Job ID = 6367448 SRX = SRX331206 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:26:36 prefetch.2.10.7: 1) Downloading 'SRR947438'... 2020-06-15T23:26:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:27:11 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:27:12 prefetch.2.10.7: 'SRR947438' is valid 2020-06-15T23:27:12 prefetch.2.10.7: 1) 'SRR947438' was downloaded successfully Read 8379896 spots for SRR947438/SRR947438.sra Written 8379896 spots for SRR947438/SRR947438.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: 00:01:00 8379896 reads; of these: 8379896 (100.00%) were unpaired; of these: 3406623 (40.65%) aligned 0 times 4214162 (50.29%) aligned exactly 1 time 759111 (9.06%) aligned >1 times 59.35% overall alignment rate Time searching: 00:01:00 Overall time: 00:01:00 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] 449160 / 4973273 = 0.0903 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 08:30:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331206/SRX331206.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331206/SRX331206.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331206/SRX331206.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331206/SRX331206.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 08:30:05: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:30:05: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:30:11: 1000000 INFO @ Tue, 16 Jun 2020 08:30:17: 2000000 INFO @ Tue, 16 Jun 2020 08:30:23: 3000000 INFO @ Tue, 16 Jun 2020 08:30:29: 4000000 INFO @ Tue, 16 Jun 2020 08:30:32: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:30:32: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:30:32: #1 total tags in treatment: 4524113 INFO @ Tue, 16 Jun 2020 08:30:32: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:30:32: #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 08:30:32: #1 tags after filtering in treatment: 4524113 INFO @ Tue, 16 Jun 2020 08:30:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:30:32: #1 finished! INFO @ Tue, 16 Jun 2020 08:30:32: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:30:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:30:33: #2 number of paired peaks: 658 WARNING @ Tue, 16 Jun 2020 08:30:33: Fewer paired peaks (658) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 658 pairs to build model! INFO @ Tue, 16 Jun 2020 08:30:33: start model_add_line... INFO @ Tue, 16 Jun 2020 08:30:33: start X-correlation... INFO @ Tue, 16 Jun 2020 08:30:33: end of X-cor INFO @ Tue, 16 Jun 2020 08:30:33: #2 finished! INFO @ Tue, 16 Jun 2020 08:30:33: #2 predicted fragment length is 147 bps INFO @ Tue, 16 Jun 2020 08:30:33: #2 alternative fragment length(s) may be 147 bps INFO @ Tue, 16 Jun 2020 08:30:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331206/SRX331206.05_model.r INFO @ Tue, 16 Jun 2020 08:30:33: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:30:33: #3 Pre-compute pvalue-qvalue table... 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 08:30:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331206/SRX331206.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331206/SRX331206.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331206/SRX331206.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331206/SRX331206.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 08:30:35: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:30:35: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:30:40: 1000000 INFO @ Tue, 16 Jun 2020 08:30:43: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:30:45: 2000000 INFO @ Tue, 16 Jun 2020 08:30:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331206/SRX331206.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:30:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331206/SRX331206.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:30:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331206/SRX331206.05_summits.bed INFO @ Tue, 16 Jun 2020 08:30:49: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2549 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:30:51: 3000000 INFO @ Tue, 16 Jun 2020 08:30:56: 4000000 INFO @ Tue, 16 Jun 2020 08:30:58: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:30:58: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:30:58: #1 total tags in treatment: 4524113 INFO @ Tue, 16 Jun 2020 08:30:58: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:30:58: #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 08:30:58: #1 tags after filtering in treatment: 4524113 INFO @ Tue, 16 Jun 2020 08:30:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:30:58: #1 finished! INFO @ Tue, 16 Jun 2020 08:30:58: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:30:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:30:59: #2 number of paired peaks: 658 WARNING @ Tue, 16 Jun 2020 08:30:59: Fewer paired peaks (658) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 658 pairs to build model! INFO @ Tue, 16 Jun 2020 08:30:59: start model_add_line... INFO @ Tue, 16 Jun 2020 08:30:59: start X-correlation... INFO @ Tue, 16 Jun 2020 08:30:59: end of X-cor INFO @ Tue, 16 Jun 2020 08:30:59: #2 finished! INFO @ Tue, 16 Jun 2020 08:30:59: #2 predicted fragment length is 147 bps INFO @ Tue, 16 Jun 2020 08:30:59: #2 alternative fragment length(s) may be 147 bps INFO @ Tue, 16 Jun 2020 08:30:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331206/SRX331206.10_model.r INFO @ Tue, 16 Jun 2020 08:30:59: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:30:59: #3 Pre-compute pvalue-qvalue table... 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 08:31:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331206/SRX331206.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331206/SRX331206.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331206/SRX331206.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331206/SRX331206.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 08:31:05: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:31:05: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:31:10: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:31:11: 1000000 INFO @ Tue, 16 Jun 2020 08:31:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331206/SRX331206.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:31:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331206/SRX331206.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:31:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331206/SRX331206.10_summits.bed INFO @ Tue, 16 Jun 2020 08:31:15: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1248 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:31:17: 2000000 INFO @ Tue, 16 Jun 2020 08:31:23: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:31:28: 4000000 INFO @ Tue, 16 Jun 2020 08:31:31: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:31:31: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:31:31: #1 total tags in treatment: 4524113 INFO @ Tue, 16 Jun 2020 08:31:31: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:31:31: #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 08:31:31: #1 tags after filtering in treatment: 4524113 INFO @ Tue, 16 Jun 2020 08:31:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:31:31: #1 finished! INFO @ Tue, 16 Jun 2020 08:31:31: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:31:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:31:32: #2 number of paired peaks: 658 WARNING @ Tue, 16 Jun 2020 08:31:32: Fewer paired peaks (658) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 658 pairs to build model! INFO @ Tue, 16 Jun 2020 08:31:32: start model_add_line... INFO @ Tue, 16 Jun 2020 08:31:32: start X-correlation... INFO @ Tue, 16 Jun 2020 08:31:32: end of X-cor INFO @ Tue, 16 Jun 2020 08:31:32: #2 finished! INFO @ Tue, 16 Jun 2020 08:31:32: #2 predicted fragment length is 147 bps INFO @ Tue, 16 Jun 2020 08:31:32: #2 alternative fragment length(s) may be 147 bps INFO @ Tue, 16 Jun 2020 08:31:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331206/SRX331206.20_model.r INFO @ Tue, 16 Jun 2020 08:31:32: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:31:32: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:31:42: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:31:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331206/SRX331206.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:31:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331206/SRX331206.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:31:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331206/SRX331206.20_summits.bed INFO @ Tue, 16 Jun 2020 08:31:47: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (482 records, 4 fields): 2 millis CompletedMACS2peakCalling