Job ID = 6366116 SRX = SRX065632 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:40:36 prefetch.2.10.7: 1) Downloading 'SRR217338'... 2020-06-15T22:40:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:41:00 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:41:00 prefetch.2.10.7: 'SRR217338' is valid 2020-06-15T22:41:00 prefetch.2.10.7: 1) 'SRR217338' was downloaded successfully Read 5463422 spots for SRR217338/SRR217338.sra Written 5463422 spots for SRR217338/SRR217338.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: 00:00:43 5463422 reads; of these: 5463422 (100.00%) were unpaired; of these: 1943939 (35.58%) aligned 0 times 2988868 (54.71%) aligned exactly 1 time 530615 (9.71%) aligned >1 times 64.42% overall alignment rate Time searching: 00:00:44 Overall time: 00:00:44 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] 803735 / 3519483 = 0.2284 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 07:43:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX065632/SRX065632.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX065632/SRX065632.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX065632/SRX065632.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX065632/SRX065632.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 07:43:10: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:43:10: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:43:15: 1000000 INFO @ Tue, 16 Jun 2020 07:43:20: 2000000 INFO @ Tue, 16 Jun 2020 07:43:24: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:43:24: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:43:24: #1 total tags in treatment: 2715748 INFO @ Tue, 16 Jun 2020 07:43:24: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:43:24: #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 07:43:24: #1 tags after filtering in treatment: 2715748 INFO @ Tue, 16 Jun 2020 07:43:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:43:24: #1 finished! INFO @ Tue, 16 Jun 2020 07:43:24: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:43:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:43:24: #2 number of paired peaks: 532 WARNING @ Tue, 16 Jun 2020 07:43:24: Fewer paired peaks (532) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 532 pairs to build model! INFO @ Tue, 16 Jun 2020 07:43:24: start model_add_line... INFO @ Tue, 16 Jun 2020 07:43:24: start X-correlation... INFO @ Tue, 16 Jun 2020 07:43:24: end of X-cor INFO @ Tue, 16 Jun 2020 07:43:24: #2 finished! INFO @ Tue, 16 Jun 2020 07:43:24: #2 predicted fragment length is 115 bps INFO @ Tue, 16 Jun 2020 07:43:24: #2 alternative fragment length(s) may be 115,587 bps INFO @ Tue, 16 Jun 2020 07:43:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX065632/SRX065632.05_model.r INFO @ Tue, 16 Jun 2020 07:43:24: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:43:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:43:31: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:43:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX065632/SRX065632.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:43:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX065632/SRX065632.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:43:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX065632/SRX065632.05_summits.bed INFO @ Tue, 16 Jun 2020 07:43:34: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1358 records, 4 fields): 3 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 07:43:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX065632/SRX065632.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX065632/SRX065632.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX065632/SRX065632.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX065632/SRX065632.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 07:43:40: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:43:40: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:43:45: 1000000 INFO @ Tue, 16 Jun 2020 07:43:49: 2000000 INFO @ Tue, 16 Jun 2020 07:43:53: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:43:53: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:43:53: #1 total tags in treatment: 2715748 INFO @ Tue, 16 Jun 2020 07:43:53: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:43:53: #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 07:43:53: #1 tags after filtering in treatment: 2715748 INFO @ Tue, 16 Jun 2020 07:43:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:43:53: #1 finished! INFO @ Tue, 16 Jun 2020 07:43:53: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:43:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:43:53: #2 number of paired peaks: 532 WARNING @ Tue, 16 Jun 2020 07:43:53: Fewer paired peaks (532) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 532 pairs to build model! INFO @ Tue, 16 Jun 2020 07:43:53: start model_add_line... INFO @ Tue, 16 Jun 2020 07:43:53: start X-correlation... INFO @ Tue, 16 Jun 2020 07:43:53: end of X-cor INFO @ Tue, 16 Jun 2020 07:43:53: #2 finished! INFO @ Tue, 16 Jun 2020 07:43:53: #2 predicted fragment length is 115 bps INFO @ Tue, 16 Jun 2020 07:43:53: #2 alternative fragment length(s) may be 115,587 bps INFO @ Tue, 16 Jun 2020 07:43:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX065632/SRX065632.10_model.r INFO @ Tue, 16 Jun 2020 07:43:53: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:43:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:44:00: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:44:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX065632/SRX065632.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:44:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX065632/SRX065632.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:44:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX065632/SRX065632.10_summits.bed INFO @ Tue, 16 Jun 2020 07:44:03: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (436 records, 4 fields): 2 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 07:44:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX065632/SRX065632.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX065632/SRX065632.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX065632/SRX065632.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX065632/SRX065632.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 07:44:10: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:44:10: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:44:15: 1000000 INFO @ Tue, 16 Jun 2020 07:44:20: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:44:23: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:44:23: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:44:23: #1 total tags in treatment: 2715748 INFO @ Tue, 16 Jun 2020 07:44:23: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:44:23: #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 07:44:23: #1 tags after filtering in treatment: 2715748 INFO @ Tue, 16 Jun 2020 07:44:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:44:23: #1 finished! INFO @ Tue, 16 Jun 2020 07:44:23: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:44:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:44:23: #2 number of paired peaks: 532 WARNING @ Tue, 16 Jun 2020 07:44:23: Fewer paired peaks (532) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 532 pairs to build model! INFO @ Tue, 16 Jun 2020 07:44:23: start model_add_line... INFO @ Tue, 16 Jun 2020 07:44:23: start X-correlation... INFO @ Tue, 16 Jun 2020 07:44:23: end of X-cor INFO @ Tue, 16 Jun 2020 07:44:23: #2 finished! INFO @ Tue, 16 Jun 2020 07:44:23: #2 predicted fragment length is 115 bps INFO @ Tue, 16 Jun 2020 07:44:23: #2 alternative fragment length(s) may be 115,587 bps INFO @ Tue, 16 Jun 2020 07:44:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX065632/SRX065632.20_model.r INFO @ Tue, 16 Jun 2020 07:44:23: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:44:23: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:44:30: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:44:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX065632/SRX065632.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:44:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX065632/SRX065632.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:44:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX065632/SRX065632.20_summits.bed INFO @ Tue, 16 Jun 2020 07:44:33: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (116 records, 4 fields): 1 millis CompletedMACS2peakCalling