Job ID = 6366390 SRX = SRX1388764 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:46:52 prefetch.2.10.7: 1) Downloading 'SRR2832480'... 2020-06-15T22:46:52 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:47:20 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:47:21 prefetch.2.10.7: 'SRR2832480' is valid 2020-06-15T22:47:21 prefetch.2.10.7: 1) 'SRR2832480' was downloaded successfully Read 6061718 spots for SRR2832480/SRR2832480.sra Written 6061718 spots for SRR2832480/SRR2832480.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: 00:01:21 6061718 reads; of these: 6061718 (100.00%) were unpaired; of these: 332116 (5.48%) aligned 0 times 4956928 (81.77%) aligned exactly 1 time 772674 (12.75%) aligned >1 times 94.52% overall alignment rate Time searching: 00:01:21 Overall time: 00:01:21 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] 578133 / 5729602 = 0.1009 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 07:50:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1388764/SRX1388764.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1388764/SRX1388764.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1388764/SRX1388764.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1388764/SRX1388764.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 07:50:42: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:50:42: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:50:47: 1000000 INFO @ Tue, 16 Jun 2020 07:50:52: 2000000 INFO @ Tue, 16 Jun 2020 07:50:57: 3000000 INFO @ Tue, 16 Jun 2020 07:51:02: 4000000 INFO @ Tue, 16 Jun 2020 07:51:07: 5000000 INFO @ Tue, 16 Jun 2020 07:51:08: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 07:51:08: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 07:51:08: #1 total tags in treatment: 5151469 INFO @ Tue, 16 Jun 2020 07:51:08: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:51:08: #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 07:51:08: #1 tags after filtering in treatment: 5151469 INFO @ Tue, 16 Jun 2020 07:51:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:51:08: #1 finished! INFO @ Tue, 16 Jun 2020 07:51:08: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:51:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:51:08: #2 number of paired peaks: 2682 INFO @ Tue, 16 Jun 2020 07:51:08: start model_add_line... INFO @ Tue, 16 Jun 2020 07:51:08: start X-correlation... INFO @ Tue, 16 Jun 2020 07:51:08: end of X-cor INFO @ Tue, 16 Jun 2020 07:51:08: #2 finished! INFO @ Tue, 16 Jun 2020 07:51:08: #2 predicted fragment length is 177 bps INFO @ Tue, 16 Jun 2020 07:51:08: #2 alternative fragment length(s) may be 177 bps INFO @ Tue, 16 Jun 2020 07:51:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1388764/SRX1388764.05_model.r INFO @ Tue, 16 Jun 2020 07:51:08: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:51:08: #3 Pre-compute pvalue-qvalue table... 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 07:51:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1388764/SRX1388764.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1388764/SRX1388764.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1388764/SRX1388764.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1388764/SRX1388764.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 07:51:12: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:51:12: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:51:17: 1000000 INFO @ Tue, 16 Jun 2020 07:51:22: 2000000 INFO @ Tue, 16 Jun 2020 07:51:23: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:51:27: 3000000 INFO @ Tue, 16 Jun 2020 07:51:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1388764/SRX1388764.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:51:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1388764/SRX1388764.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:51:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1388764/SRX1388764.05_summits.bed INFO @ Tue, 16 Jun 2020 07:51:31: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (4137 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:51:32: 4000000 INFO @ Tue, 16 Jun 2020 07:51:37: 5000000 INFO @ Tue, 16 Jun 2020 07:51:38: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 07:51:38: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 07:51:38: #1 total tags in treatment: 5151469 INFO @ Tue, 16 Jun 2020 07:51:38: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:51:38: #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 07:51:38: #1 tags after filtering in treatment: 5151469 INFO @ Tue, 16 Jun 2020 07:51:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:51:38: #1 finished! INFO @ Tue, 16 Jun 2020 07:51:38: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:51:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:51:39: #2 number of paired peaks: 2682 INFO @ Tue, 16 Jun 2020 07:51:39: start model_add_line... INFO @ Tue, 16 Jun 2020 07:51:39: start X-correlation... INFO @ Tue, 16 Jun 2020 07:51:39: end of X-cor INFO @ Tue, 16 Jun 2020 07:51:39: #2 finished! INFO @ Tue, 16 Jun 2020 07:51:39: #2 predicted fragment length is 177 bps INFO @ Tue, 16 Jun 2020 07:51:39: #2 alternative fragment length(s) may be 177 bps INFO @ Tue, 16 Jun 2020 07:51:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1388764/SRX1388764.10_model.r INFO @ Tue, 16 Jun 2020 07:51:39: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:51:39: #3 Pre-compute pvalue-qvalue table... 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 07:51:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1388764/SRX1388764.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1388764/SRX1388764.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1388764/SRX1388764.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1388764/SRX1388764.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 07:51:42: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:51:42: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:51:47: 1000000 INFO @ Tue, 16 Jun 2020 07:51:52: 2000000 INFO @ Tue, 16 Jun 2020 07:51:54: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:51:57: 3000000 INFO @ Tue, 16 Jun 2020 07:52:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1388764/SRX1388764.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:52:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1388764/SRX1388764.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:52:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1388764/SRX1388764.10_summits.bed INFO @ Tue, 16 Jun 2020 07:52:01: Done! INFO @ Tue, 16 Jun 2020 07:52:02: 4000000 pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2242 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:52:07: 5000000 INFO @ Tue, 16 Jun 2020 07:52:08: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 07:52:08: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 07:52:08: #1 total tags in treatment: 5151469 INFO @ Tue, 16 Jun 2020 07:52:08: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:52:08: #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 07:52:08: #1 tags after filtering in treatment: 5151469 INFO @ Tue, 16 Jun 2020 07:52:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:52:08: #1 finished! INFO @ Tue, 16 Jun 2020 07:52:08: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:52:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:52:08: #2 number of paired peaks: 2682 INFO @ Tue, 16 Jun 2020 07:52:08: start model_add_line... INFO @ Tue, 16 Jun 2020 07:52:08: start X-correlation... INFO @ Tue, 16 Jun 2020 07:52:08: end of X-cor INFO @ Tue, 16 Jun 2020 07:52:08: #2 finished! INFO @ Tue, 16 Jun 2020 07:52:08: #2 predicted fragment length is 177 bps INFO @ Tue, 16 Jun 2020 07:52:08: #2 alternative fragment length(s) may be 177 bps INFO @ Tue, 16 Jun 2020 07:52:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1388764/SRX1388764.20_model.r INFO @ Tue, 16 Jun 2020 07:52:08: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:52:08: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:52:23: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:52:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1388764/SRX1388764.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:52:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1388764/SRX1388764.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:52:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1388764/SRX1388764.20_summits.bed INFO @ Tue, 16 Jun 2020 07:52:30: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (774 records, 4 fields): 4 millis CompletedMACS2peakCalling