Job ID = 6366384 SRX = SRX1388758 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:44:37 prefetch.2.10.7: 1) Downloading 'SRR2832474'... 2020-06-15T22:44:37 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:45:06 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:45:07 prefetch.2.10.7: 'SRR2832474' is valid 2020-06-15T22:45:07 prefetch.2.10.7: 1) 'SRR2832474' was downloaded successfully Read 4494469 spots for SRR2832474/SRR2832474.sra Written 4494469 spots for SRR2832474/SRR2832474.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: 00:01:02 4494469 reads; of these: 4494469 (100.00%) were unpaired; of these: 180594 (4.02%) aligned 0 times 3793488 (84.40%) aligned exactly 1 time 520387 (11.58%) aligned >1 times 95.98% overall alignment rate Time searching: 00:01:02 Overall time: 00:01:02 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 398729 / 4313875 = 0.0924 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 07:47:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1388758/SRX1388758.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1388758/SRX1388758.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1388758/SRX1388758.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1388758/SRX1388758.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 07:47:52: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:47:52: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:47:58: 1000000 INFO @ Tue, 16 Jun 2020 07:48:03: 2000000 INFO @ Tue, 16 Jun 2020 07:48:08: 3000000 INFO @ Tue, 16 Jun 2020 07:48:13: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 07:48:13: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 07:48:13: #1 total tags in treatment: 3915146 INFO @ Tue, 16 Jun 2020 07:48:13: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:48:13: #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 07:48:13: #1 tags after filtering in treatment: 3915146 INFO @ Tue, 16 Jun 2020 07:48:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:48:13: #1 finished! INFO @ Tue, 16 Jun 2020 07:48:13: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:48:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:48:14: #2 number of paired peaks: 3273 INFO @ Tue, 16 Jun 2020 07:48:14: start model_add_line... INFO @ Tue, 16 Jun 2020 07:48:14: start X-correlation... INFO @ Tue, 16 Jun 2020 07:48:14: end of X-cor INFO @ Tue, 16 Jun 2020 07:48:14: #2 finished! INFO @ Tue, 16 Jun 2020 07:48:14: #2 predicted fragment length is 186 bps INFO @ Tue, 16 Jun 2020 07:48:14: #2 alternative fragment length(s) may be 186 bps INFO @ Tue, 16 Jun 2020 07:48:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1388758/SRX1388758.05_model.r INFO @ Tue, 16 Jun 2020 07:48:14: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:48:14: #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 07:48:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1388758/SRX1388758.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1388758/SRX1388758.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1388758/SRX1388758.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1388758/SRX1388758.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 07:48:22: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:48:22: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:48:25: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:48:28: 1000000 INFO @ Tue, 16 Jun 2020 07:48:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1388758/SRX1388758.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:48:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1388758/SRX1388758.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:48:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1388758/SRX1388758.05_summits.bed INFO @ Tue, 16 Jun 2020 07:48:31: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3452 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:48:33: 2000000 INFO @ Tue, 16 Jun 2020 07:48:39: 3000000 INFO @ Tue, 16 Jun 2020 07:48:44: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 07:48:44: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 07:48:44: #1 total tags in treatment: 3915146 INFO @ Tue, 16 Jun 2020 07:48:44: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:48:44: #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 07:48:44: #1 tags after filtering in treatment: 3915146 INFO @ Tue, 16 Jun 2020 07:48:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:48:44: #1 finished! INFO @ Tue, 16 Jun 2020 07:48:44: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:48:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:48:45: #2 number of paired peaks: 3273 INFO @ Tue, 16 Jun 2020 07:48:45: start model_add_line... INFO @ Tue, 16 Jun 2020 07:48:45: start X-correlation... INFO @ Tue, 16 Jun 2020 07:48:45: end of X-cor INFO @ Tue, 16 Jun 2020 07:48:45: #2 finished! INFO @ Tue, 16 Jun 2020 07:48:45: #2 predicted fragment length is 186 bps INFO @ Tue, 16 Jun 2020 07:48:45: #2 alternative fragment length(s) may be 186 bps INFO @ Tue, 16 Jun 2020 07:48:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1388758/SRX1388758.10_model.r INFO @ Tue, 16 Jun 2020 07:48:45: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:48:45: #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 07:48:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1388758/SRX1388758.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1388758/SRX1388758.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1388758/SRX1388758.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1388758/SRX1388758.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 07:48:52: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:48:52: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:48:56: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:48:58: 1000000 INFO @ Tue, 16 Jun 2020 07:49:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1388758/SRX1388758.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:49:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1388758/SRX1388758.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:49:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1388758/SRX1388758.10_summits.bed INFO @ Tue, 16 Jun 2020 07:49:02: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (1665 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:49:03: 2000000 INFO @ Tue, 16 Jun 2020 07:49:09: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:49:13: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 07:49:13: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 07:49:13: #1 total tags in treatment: 3915146 INFO @ Tue, 16 Jun 2020 07:49:13: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:49:13: #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 07:49:14: #1 tags after filtering in treatment: 3915146 INFO @ Tue, 16 Jun 2020 07:49:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:49:14: #1 finished! INFO @ Tue, 16 Jun 2020 07:49:14: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:49:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:49:14: #2 number of paired peaks: 3273 INFO @ Tue, 16 Jun 2020 07:49:14: start model_add_line... INFO @ Tue, 16 Jun 2020 07:49:14: start X-correlation... INFO @ Tue, 16 Jun 2020 07:49:14: end of X-cor INFO @ Tue, 16 Jun 2020 07:49:14: #2 finished! INFO @ Tue, 16 Jun 2020 07:49:14: #2 predicted fragment length is 186 bps INFO @ Tue, 16 Jun 2020 07:49:14: #2 alternative fragment length(s) may be 186 bps INFO @ Tue, 16 Jun 2020 07:49:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1388758/SRX1388758.20_model.r INFO @ Tue, 16 Jun 2020 07:49:14: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:49:14: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:49:25: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:49:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1388758/SRX1388758.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:49:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1388758/SRX1388758.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:49:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1388758/SRX1388758.20_summits.bed INFO @ Tue, 16 Jun 2020 07:49:30: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (617 records, 4 fields): 1 millis CompletedMACS2peakCalling