Job ID = 6368487 SRX = SRX5020717 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:21:51 prefetch.2.10.7: 1) Downloading 'SRR8201340'... 2020-06-16T00:21:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:22:47 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:22:48 prefetch.2.10.7: 'SRR8201340' is valid 2020-06-16T00:22:48 prefetch.2.10.7: 1) 'SRR8201340' was downloaded successfully Read 8587074 spots for SRR8201340/SRR8201340.sra Written 8587074 spots for SRR8201340/SRR8201340.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: 00:01:54 8587074 reads; of these: 8587074 (100.00%) were unpaired; of these: 481784 (5.61%) aligned 0 times 6762516 (78.75%) aligned exactly 1 time 1342774 (15.64%) aligned >1 times 94.39% overall alignment rate Time searching: 00:01:55 Overall time: 00:01:55 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 629777 / 8105290 = 0.0777 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, 16 Jun 2020 09:28:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020717/SRX5020717.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020717/SRX5020717.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020717/SRX5020717.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020717/SRX5020717.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 16 Jun 2020 09:28:20: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:28:20: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:28:25: 1000000 INFO @ Tue, 16 Jun 2020 09:28:31: 2000000 INFO @ Tue, 16 Jun 2020 09:28:36: 3000000 INFO @ Tue, 16 Jun 2020 09:28:42: 4000000 INFO @ Tue, 16 Jun 2020 09:28:47: 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, 16 Jun 2020 09:28:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020717/SRX5020717.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020717/SRX5020717.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020717/SRX5020717.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020717/SRX5020717.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 16 Jun 2020 09:28:50: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:28:50: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:28:53: 6000000 INFO @ Tue, 16 Jun 2020 09:28:56: 1000000 INFO @ Tue, 16 Jun 2020 09:28:59: 7000000 INFO @ Tue, 16 Jun 2020 09:29:01: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:29:01: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:29:01: #1 total tags in treatment: 7475513 INFO @ Tue, 16 Jun 2020 09:29:01: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:29:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:29:01: #1 tags after filtering in treatment: 7475513 INFO @ Tue, 16 Jun 2020 09:29:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:29:01: #1 finished! INFO @ Tue, 16 Jun 2020 09:29:01: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:29:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:29:02: 2000000 INFO @ Tue, 16 Jun 2020 09:29:02: #2 number of paired peaks: 422 WARNING @ Tue, 16 Jun 2020 09:29:02: Fewer paired peaks (422) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 422 pairs to build model! INFO @ Tue, 16 Jun 2020 09:29:02: start model_add_line... INFO @ Tue, 16 Jun 2020 09:29:02: start X-correlation... INFO @ Tue, 16 Jun 2020 09:29:02: end of X-cor INFO @ Tue, 16 Jun 2020 09:29:02: #2 finished! INFO @ Tue, 16 Jun 2020 09:29:02: #2 predicted fragment length is 108 bps INFO @ Tue, 16 Jun 2020 09:29:02: #2 alternative fragment length(s) may be 108,120,123 bps INFO @ Tue, 16 Jun 2020 09:29:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020717/SRX5020717.05_model.r INFO @ Tue, 16 Jun 2020 09:29:02: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:29:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:29:07: 3000000 INFO @ Tue, 16 Jun 2020 09:29:13: 4000000 INFO @ Tue, 16 Jun 2020 09:29:18: #3 Call peaks for each chromosome... 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, 16 Jun 2020 09:29:18: 5000000 INFO @ Tue, 16 Jun 2020 09:29:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020717/SRX5020717.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020717/SRX5020717.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020717/SRX5020717.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020717/SRX5020717.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 16 Jun 2020 09:29:20: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:29:20: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:29:24: 6000000 INFO @ Tue, 16 Jun 2020 09:29:26: 1000000 INFO @ Tue, 16 Jun 2020 09:29:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020717/SRX5020717.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:29:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020717/SRX5020717.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:29:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020717/SRX5020717.05_summits.bed INFO @ Tue, 16 Jun 2020 09:29:26: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1847 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:29:29: 7000000 INFO @ Tue, 16 Jun 2020 09:29:32: 2000000 INFO @ Tue, 16 Jun 2020 09:29:32: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:29:32: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:29:32: #1 total tags in treatment: 7475513 INFO @ Tue, 16 Jun 2020 09:29:32: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:29:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:29:32: #1 tags after filtering in treatment: 7475513 INFO @ Tue, 16 Jun 2020 09:29:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:29:32: #1 finished! INFO @ Tue, 16 Jun 2020 09:29:32: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:29:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:29:33: #2 number of paired peaks: 422 WARNING @ Tue, 16 Jun 2020 09:29:33: Fewer paired peaks (422) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 422 pairs to build model! INFO @ Tue, 16 Jun 2020 09:29:33: start model_add_line... INFO @ Tue, 16 Jun 2020 09:29:33: start X-correlation... INFO @ Tue, 16 Jun 2020 09:29:33: end of X-cor INFO @ Tue, 16 Jun 2020 09:29:33: #2 finished! INFO @ Tue, 16 Jun 2020 09:29:33: #2 predicted fragment length is 108 bps INFO @ Tue, 16 Jun 2020 09:29:33: #2 alternative fragment length(s) may be 108,120,123 bps INFO @ Tue, 16 Jun 2020 09:29:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020717/SRX5020717.10_model.r INFO @ Tue, 16 Jun 2020 09:29:33: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:29:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:29:37: 3000000 INFO @ Tue, 16 Jun 2020 09:29:43: 4000000 INFO @ Tue, 16 Jun 2020 09:29:48: 5000000 INFO @ Tue, 16 Jun 2020 09:29:48: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:29:53: 6000000 INFO @ Tue, 16 Jun 2020 09:29:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020717/SRX5020717.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:29:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020717/SRX5020717.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:29:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020717/SRX5020717.10_summits.bed INFO @ Tue, 16 Jun 2020 09:29:57: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (560 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:29:59: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:30:01: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:30:01: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:30:01: #1 total tags in treatment: 7475513 INFO @ Tue, 16 Jun 2020 09:30:01: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:30:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:30:02: #1 tags after filtering in treatment: 7475513 INFO @ Tue, 16 Jun 2020 09:30:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:30:02: #1 finished! INFO @ Tue, 16 Jun 2020 09:30:02: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:30:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:30:02: #2 number of paired peaks: 422 WARNING @ Tue, 16 Jun 2020 09:30:02: Fewer paired peaks (422) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 422 pairs to build model! INFO @ Tue, 16 Jun 2020 09:30:02: start model_add_line... INFO @ Tue, 16 Jun 2020 09:30:02: start X-correlation... INFO @ Tue, 16 Jun 2020 09:30:02: end of X-cor INFO @ Tue, 16 Jun 2020 09:30:02: #2 finished! INFO @ Tue, 16 Jun 2020 09:30:02: #2 predicted fragment length is 108 bps INFO @ Tue, 16 Jun 2020 09:30:02: #2 alternative fragment length(s) may be 108,120,123 bps INFO @ Tue, 16 Jun 2020 09:30:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020717/SRX5020717.20_model.r INFO @ Tue, 16 Jun 2020 09:30:02: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:30:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:30:17: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:30:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020717/SRX5020717.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:30:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020717/SRX5020717.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:30:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020717/SRX5020717.20_summits.bed INFO @ Tue, 16 Jun 2020 09:30:25: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (193 records, 4 fields): 1 millis CompletedMACS2peakCalling