Job ID = 6366703 SRX = SRX2228859 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:50:26 prefetch.2.10.7: 1) Downloading 'SRR4380315'... 2020-06-15T22:50:26 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:51:04 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:51:04 prefetch.2.10.7: 'SRR4380315' is valid 2020-06-15T22:51:04 prefetch.2.10.7: 1) 'SRR4380315' was downloaded successfully Read 12255316 spots for SRR4380315/SRR4380315.sra Written 12255316 spots for SRR4380315/SRR4380315.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: 00:01:02 12255316 reads; of these: 12255316 (100.00%) were unpaired; of these: 8643373 (70.53%) aligned 0 times 3002973 (24.50%) aligned exactly 1 time 608970 (4.97%) aligned >1 times 29.47% overall alignment rate Time searching: 00:01:02 Overall time: 00:01:02 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] 1882624 / 3611943 = 0.5212 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 07:53:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228859/SRX2228859.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228859/SRX2228859.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228859/SRX2228859.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228859/SRX2228859.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 07:53:43: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:53:43: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:53:48: 1000000 INFO @ Tue, 16 Jun 2020 07:53:52: #1 tag size is determined as 35 bps INFO @ Tue, 16 Jun 2020 07:53:52: #1 tag size = 35 INFO @ Tue, 16 Jun 2020 07:53:52: #1 total tags in treatment: 1729319 INFO @ Tue, 16 Jun 2020 07:53:52: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:53:52: #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 07:53:52: #1 tags after filtering in treatment: 1729319 INFO @ Tue, 16 Jun 2020 07:53:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:53:52: #1 finished! INFO @ Tue, 16 Jun 2020 07:53:52: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:53:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:53:52: #2 number of paired peaks: 620 WARNING @ Tue, 16 Jun 2020 07:53:52: Fewer paired peaks (620) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 620 pairs to build model! INFO @ Tue, 16 Jun 2020 07:53:52: start model_add_line... INFO @ Tue, 16 Jun 2020 07:53:52: start X-correlation... INFO @ Tue, 16 Jun 2020 07:53:52: end of X-cor INFO @ Tue, 16 Jun 2020 07:53:52: #2 finished! INFO @ Tue, 16 Jun 2020 07:53:52: #2 predicted fragment length is 92 bps INFO @ Tue, 16 Jun 2020 07:53:52: #2 alternative fragment length(s) may be 92,567 bps INFO @ Tue, 16 Jun 2020 07:53:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228859/SRX2228859.05_model.r INFO @ Tue, 16 Jun 2020 07:53:52: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:53:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:53:56: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:53:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228859/SRX2228859.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:53:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228859/SRX2228859.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:53:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228859/SRX2228859.05_summits.bed INFO @ Tue, 16 Jun 2020 07:53:58: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (443 records, 4 fields): 2 millis CompletedMACS2peakCalling 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 07:54:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228859/SRX2228859.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228859/SRX2228859.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228859/SRX2228859.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228859/SRX2228859.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 07:54:13: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:54:13: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:54:18: 1000000 INFO @ Tue, 16 Jun 2020 07:54:21: #1 tag size is determined as 35 bps INFO @ Tue, 16 Jun 2020 07:54:21: #1 tag size = 35 INFO @ Tue, 16 Jun 2020 07:54:21: #1 total tags in treatment: 1729319 INFO @ Tue, 16 Jun 2020 07:54:21: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:54:21: #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 07:54:21: #1 tags after filtering in treatment: 1729319 INFO @ Tue, 16 Jun 2020 07:54:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:54:21: #1 finished! INFO @ Tue, 16 Jun 2020 07:54:21: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:54:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:54:22: #2 number of paired peaks: 620 WARNING @ Tue, 16 Jun 2020 07:54:22: Fewer paired peaks (620) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 620 pairs to build model! INFO @ Tue, 16 Jun 2020 07:54:22: start model_add_line... INFO @ Tue, 16 Jun 2020 07:54:22: start X-correlation... INFO @ Tue, 16 Jun 2020 07:54:22: end of X-cor INFO @ Tue, 16 Jun 2020 07:54:22: #2 finished! INFO @ Tue, 16 Jun 2020 07:54:22: #2 predicted fragment length is 92 bps INFO @ Tue, 16 Jun 2020 07:54:22: #2 alternative fragment length(s) may be 92,567 bps INFO @ Tue, 16 Jun 2020 07:54:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228859/SRX2228859.10_model.r INFO @ Tue, 16 Jun 2020 07:54:22: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:54:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:54:26: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:54:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228859/SRX2228859.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:54:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228859/SRX2228859.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:54:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228859/SRX2228859.10_summits.bed INFO @ Tue, 16 Jun 2020 07:54:27: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (228 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 07:54:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228859/SRX2228859.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228859/SRX2228859.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228859/SRX2228859.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228859/SRX2228859.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 07:54:43: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:54:43: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:54:49: 1000000 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:54:54: #1 tag size is determined as 35 bps INFO @ Tue, 16 Jun 2020 07:54:54: #1 tag size = 35 INFO @ Tue, 16 Jun 2020 07:54:54: #1 total tags in treatment: 1729319 INFO @ Tue, 16 Jun 2020 07:54:54: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:54:54: #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 07:54:54: #1 tags after filtering in treatment: 1729319 INFO @ Tue, 16 Jun 2020 07:54:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:54:54: #1 finished! INFO @ Tue, 16 Jun 2020 07:54:54: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:54:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:54:54: #2 number of paired peaks: 620 WARNING @ Tue, 16 Jun 2020 07:54:54: Fewer paired peaks (620) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 620 pairs to build model! INFO @ Tue, 16 Jun 2020 07:54:54: start model_add_line... INFO @ Tue, 16 Jun 2020 07:54:54: start X-correlation... INFO @ Tue, 16 Jun 2020 07:54:54: end of X-cor INFO @ Tue, 16 Jun 2020 07:54:54: #2 finished! INFO @ Tue, 16 Jun 2020 07:54:54: #2 predicted fragment length is 92 bps INFO @ Tue, 16 Jun 2020 07:54:54: #2 alternative fragment length(s) may be 92,567 bps INFO @ Tue, 16 Jun 2020 07:54:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228859/SRX2228859.20_model.r INFO @ Tue, 16 Jun 2020 07:54:54: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:54:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:54:58: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:55:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228859/SRX2228859.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:55:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228859/SRX2228859.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:55:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228859/SRX2228859.20_summits.bed INFO @ Tue, 16 Jun 2020 07:55:00: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (112 records, 4 fields): 1 millis CompletedMACS2peakCalling