Job ID = 6366037 SRX = SRX054265 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:42:37 prefetch.2.10.7: 1) Downloading 'SRR164272'... 2020-06-15T22:42:37 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:43:06 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:43:06 prefetch.2.10.7: 'SRR164272' is valid 2020-06-15T22:43:06 prefetch.2.10.7: 1) 'SRR164272' was downloaded successfully Read 3994945 spots for SRR164272/SRR164272.sra Written 3994945 spots for SRR164272/SRR164272.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: 00:00:25 3994945 reads; of these: 3994945 (100.00%) were unpaired; of these: 2566191 (64.24%) aligned 0 times 1241275 (31.07%) aligned exactly 1 time 187479 (4.69%) aligned >1 times 35.76% overall alignment rate Time searching: 00:00:25 Overall time: 00:00:25 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] 223873 / 1428754 = 0.1567 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 07:44:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX054265/SRX054265.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX054265/SRX054265.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX054265/SRX054265.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX054265/SRX054265.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 07:44:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:44:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:44:44: 1000000 INFO @ Tue, 16 Jun 2020 07:44:46: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:44:46: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:44:46: #1 total tags in treatment: 1204881 INFO @ Tue, 16 Jun 2020 07:44:46: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:44:46: #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 07:44:46: #1 tags after filtering in treatment: 1204881 INFO @ Tue, 16 Jun 2020 07:44:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:44:46: #1 finished! INFO @ Tue, 16 Jun 2020 07:44:46: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:44:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:44:46: #2 number of paired peaks: 699 WARNING @ Tue, 16 Jun 2020 07:44:46: Fewer paired peaks (699) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 699 pairs to build model! INFO @ Tue, 16 Jun 2020 07:44:46: start model_add_line... INFO @ Tue, 16 Jun 2020 07:44:46: start X-correlation... INFO @ Tue, 16 Jun 2020 07:44:46: end of X-cor INFO @ Tue, 16 Jun 2020 07:44:46: #2 finished! INFO @ Tue, 16 Jun 2020 07:44:46: #2 predicted fragment length is 154 bps INFO @ Tue, 16 Jun 2020 07:44:46: #2 alternative fragment length(s) may be 154 bps INFO @ Tue, 16 Jun 2020 07:44:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX054265/SRX054265.05_model.r INFO @ Tue, 16 Jun 2020 07:44:46: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:44:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:44:49: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:44:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX054265/SRX054265.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:44:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX054265/SRX054265.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:44:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX054265/SRX054265.05_summits.bed INFO @ Tue, 16 Jun 2020 07:44:50: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (947 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 07:45:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX054265/SRX054265.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX054265/SRX054265.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX054265/SRX054265.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX054265/SRX054265.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 07:45:07: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:45:07: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:45:14: 1000000 INFO @ Tue, 16 Jun 2020 07:45:15: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:45:15: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:45:15: #1 total tags in treatment: 1204881 INFO @ Tue, 16 Jun 2020 07:45:15: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:45:15: #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 07:45:15: #1 tags after filtering in treatment: 1204881 INFO @ Tue, 16 Jun 2020 07:45:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:45:15: #1 finished! INFO @ Tue, 16 Jun 2020 07:45:15: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:45:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:45:16: #2 number of paired peaks: 699 WARNING @ Tue, 16 Jun 2020 07:45:16: Fewer paired peaks (699) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 699 pairs to build model! INFO @ Tue, 16 Jun 2020 07:45:16: start model_add_line... INFO @ Tue, 16 Jun 2020 07:45:16: start X-correlation... INFO @ Tue, 16 Jun 2020 07:45:16: end of X-cor INFO @ Tue, 16 Jun 2020 07:45:16: #2 finished! INFO @ Tue, 16 Jun 2020 07:45:16: #2 predicted fragment length is 154 bps INFO @ Tue, 16 Jun 2020 07:45:16: #2 alternative fragment length(s) may be 154 bps INFO @ Tue, 16 Jun 2020 07:45:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX054265/SRX054265.10_model.r INFO @ Tue, 16 Jun 2020 07:45:16: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:45:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:45:18: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:45:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX054265/SRX054265.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:45:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX054265/SRX054265.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:45:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX054265/SRX054265.10_summits.bed INFO @ Tue, 16 Jun 2020 07:45:20: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (284 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 07:45:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX054265/SRX054265.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX054265/SRX054265.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX054265/SRX054265.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX054265/SRX054265.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 07:45:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:45:38: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:45:44: 1000000 INFO @ Tue, 16 Jun 2020 07:45:45: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:45:45: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:45:45: #1 total tags in treatment: 1204881 INFO @ Tue, 16 Jun 2020 07:45:45: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:45:45: #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 07:45:45: #1 tags after filtering in treatment: 1204881 INFO @ Tue, 16 Jun 2020 07:45:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:45:45: #1 finished! INFO @ Tue, 16 Jun 2020 07:45:45: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:45:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:45:45: #2 number of paired peaks: 699 WARNING @ Tue, 16 Jun 2020 07:45:45: Fewer paired peaks (699) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 699 pairs to build model! INFO @ Tue, 16 Jun 2020 07:45:45: start model_add_line... INFO @ Tue, 16 Jun 2020 07:45:45: start X-correlation... INFO @ Tue, 16 Jun 2020 07:45:45: end of X-cor INFO @ Tue, 16 Jun 2020 07:45:45: #2 finished! INFO @ Tue, 16 Jun 2020 07:45:45: #2 predicted fragment length is 154 bps INFO @ Tue, 16 Jun 2020 07:45:45: #2 alternative fragment length(s) may be 154 bps INFO @ Tue, 16 Jun 2020 07:45:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX054265/SRX054265.20_model.r INFO @ Tue, 16 Jun 2020 07:45:45: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:45:45: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:45:48: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:45:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX054265/SRX054265.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:45:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX054265/SRX054265.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:45:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX054265/SRX054265.20_summits.bed INFO @ Tue, 16 Jun 2020 07:45:50: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (54 records, 4 fields): 1 millis CompletedMACS2peakCalling