Job ID = 6366260 SRX = SRX1007132 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:26:59 prefetch.2.10.7: 1) Downloading 'SRR1993092'... 2020-06-15T22:26:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:27:22 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:27:22 prefetch.2.10.7: 'SRR1993092' is valid 2020-06-15T22:27:22 prefetch.2.10.7: 1) 'SRR1993092' was downloaded successfully Read 2905382 spots for SRR1993092/SRR1993092.sra Written 2905382 spots for SRR1993092/SRR1993092.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: 00:00:11 2905382 reads; of these: 2905382 (100.00%) were unpaired; of these: 2602105 (89.56%) aligned 0 times 253965 (8.74%) aligned exactly 1 time 49312 (1.70%) aligned >1 times 10.44% overall alignment rate Time searching: 00:00:11 Overall time: 00:00:11 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] 21070 / 303277 = 0.0695 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 07:28:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1007132/SRX1007132.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1007132/SRX1007132.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1007132/SRX1007132.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1007132/SRX1007132.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 07:28:17: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:28:17: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:28:19: #1 tag size is determined as 40 bps INFO @ Tue, 16 Jun 2020 07:28:19: #1 tag size = 40 INFO @ Tue, 16 Jun 2020 07:28:19: #1 total tags in treatment: 282207 INFO @ Tue, 16 Jun 2020 07:28:19: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:28:19: #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 07:28:19: #1 tags after filtering in treatment: 282207 INFO @ Tue, 16 Jun 2020 07:28:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:28:19: #1 finished! INFO @ Tue, 16 Jun 2020 07:28:19: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:28:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:28:19: #2 number of paired peaks: 2095 INFO @ Tue, 16 Jun 2020 07:28:19: start model_add_line... INFO @ Tue, 16 Jun 2020 07:28:19: start X-correlation... INFO @ Tue, 16 Jun 2020 07:28:19: end of X-cor INFO @ Tue, 16 Jun 2020 07:28:19: #2 finished! INFO @ Tue, 16 Jun 2020 07:28:19: #2 predicted fragment length is 83 bps INFO @ Tue, 16 Jun 2020 07:28:19: #2 alternative fragment length(s) may be 83 bps INFO @ Tue, 16 Jun 2020 07:28:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1007132/SRX1007132.05_model.r INFO @ Tue, 16 Jun 2020 07:28:19: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:28:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:28:19: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:28:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1007132/SRX1007132.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:28:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1007132/SRX1007132.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:28:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1007132/SRX1007132.05_summits.bed INFO @ Tue, 16 Jun 2020 07:28:20: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1680 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 07:28:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1007132/SRX1007132.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1007132/SRX1007132.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1007132/SRX1007132.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1007132/SRX1007132.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 07:28:47: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:28:47: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:28:49: #1 tag size is determined as 40 bps INFO @ Tue, 16 Jun 2020 07:28:49: #1 tag size = 40 INFO @ Tue, 16 Jun 2020 07:28:49: #1 total tags in treatment: 282207 INFO @ Tue, 16 Jun 2020 07:28:49: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:28:49: #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 07:28:49: #1 tags after filtering in treatment: 282207 INFO @ Tue, 16 Jun 2020 07:28:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:28:49: #1 finished! INFO @ Tue, 16 Jun 2020 07:28:49: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:28:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:28:49: #2 number of paired peaks: 2095 INFO @ Tue, 16 Jun 2020 07:28:49: start model_add_line... INFO @ Tue, 16 Jun 2020 07:28:49: start X-correlation... INFO @ Tue, 16 Jun 2020 07:28:49: end of X-cor INFO @ Tue, 16 Jun 2020 07:28:49: #2 finished! INFO @ Tue, 16 Jun 2020 07:28:49: #2 predicted fragment length is 83 bps INFO @ Tue, 16 Jun 2020 07:28:49: #2 alternative fragment length(s) may be 83 bps INFO @ Tue, 16 Jun 2020 07:28:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1007132/SRX1007132.10_model.r INFO @ Tue, 16 Jun 2020 07:28:49: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:28:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:28:50: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:28:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1007132/SRX1007132.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:28:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1007132/SRX1007132.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:28:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1007132/SRX1007132.10_summits.bed INFO @ Tue, 16 Jun 2020 07:28:50: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (722 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 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:29:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1007132/SRX1007132.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1007132/SRX1007132.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1007132/SRX1007132.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1007132/SRX1007132.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 07:29:17: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:29:17: #1 read treatment tags... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:29:19: #1 tag size is determined as 40 bps INFO @ Tue, 16 Jun 2020 07:29:19: #1 tag size = 40 INFO @ Tue, 16 Jun 2020 07:29:19: #1 total tags in treatment: 282207 INFO @ Tue, 16 Jun 2020 07:29:19: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:29:19: #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 07:29:19: #1 tags after filtering in treatment: 282207 INFO @ Tue, 16 Jun 2020 07:29:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:29:19: #1 finished! INFO @ Tue, 16 Jun 2020 07:29:19: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:29:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:29:19: #2 number of paired peaks: 2095 INFO @ Tue, 16 Jun 2020 07:29:19: start model_add_line... INFO @ Tue, 16 Jun 2020 07:29:19: start X-correlation... INFO @ Tue, 16 Jun 2020 07:29:19: end of X-cor INFO @ Tue, 16 Jun 2020 07:29:19: #2 finished! INFO @ Tue, 16 Jun 2020 07:29:19: #2 predicted fragment length is 83 bps INFO @ Tue, 16 Jun 2020 07:29:19: #2 alternative fragment length(s) may be 83 bps INFO @ Tue, 16 Jun 2020 07:29:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1007132/SRX1007132.20_model.r INFO @ Tue, 16 Jun 2020 07:29:19: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:29:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:29:20: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:29:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1007132/SRX1007132.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:29:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1007132/SRX1007132.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:29:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1007132/SRX1007132.20_summits.bed INFO @ Tue, 16 Jun 2020 07:29:20: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (228 records, 4 fields): 2 millis CompletedMACS2peakCalling