Job ID = 6365909 SRX = SRX027211 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:18:57 prefetch.2.10.7: 1) Downloading 'SRR066594'... 2020-06-15T22:18:57 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:19:50 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:19:51 prefetch.2.10.7: 'SRR066594' is valid 2020-06-15T22:19:51 prefetch.2.10.7: 1) 'SRR066594' was downloaded successfully Read 16264926 spots for SRR066594/SRR066594.sra Written 16264926 spots for SRR066594/SRR066594.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 16264926 reads; of these: 16264926 (100.00%) were unpaired; of these: 10752796 (66.11%) aligned 0 times 4783539 (29.41%) aligned exactly 1 time 728591 (4.48%) aligned >1 times 33.89% 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] 660468 / 5512130 = 0.1198 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 07:23:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX027211/SRX027211.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX027211/SRX027211.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX027211/SRX027211.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX027211/SRX027211.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 07:23:34: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:23:34: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:23:39: 1000000 INFO @ Tue, 16 Jun 2020 07:23:45: 2000000 INFO @ Tue, 16 Jun 2020 07:23:50: 3000000 INFO @ Tue, 16 Jun 2020 07:23:55: 4000000 INFO @ Tue, 16 Jun 2020 07:24:00: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:24:00: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:24:00: #1 total tags in treatment: 4851662 INFO @ Tue, 16 Jun 2020 07:24:00: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:24:00: #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 07:24:00: #1 tags after filtering in treatment: 4851662 INFO @ Tue, 16 Jun 2020 07:24:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:24:00: #1 finished! INFO @ Tue, 16 Jun 2020 07:24:00: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:24:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:24:00: #2 number of paired peaks: 2973 INFO @ Tue, 16 Jun 2020 07:24:00: start model_add_line... INFO @ Tue, 16 Jun 2020 07:24:00: start X-correlation... INFO @ Tue, 16 Jun 2020 07:24:00: end of X-cor INFO @ Tue, 16 Jun 2020 07:24:00: #2 finished! INFO @ Tue, 16 Jun 2020 07:24:00: #2 predicted fragment length is 243 bps INFO @ Tue, 16 Jun 2020 07:24:00: #2 alternative fragment length(s) may be 243 bps INFO @ Tue, 16 Jun 2020 07:24:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX027211/SRX027211.05_model.r INFO @ Tue, 16 Jun 2020 07:24:00: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:24:00: #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 07:24:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX027211/SRX027211.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX027211/SRX027211.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX027211/SRX027211.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX027211/SRX027211.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 07:24:08: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:24:08: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:24:14: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:24:14: 1000000 INFO @ Tue, 16 Jun 2020 07:24:20: 2000000 INFO @ Tue, 16 Jun 2020 07:24:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX027211/SRX027211.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:24:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX027211/SRX027211.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:24:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX027211/SRX027211.05_summits.bed INFO @ Tue, 16 Jun 2020 07:24:21: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3894 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:24:27: 3000000 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 07:24:33: 4000000 INFO @ Tue, 16 Jun 2020 07:24:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX027211/SRX027211.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX027211/SRX027211.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX027211/SRX027211.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX027211/SRX027211.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 07:24:34: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:24:34: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:24:39: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:24:39: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:24:39: #1 total tags in treatment: 4851662 INFO @ Tue, 16 Jun 2020 07:24:39: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:24:39: #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 07:24:39: #1 tags after filtering in treatment: 4851662 INFO @ Tue, 16 Jun 2020 07:24:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:24:39: #1 finished! INFO @ Tue, 16 Jun 2020 07:24:39: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:24:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:24:39: #2 number of paired peaks: 2973 INFO @ Tue, 16 Jun 2020 07:24:39: start model_add_line... INFO @ Tue, 16 Jun 2020 07:24:39: start X-correlation... INFO @ Tue, 16 Jun 2020 07:24:39: end of X-cor INFO @ Tue, 16 Jun 2020 07:24:39: #2 finished! INFO @ Tue, 16 Jun 2020 07:24:39: #2 predicted fragment length is 243 bps INFO @ Tue, 16 Jun 2020 07:24:39: #2 alternative fragment length(s) may be 243 bps INFO @ Tue, 16 Jun 2020 07:24:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX027211/SRX027211.10_model.r INFO @ Tue, 16 Jun 2020 07:24:39: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:24:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:24:40: 1000000 INFO @ Tue, 16 Jun 2020 07:24:45: 2000000 INFO @ Tue, 16 Jun 2020 07:24:51: 3000000 INFO @ Tue, 16 Jun 2020 07:24:53: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:24:56: 4000000 INFO @ Tue, 16 Jun 2020 07:25:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX027211/SRX027211.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:25:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX027211/SRX027211.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:25:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX027211/SRX027211.10_summits.bed INFO @ Tue, 16 Jun 2020 07:25:00: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3107 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:25:00: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:25:00: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:25:00: #1 total tags in treatment: 4851662 INFO @ Tue, 16 Jun 2020 07:25:00: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:25:00: #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 07:25:00: #1 tags after filtering in treatment: 4851662 INFO @ Tue, 16 Jun 2020 07:25:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:25:00: #1 finished! INFO @ Tue, 16 Jun 2020 07:25:00: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:25:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:25:01: #2 number of paired peaks: 2973 INFO @ Tue, 16 Jun 2020 07:25:01: start model_add_line... INFO @ Tue, 16 Jun 2020 07:25:01: start X-correlation... INFO @ Tue, 16 Jun 2020 07:25:01: end of X-cor INFO @ Tue, 16 Jun 2020 07:25:01: #2 finished! INFO @ Tue, 16 Jun 2020 07:25:01: #2 predicted fragment length is 243 bps INFO @ Tue, 16 Jun 2020 07:25:01: #2 alternative fragment length(s) may be 243 bps INFO @ Tue, 16 Jun 2020 07:25:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX027211/SRX027211.20_model.r INFO @ Tue, 16 Jun 2020 07:25:01: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:25:01: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:25:14: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:25:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX027211/SRX027211.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:25:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX027211/SRX027211.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:25:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX027211/SRX027211.20_summits.bed INFO @ Tue, 16 Jun 2020 07:25:20: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2162 records, 4 fields): 4 millis CompletedMACS2peakCalling