Job ID = 6367122 SRX = SRX277079 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:09:31 prefetch.2.10.7: 1) Downloading 'SRR849755'... 2020-06-15T23:09:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:10:09 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:10:09 prefetch.2.10.7: 'SRR849755' is valid 2020-06-15T23:10:09 prefetch.2.10.7: 1) 'SRR849755' was downloaded successfully Read 7279156 spots for SRR849755/SRR849755.sra Written 7279156 spots for SRR849755/SRR849755.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: 00:01:01 7279156 reads; of these: 7279156 (100.00%) were unpaired; of these: 1216803 (16.72%) aligned 0 times 5133000 (70.52%) aligned exactly 1 time 929353 (12.77%) aligned >1 times 83.28% overall alignment rate Time searching: 00:01:01 Overall time: 00:01:01 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] 438223 / 6062353 = 0.0723 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 08:13:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX277079/SRX277079.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX277079/SRX277079.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX277079/SRX277079.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX277079/SRX277079.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 08:13:07: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:13:07: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:13:11: 1000000 INFO @ Tue, 16 Jun 2020 08:13:16: 2000000 INFO @ Tue, 16 Jun 2020 08:13:20: 3000000 INFO @ Tue, 16 Jun 2020 08:13:25: 4000000 INFO @ Tue, 16 Jun 2020 08:13:29: 5000000 INFO @ Tue, 16 Jun 2020 08:13:32: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:13:32: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:13:32: #1 total tags in treatment: 5624130 INFO @ Tue, 16 Jun 2020 08:13:32: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:13:32: #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 08:13:32: #1 tags after filtering in treatment: 5624130 INFO @ Tue, 16 Jun 2020 08:13:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:13:32: #1 finished! INFO @ Tue, 16 Jun 2020 08:13:32: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:13:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:13:33: #2 number of paired peaks: 651 WARNING @ Tue, 16 Jun 2020 08:13:33: Fewer paired peaks (651) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 651 pairs to build model! INFO @ Tue, 16 Jun 2020 08:13:33: start model_add_line... INFO @ Tue, 16 Jun 2020 08:13:33: start X-correlation... INFO @ Tue, 16 Jun 2020 08:13:33: end of X-cor INFO @ Tue, 16 Jun 2020 08:13:33: #2 finished! INFO @ Tue, 16 Jun 2020 08:13:33: #2 predicted fragment length is 129 bps INFO @ Tue, 16 Jun 2020 08:13:33: #2 alternative fragment length(s) may be 129 bps INFO @ Tue, 16 Jun 2020 08:13:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX277079/SRX277079.05_model.r INFO @ Tue, 16 Jun 2020 08:13:33: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:13:33: #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 08:13:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX277079/SRX277079.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX277079/SRX277079.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX277079/SRX277079.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX277079/SRX277079.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 08:13:37: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:13:37: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:13:43: 1000000 INFO @ Tue, 16 Jun 2020 08:13:44: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:13:49: 2000000 INFO @ Tue, 16 Jun 2020 08:13:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX277079/SRX277079.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:13:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX277079/SRX277079.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:13:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX277079/SRX277079.05_summits.bed INFO @ Tue, 16 Jun 2020 08:13:50: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1587 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:13:54: 3000000 INFO @ Tue, 16 Jun 2020 08:14:00: 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 @ Tue, 16 Jun 2020 08:14:05: 5000000 INFO @ Tue, 16 Jun 2020 08:14:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX277079/SRX277079.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX277079/SRX277079.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX277079/SRX277079.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX277079/SRX277079.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 08:14:07: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:14:07: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:14:09: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:14:09: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:14:09: #1 total tags in treatment: 5624130 INFO @ Tue, 16 Jun 2020 08:14:09: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:14:09: #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 08:14:09: #1 tags after filtering in treatment: 5624130 INFO @ Tue, 16 Jun 2020 08:14:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:14:09: #1 finished! INFO @ Tue, 16 Jun 2020 08:14:09: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:14:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:14:09: #2 number of paired peaks: 651 WARNING @ Tue, 16 Jun 2020 08:14:09: Fewer paired peaks (651) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 651 pairs to build model! INFO @ Tue, 16 Jun 2020 08:14:09: start model_add_line... INFO @ Tue, 16 Jun 2020 08:14:09: start X-correlation... INFO @ Tue, 16 Jun 2020 08:14:09: end of X-cor INFO @ Tue, 16 Jun 2020 08:14:09: #2 finished! INFO @ Tue, 16 Jun 2020 08:14:09: #2 predicted fragment length is 129 bps INFO @ Tue, 16 Jun 2020 08:14:09: #2 alternative fragment length(s) may be 129 bps INFO @ Tue, 16 Jun 2020 08:14:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX277079/SRX277079.10_model.r INFO @ Tue, 16 Jun 2020 08:14:09: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:14:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:14:12: 1000000 INFO @ Tue, 16 Jun 2020 08:14:17: 2000000 INFO @ Tue, 16 Jun 2020 08:14:21: 3000000 INFO @ Tue, 16 Jun 2020 08:14:22: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:14:26: 4000000 INFO @ Tue, 16 Jun 2020 08:14:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX277079/SRX277079.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:14:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX277079/SRX277079.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:14:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX277079/SRX277079.10_summits.bed INFO @ Tue, 16 Jun 2020 08:14:29: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (874 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:14:31: 5000000 INFO @ Tue, 16 Jun 2020 08:14:34: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:14:34: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:14:34: #1 total tags in treatment: 5624130 INFO @ Tue, 16 Jun 2020 08:14:34: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:14:34: #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 08:14:34: #1 tags after filtering in treatment: 5624130 INFO @ Tue, 16 Jun 2020 08:14:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:14:34: #1 finished! INFO @ Tue, 16 Jun 2020 08:14:34: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:14:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:14:34: #2 number of paired peaks: 651 WARNING @ Tue, 16 Jun 2020 08:14:34: Fewer paired peaks (651) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 651 pairs to build model! INFO @ Tue, 16 Jun 2020 08:14:34: start model_add_line... INFO @ Tue, 16 Jun 2020 08:14:34: start X-correlation... INFO @ Tue, 16 Jun 2020 08:14:34: end of X-cor INFO @ Tue, 16 Jun 2020 08:14:34: #2 finished! INFO @ Tue, 16 Jun 2020 08:14:34: #2 predicted fragment length is 129 bps INFO @ Tue, 16 Jun 2020 08:14:34: #2 alternative fragment length(s) may be 129 bps INFO @ Tue, 16 Jun 2020 08:14:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX277079/SRX277079.20_model.r INFO @ Tue, 16 Jun 2020 08:14:34: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:14:34: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:14:46: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:14:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX277079/SRX277079.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:14:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX277079/SRX277079.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:14:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX277079/SRX277079.20_summits.bed INFO @ Tue, 16 Jun 2020 08:14:53: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (428 records, 4 fields): 1 millis CompletedMACS2peakCalling