Job ID = 6454817 SRX = SRX2592416 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:37:25 prefetch.2.10.7: 1) Downloading 'SRR5289693'... 2020-06-21T09:37:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:37:37 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:37:37 prefetch.2.10.7: 'SRR5289693' is valid 2020-06-21T09:37:37 prefetch.2.10.7: 1) 'SRR5289693' was downloaded successfully Read 126212 spots for SRR5289693/SRR5289693.sra Written 126212 spots for SRR5289693/SRR5289693.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: 00:00:02 126212 reads; of these: 126212 (100.00%) were unpaired; of these: 23170 (18.36%) aligned 0 times 76470 (60.59%) aligned exactly 1 time 26572 (21.05%) aligned >1 times 81.64% overall alignment rate Time searching: 00:00:02 Overall time: 00:00:02 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_rmdupse_core] 46829 / 103042 = 0.4545 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 @ Sun, 21 Jun 2020 18:38:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592416/SRX2592416.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592416/SRX2592416.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592416/SRX2592416.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592416/SRX2592416.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 18:38:14: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:38:14: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:38:14: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:38:14: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:38:14: #1 total tags in treatment: 56213 INFO @ Sun, 21 Jun 2020 18:38:14: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:38:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:38:14: #1 tags after filtering in treatment: 55535 INFO @ Sun, 21 Jun 2020 18:38:14: #1 Redundant rate of treatment: 0.01 INFO @ Sun, 21 Jun 2020 18:38:14: #1 finished! INFO @ Sun, 21 Jun 2020 18:38:14: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:38:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:38:14: #2 number of paired peaks: 1487 INFO @ Sun, 21 Jun 2020 18:38:14: start model_add_line... INFO @ Sun, 21 Jun 2020 18:38:14: start X-correlation... INFO @ Sun, 21 Jun 2020 18:38:14: end of X-cor INFO @ Sun, 21 Jun 2020 18:38:14: #2 finished! INFO @ Sun, 21 Jun 2020 18:38:14: #2 predicted fragment length is 291 bps INFO @ Sun, 21 Jun 2020 18:38:14: #2 alternative fragment length(s) may be 205,291 bps INFO @ Sun, 21 Jun 2020 18:38:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592416/SRX2592416.05_model.r INFO @ Sun, 21 Jun 2020 18:38:14: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:38:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:38:15: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:38:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592416/SRX2592416.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:38:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592416/SRX2592416.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:38:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592416/SRX2592416.05_summits.bed INFO @ Sun, 21 Jun 2020 18:38:15: Done! pass1 - making usageList (30 chroms): 1 millis pass2 - checking and writing primary data (52 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 @ Sun, 21 Jun 2020 18:38:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592416/SRX2592416.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592416/SRX2592416.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592416/SRX2592416.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592416/SRX2592416.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 18:38:44: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:38:44: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:38:44: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:38:44: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:38:44: #1 total tags in treatment: 56213 INFO @ Sun, 21 Jun 2020 18:38:44: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:38:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:38:44: #1 tags after filtering in treatment: 55535 INFO @ Sun, 21 Jun 2020 18:38:44: #1 Redundant rate of treatment: 0.01 INFO @ Sun, 21 Jun 2020 18:38:44: #1 finished! INFO @ Sun, 21 Jun 2020 18:38:44: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:38:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:38:45: #2 number of paired peaks: 1487 INFO @ Sun, 21 Jun 2020 18:38:45: start model_add_line... INFO @ Sun, 21 Jun 2020 18:38:45: start X-correlation... INFO @ Sun, 21 Jun 2020 18:38:45: end of X-cor INFO @ Sun, 21 Jun 2020 18:38:45: #2 finished! INFO @ Sun, 21 Jun 2020 18:38:45: #2 predicted fragment length is 291 bps INFO @ Sun, 21 Jun 2020 18:38:45: #2 alternative fragment length(s) may be 205,291 bps INFO @ Sun, 21 Jun 2020 18:38:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592416/SRX2592416.10_model.r INFO @ Sun, 21 Jun 2020 18:38:45: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:38:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:38:45: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:38:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592416/SRX2592416.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:38:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592416/SRX2592416.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:38:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592416/SRX2592416.10_summits.bed INFO @ Sun, 21 Jun 2020 18:38:45: Done! pass1 - making usageList (18 chroms): 1 millis pass2 - checking and writing primary data (24 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 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:39:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592416/SRX2592416.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592416/SRX2592416.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592416/SRX2592416.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592416/SRX2592416.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 18:39:14: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:39:14: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:39:14: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:39:14: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:39:14: #1 total tags in treatment: 56213 INFO @ Sun, 21 Jun 2020 18:39:14: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:39:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:39:14: #1 tags after filtering in treatment: 55535 INFO @ Sun, 21 Jun 2020 18:39:14: #1 Redundant rate of treatment: 0.01 INFO @ Sun, 21 Jun 2020 18:39:14: #1 finished! INFO @ Sun, 21 Jun 2020 18:39:14: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:39:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:39:14: #2 number of paired peaks: 1487 INFO @ Sun, 21 Jun 2020 18:39:14: start model_add_line... INFO @ Sun, 21 Jun 2020 18:39:14: start X-correlation... INFO @ Sun, 21 Jun 2020 18:39:14: end of X-cor INFO @ Sun, 21 Jun 2020 18:39:14: #2 finished! INFO @ Sun, 21 Jun 2020 18:39:14: #2 predicted fragment length is 291 bps INFO @ Sun, 21 Jun 2020 18:39:14: #2 alternative fragment length(s) may be 205,291 bps INFO @ Sun, 21 Jun 2020 18:39:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592416/SRX2592416.20_model.r INFO @ Sun, 21 Jun 2020 18:39:14: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:39:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:39:15: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:39:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592416/SRX2592416.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:39:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592416/SRX2592416.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:39:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592416/SRX2592416.20_summits.bed INFO @ Sun, 21 Jun 2020 18:39:15: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (7 records, 4 fields): 1 millis CompletedMACS2peakCalling