Job ID = 6366047 SRX = SRX054311 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:38:51 prefetch.2.10.7: 1) Downloading 'SRR164282'... 2020-06-15T22:38:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:39:33 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:39:33 prefetch.2.10.7: 'SRR164282' is valid 2020-06-15T22:39:33 prefetch.2.10.7: 1) 'SRR164282' was downloaded successfully Read 4502986 spots for SRR164282/SRR164282.sra Written 4502986 spots for SRR164282/SRR164282.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: 00:00:22 4502986 reads; of these: 4502986 (100.00%) were unpaired; of these: 3722508 (82.67%) aligned 0 times 693789 (15.41%) aligned exactly 1 time 86689 (1.93%) aligned >1 times 17.33% overall alignment rate Time searching: 00:00:22 Overall time: 00:00:22 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] 25222 / 780478 = 0.0323 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 07:40:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX054311/SRX054311.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX054311/SRX054311.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX054311/SRX054311.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX054311/SRX054311.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 07:40:54: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:40:54: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:40:58: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:40:58: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:40:58: #1 total tags in treatment: 755256 INFO @ Tue, 16 Jun 2020 07:40:58: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:40:58: #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 07:40:58: #1 tags after filtering in treatment: 755256 INFO @ Tue, 16 Jun 2020 07:40:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:40:58: #1 finished! INFO @ Tue, 16 Jun 2020 07:40:58: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:40:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:40:58: #2 number of paired peaks: 975 WARNING @ Tue, 16 Jun 2020 07:40:58: Fewer paired peaks (975) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 975 pairs to build model! INFO @ Tue, 16 Jun 2020 07:40:58: start model_add_line... INFO @ Tue, 16 Jun 2020 07:40:58: start X-correlation... INFO @ Tue, 16 Jun 2020 07:40:58: end of X-cor INFO @ Tue, 16 Jun 2020 07:40:58: #2 finished! INFO @ Tue, 16 Jun 2020 07:40:58: #2 predicted fragment length is 169 bps INFO @ Tue, 16 Jun 2020 07:40:58: #2 alternative fragment length(s) may be 169 bps INFO @ Tue, 16 Jun 2020 07:40:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX054311/SRX054311.05_model.r INFO @ Tue, 16 Jun 2020 07:40:58: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:40:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:41:00: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:41:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX054311/SRX054311.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:41:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX054311/SRX054311.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:41:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX054311/SRX054311.05_summits.bed INFO @ Tue, 16 Jun 2020 07:41:01: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (650 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 07:41:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX054311/SRX054311.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX054311/SRX054311.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX054311/SRX054311.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX054311/SRX054311.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 07:41:24: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:41:24: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:41:28: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:41:28: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:41:28: #1 total tags in treatment: 755256 INFO @ Tue, 16 Jun 2020 07:41:28: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:41:28: #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 07:41:28: #1 tags after filtering in treatment: 755256 INFO @ Tue, 16 Jun 2020 07:41:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:41:28: #1 finished! INFO @ Tue, 16 Jun 2020 07:41:28: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:41:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:41:28: #2 number of paired peaks: 975 WARNING @ Tue, 16 Jun 2020 07:41:28: Fewer paired peaks (975) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 975 pairs to build model! INFO @ Tue, 16 Jun 2020 07:41:28: start model_add_line... INFO @ Tue, 16 Jun 2020 07:41:28: start X-correlation... INFO @ Tue, 16 Jun 2020 07:41:28: end of X-cor INFO @ Tue, 16 Jun 2020 07:41:28: #2 finished! INFO @ Tue, 16 Jun 2020 07:41:28: #2 predicted fragment length is 169 bps INFO @ Tue, 16 Jun 2020 07:41:28: #2 alternative fragment length(s) may be 169 bps INFO @ Tue, 16 Jun 2020 07:41:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX054311/SRX054311.10_model.r INFO @ Tue, 16 Jun 2020 07:41:28: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:41:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:41:30: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:41:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX054311/SRX054311.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:41:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX054311/SRX054311.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:41:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX054311/SRX054311.10_summits.bed INFO @ Tue, 16 Jun 2020 07:41:31: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (104 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 07:41:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX054311/SRX054311.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX054311/SRX054311.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX054311/SRX054311.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX054311/SRX054311.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 07:41:54: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:41:54: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:41:58: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:41:58: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:41:58: #1 total tags in treatment: 755256 INFO @ Tue, 16 Jun 2020 07:41:58: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:41:58: #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 07:41:58: #1 tags after filtering in treatment: 755256 INFO @ Tue, 16 Jun 2020 07:41:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:41:58: #1 finished! INFO @ Tue, 16 Jun 2020 07:41:58: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:41:58: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:41:58: #2 number of paired peaks: 975 WARNING @ Tue, 16 Jun 2020 07:41:58: Fewer paired peaks (975) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 975 pairs to build model! INFO @ Tue, 16 Jun 2020 07:41:58: start model_add_line... INFO @ Tue, 16 Jun 2020 07:41:58: start X-correlation... INFO @ Tue, 16 Jun 2020 07:41:58: end of X-cor INFO @ Tue, 16 Jun 2020 07:41:58: #2 finished! INFO @ Tue, 16 Jun 2020 07:41:58: #2 predicted fragment length is 169 bps INFO @ Tue, 16 Jun 2020 07:41:58: #2 alternative fragment length(s) may be 169 bps INFO @ Tue, 16 Jun 2020 07:41:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX054311/SRX054311.20_model.r INFO @ Tue, 16 Jun 2020 07:41:58: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:41:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:42:00: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:42:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX054311/SRX054311.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:42:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX054311/SRX054311.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:42:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX054311/SRX054311.20_summits.bed INFO @ Tue, 16 Jun 2020 07:42:01: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (11 records, 4 fields): 1 millis CompletedMACS2peakCalling