Job ID = 6366152 SRX = SRX065677 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:28:59 prefetch.2.10.7: 1) Downloading 'SRR217383'... 2020-06-15T22:28:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:29:32 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:29:32 prefetch.2.10.7: 'SRR217383' is valid 2020-06-15T22:29:32 prefetch.2.10.7: 1) 'SRR217383' was downloaded successfully Read 6611858 spots for SRR217383/SRR217383.sra Written 6611858 spots for SRR217383/SRR217383.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: 00:00:26 6611858 reads; of these: 6611858 (100.00%) were unpaired; of these: 5442532 (82.31%) aligned 0 times 977371 (14.78%) aligned exactly 1 time 191955 (2.90%) aligned >1 times 17.69% overall alignment rate Time searching: 00:00:26 Overall time: 00:00:26 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] 133854 / 1169326 = 0.1145 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 07:31:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX065677/SRX065677.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX065677/SRX065677.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX065677/SRX065677.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX065677/SRX065677.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 07:31:02: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:31:02: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:31:06: 1000000 INFO @ Tue, 16 Jun 2020 07:31:07: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:31:07: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:31:07: #1 total tags in treatment: 1035472 INFO @ Tue, 16 Jun 2020 07:31:07: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:31:07: #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 07:31:07: #1 tags after filtering in treatment: 1035472 INFO @ Tue, 16 Jun 2020 07:31:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:31:07: #1 finished! INFO @ Tue, 16 Jun 2020 07:31:07: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:31:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:31:07: #2 number of paired peaks: 709 WARNING @ Tue, 16 Jun 2020 07:31:07: Fewer paired peaks (709) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 709 pairs to build model! INFO @ Tue, 16 Jun 2020 07:31:07: start model_add_line... INFO @ Tue, 16 Jun 2020 07:31:07: start X-correlation... INFO @ Tue, 16 Jun 2020 07:31:07: end of X-cor INFO @ Tue, 16 Jun 2020 07:31:07: #2 finished! INFO @ Tue, 16 Jun 2020 07:31:07: #2 predicted fragment length is 124 bps INFO @ Tue, 16 Jun 2020 07:31:07: #2 alternative fragment length(s) may be 124 bps INFO @ Tue, 16 Jun 2020 07:31:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX065677/SRX065677.05_model.r INFO @ Tue, 16 Jun 2020 07:31:07: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:31:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:31:09: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:31:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX065677/SRX065677.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:31:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX065677/SRX065677.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:31:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX065677/SRX065677.05_summits.bed INFO @ Tue, 16 Jun 2020 07:31:11: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (698 records, 4 fields): 1 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 07:31:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX065677/SRX065677.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX065677/SRX065677.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX065677/SRX065677.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX065677/SRX065677.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 07:31:32: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:31:32: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:31:37: 1000000 INFO @ Tue, 16 Jun 2020 07:31:37: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:31:37: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:31:37: #1 total tags in treatment: 1035472 INFO @ Tue, 16 Jun 2020 07:31:37: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:31:37: #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 07:31:37: #1 tags after filtering in treatment: 1035472 INFO @ Tue, 16 Jun 2020 07:31:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:31:37: #1 finished! INFO @ Tue, 16 Jun 2020 07:31:37: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:31:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:31:37: #2 number of paired peaks: 709 WARNING @ Tue, 16 Jun 2020 07:31:37: Fewer paired peaks (709) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 709 pairs to build model! INFO @ Tue, 16 Jun 2020 07:31:37: start model_add_line... INFO @ Tue, 16 Jun 2020 07:31:37: start X-correlation... INFO @ Tue, 16 Jun 2020 07:31:37: end of X-cor INFO @ Tue, 16 Jun 2020 07:31:37: #2 finished! INFO @ Tue, 16 Jun 2020 07:31:37: #2 predicted fragment length is 124 bps INFO @ Tue, 16 Jun 2020 07:31:37: #2 alternative fragment length(s) may be 124 bps INFO @ Tue, 16 Jun 2020 07:31:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX065677/SRX065677.10_model.r INFO @ Tue, 16 Jun 2020 07:31:37: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:31:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:31:40: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:31:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX065677/SRX065677.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:31:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX065677/SRX065677.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:31:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX065677/SRX065677.10_summits.bed INFO @ Tue, 16 Jun 2020 07:31:41: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (247 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 07:32:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX065677/SRX065677.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX065677/SRX065677.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX065677/SRX065677.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX065677/SRX065677.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 07:32:02: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:32:02: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:32:07: 1000000 INFO @ Tue, 16 Jun 2020 07:32:07: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:32:07: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:32:07: #1 total tags in treatment: 1035472 INFO @ Tue, 16 Jun 2020 07:32:07: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:32:07: #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 07:32:07: #1 tags after filtering in treatment: 1035472 INFO @ Tue, 16 Jun 2020 07:32:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:32:07: #1 finished! INFO @ Tue, 16 Jun 2020 07:32:07: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:32:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:32:07: #2 number of paired peaks: 709 WARNING @ Tue, 16 Jun 2020 07:32:07: Fewer paired peaks (709) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 709 pairs to build model! INFO @ Tue, 16 Jun 2020 07:32:07: start model_add_line... INFO @ Tue, 16 Jun 2020 07:32:07: start X-correlation... INFO @ Tue, 16 Jun 2020 07:32:07: end of X-cor INFO @ Tue, 16 Jun 2020 07:32:07: #2 finished! INFO @ Tue, 16 Jun 2020 07:32:07: #2 predicted fragment length is 124 bps INFO @ Tue, 16 Jun 2020 07:32:07: #2 alternative fragment length(s) may be 124 bps INFO @ Tue, 16 Jun 2020 07:32:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX065677/SRX065677.20_model.r INFO @ Tue, 16 Jun 2020 07:32:07: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:32:07: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:32:10: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:32:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX065677/SRX065677.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:32:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX065677/SRX065677.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:32:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX065677/SRX065677.20_summits.bed INFO @ Tue, 16 Jun 2020 07:32:11: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (72 records, 4 fields): 1 millis CompletedMACS2peakCalling