Job ID = 6366497 SRX = SRX148639 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:47:22 prefetch.2.10.7: 1) Downloading 'SRR498192'... 2020-06-15T22:47:22 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:48:18 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:48:19 prefetch.2.10.7: 'SRR498192' is valid 2020-06-15T22:48:19 prefetch.2.10.7: 1) 'SRR498192' was downloaded successfully Read 14860990 spots for SRR498192/SRR498192.sra Written 14860990 spots for SRR498192/SRR498192.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:40 14860990 reads; of these: 14860990 (100.00%) were unpaired; of these: 1294199 (8.71%) aligned 0 times 9196139 (61.88%) aligned exactly 1 time 4370652 (29.41%) aligned >1 times 91.29% overall alignment rate Time searching: 00:03:41 Overall time: 00:03:41 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] 11532075 / 13566791 = 0.8500 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 07:55:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX148639/SRX148639.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX148639/SRX148639.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX148639/SRX148639.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX148639/SRX148639.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 07:55:17: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:55:17: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:55:24: 1000000 INFO @ Tue, 16 Jun 2020 07:55:31: 2000000 INFO @ Tue, 16 Jun 2020 07:55:31: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:55:31: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:55:31: #1 total tags in treatment: 2034716 INFO @ Tue, 16 Jun 2020 07:55:31: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:55:31: #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 07:55:31: #1 tags after filtering in treatment: 2034716 INFO @ Tue, 16 Jun 2020 07:55:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:55:31: #1 finished! INFO @ Tue, 16 Jun 2020 07:55:31: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:55:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:55:31: #2 number of paired peaks: 3624 INFO @ Tue, 16 Jun 2020 07:55:31: start model_add_line... INFO @ Tue, 16 Jun 2020 07:55:31: start X-correlation... INFO @ Tue, 16 Jun 2020 07:55:31: end of X-cor INFO @ Tue, 16 Jun 2020 07:55:31: #2 finished! INFO @ Tue, 16 Jun 2020 07:55:31: #2 predicted fragment length is 153 bps INFO @ Tue, 16 Jun 2020 07:55:31: #2 alternative fragment length(s) may be 3,153 bps INFO @ Tue, 16 Jun 2020 07:55:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX148639/SRX148639.05_model.r INFO @ Tue, 16 Jun 2020 07:55:31: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:55:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:55:37: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:55:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX148639/SRX148639.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:55:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX148639/SRX148639.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:55:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX148639/SRX148639.05_summits.bed INFO @ Tue, 16 Jun 2020 07:55:40: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1450 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 07:55:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX148639/SRX148639.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX148639/SRX148639.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX148639/SRX148639.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX148639/SRX148639.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 07:55:47: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:55:47: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:55:54: 1000000 INFO @ Tue, 16 Jun 2020 07:55:59: 2000000 INFO @ Tue, 16 Jun 2020 07:55:59: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:55:59: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:55:59: #1 total tags in treatment: 2034716 INFO @ Tue, 16 Jun 2020 07:55:59: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:55:59: #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 07:55:59: #1 tags after filtering in treatment: 2034716 INFO @ Tue, 16 Jun 2020 07:55:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:55:59: #1 finished! INFO @ Tue, 16 Jun 2020 07:55:59: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:55:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:56:00: #2 number of paired peaks: 3624 INFO @ Tue, 16 Jun 2020 07:56:00: start model_add_line... INFO @ Tue, 16 Jun 2020 07:56:00: start X-correlation... INFO @ Tue, 16 Jun 2020 07:56:00: end of X-cor INFO @ Tue, 16 Jun 2020 07:56:00: #2 finished! INFO @ Tue, 16 Jun 2020 07:56:00: #2 predicted fragment length is 153 bps INFO @ Tue, 16 Jun 2020 07:56:00: #2 alternative fragment length(s) may be 3,153 bps INFO @ Tue, 16 Jun 2020 07:56:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX148639/SRX148639.10_model.r INFO @ Tue, 16 Jun 2020 07:56:00: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:56:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:56:06: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:56:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX148639/SRX148639.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:56:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX148639/SRX148639.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:56:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX148639/SRX148639.10_summits.bed INFO @ Tue, 16 Jun 2020 07:56:09: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (604 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 INFO @ Tue, 16 Jun 2020 07:56:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX148639/SRX148639.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX148639/SRX148639.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX148639/SRX148639.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX148639/SRX148639.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 07:56:17: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:56:17: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:56:23: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:56:29: 2000000 INFO @ Tue, 16 Jun 2020 07:56:29: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:56:29: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:56:29: #1 total tags in treatment: 2034716 INFO @ Tue, 16 Jun 2020 07:56:29: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:56:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:56:29: #1 tags after filtering in treatment: 2034716 INFO @ Tue, 16 Jun 2020 07:56:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:56:29: #1 finished! INFO @ Tue, 16 Jun 2020 07:56:29: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:56:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:56:29: #2 number of paired peaks: 3624 INFO @ Tue, 16 Jun 2020 07:56:29: start model_add_line... INFO @ Tue, 16 Jun 2020 07:56:29: start X-correlation... INFO @ Tue, 16 Jun 2020 07:56:29: end of X-cor INFO @ Tue, 16 Jun 2020 07:56:29: #2 finished! INFO @ Tue, 16 Jun 2020 07:56:29: #2 predicted fragment length is 153 bps INFO @ Tue, 16 Jun 2020 07:56:29: #2 alternative fragment length(s) may be 3,153 bps INFO @ Tue, 16 Jun 2020 07:56:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX148639/SRX148639.20_model.r INFO @ Tue, 16 Jun 2020 07:56:29: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:56:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:56:35: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:56:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX148639/SRX148639.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:56:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX148639/SRX148639.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:56:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX148639/SRX148639.20_summits.bed INFO @ Tue, 16 Jun 2020 07:56:38: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (239 records, 4 fields): 1 millis CompletedMACS2peakCalling