFO @ Sun, 21 Jun 2020 17:32:21: #1 tag size is determined as 18 bps INFO @ Sun, 21 Jun 2020 17:32:21: #1 tag size = 18 INFO @ Sun, 21 Jun 2020 17:32:21: #1 total tags in treatment: 13875876 INFO @ Sun, 21 Jun 2020 17:32:21: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:32:21: #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 17:32:21: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:32:21: #1 tags after filtering in treatment: 13875876 INFO @ Sun, 21 Jun 2020 17:32:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:32:21: #1 finished! INFO @ Sun, 21 Jun 2020 17:32:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:32:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:32:22: #2 number of paired peaks: 635 WARNING @ Sun, 21 Jun 2020 17:32:22: Fewer paired peaks (635) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 635 pairs to build model! INFO @ Sun, 21 Jun 2020 17:32:22: start model_add_line... INFO @ Sun, 21 Jun 2020 17:32:22: start X-correlation... INFO @ Sun, 21 Jun 2020 17:32:22: end of X-cor INFO @ Sun, 21 Jun 2020 17:32:22: #2 finished! INFO @ Sun, 21 Jun 2020 17:32:22: #2 predicted fragment length is 58 bps INFO @ Sun, 21 Jun 2020 17:32:22: #2 alternative fragment length(s) may be 4,58 bps INFO @ Sun, 21 Jun 2020 17:32:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX110785/SRX110785.20_model.r INFO @ Sun, 21 Jun 2020 17:32:22: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:32:22: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:32:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX110785/SRX110785.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:32:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX110785/SRX110785.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:32:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX110785/SRX110785.10_summits.bed INFO @ Sun, 21 Jun 2020 17:32:35: Done! pass1 - making usageList (107 chroms): 1 millis pass2 - checking and writing primary data (1405 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:32:52: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:33:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX110785/SRX110785.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:33:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX110785/SRX110785.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:33:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX110785/SRX110785.20_summits.bed INFO @ Sun, 21 Jun 2020 17:33:08: Done! pass1 - making usageList (67 chroms): 1 millis pass2 - checking and writing primary data (199 records, 4 fields): 4 millis CompletedMACS2peakCalling