Job ID = 6366873 SRX = SRX245916 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:56:14 prefetch.2.10.7: 1) Downloading 'SRR765973'... 2020-06-15T22:56:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:57:26 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:57:27 prefetch.2.10.7: 'SRR765973' is valid 2020-06-15T22:57:27 prefetch.2.10.7: 1) 'SRR765973' was downloaded successfully Read 25703370 spots for SRR765973/SRR765973.sra Written 25703370 spots for SRR765973/SRR765973.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: 00:01:58 25703370 reads; of these: 25703370 (100.00%) were unpaired; of these: 18478075 (71.89%) aligned 0 times 6092548 (23.70%) aligned exactly 1 time 1132747 (4.41%) aligned >1 times 28.11% overall alignment rate Time searching: 00:01:58 Overall time: 00:01:58 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] 3668636 / 7225295 = 0.5077 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 08:02:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX245916/SRX245916.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX245916/SRX245916.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX245916/SRX245916.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX245916/SRX245916.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 08:02:26: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:02:26: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:02:31: 1000000 INFO @ Tue, 16 Jun 2020 08:02:37: 2000000 INFO @ Tue, 16 Jun 2020 08:02:42: 3000000 INFO @ Tue, 16 Jun 2020 08:02:45: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 08:02:45: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 08:02:45: #1 total tags in treatment: 3556659 INFO @ Tue, 16 Jun 2020 08:02:45: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:02:45: #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 08:02:45: #1 tags after filtering in treatment: 3556659 INFO @ Tue, 16 Jun 2020 08:02:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:02:45: #1 finished! INFO @ Tue, 16 Jun 2020 08:02:45: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:02:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:02:46: #2 number of paired peaks: 1051 INFO @ Tue, 16 Jun 2020 08:02:46: start model_add_line... INFO @ Tue, 16 Jun 2020 08:02:46: start X-correlation... INFO @ Tue, 16 Jun 2020 08:02:46: end of X-cor INFO @ Tue, 16 Jun 2020 08:02:46: #2 finished! INFO @ Tue, 16 Jun 2020 08:02:46: #2 predicted fragment length is 106 bps INFO @ Tue, 16 Jun 2020 08:02:46: #2 alternative fragment length(s) may be 106 bps INFO @ Tue, 16 Jun 2020 08:02:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX245916/SRX245916.05_model.r INFO @ Tue, 16 Jun 2020 08:02:46: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:02:46: #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 08:02:54: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:02:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX245916/SRX245916.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX245916/SRX245916.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX245916/SRX245916.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX245916/SRX245916.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 08:02:56: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:02:56: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:02:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX245916/SRX245916.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:02:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX245916/SRX245916.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:02:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX245916/SRX245916.05_summits.bed INFO @ Tue, 16 Jun 2020 08:02:59: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3277 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:03:01: 1000000 INFO @ Tue, 16 Jun 2020 08:03:07: 2000000 INFO @ Tue, 16 Jun 2020 08:03:13: 3000000 INFO @ Tue, 16 Jun 2020 08:03:16: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 08:03:16: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 08:03:16: #1 total tags in treatment: 3556659 INFO @ Tue, 16 Jun 2020 08:03:16: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:03:16: #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 08:03:16: #1 tags after filtering in treatment: 3556659 INFO @ Tue, 16 Jun 2020 08:03:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:03:16: #1 finished! INFO @ Tue, 16 Jun 2020 08:03:16: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:03:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:03:16: #2 number of paired peaks: 1051 INFO @ Tue, 16 Jun 2020 08:03:16: start model_add_line... INFO @ Tue, 16 Jun 2020 08:03:16: start X-correlation... INFO @ Tue, 16 Jun 2020 08:03:16: end of X-cor INFO @ Tue, 16 Jun 2020 08:03:16: #2 finished! INFO @ Tue, 16 Jun 2020 08:03:16: #2 predicted fragment length is 106 bps INFO @ Tue, 16 Jun 2020 08:03:16: #2 alternative fragment length(s) may be 106 bps INFO @ Tue, 16 Jun 2020 08:03:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX245916/SRX245916.10_model.r INFO @ Tue, 16 Jun 2020 08:03:16: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:03:16: #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 08:03:25: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:03:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX245916/SRX245916.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX245916/SRX245916.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX245916/SRX245916.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX245916/SRX245916.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 08:03:26: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:03:26: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:03:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX245916/SRX245916.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:03:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX245916/SRX245916.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:03:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX245916/SRX245916.10_summits.bed INFO @ Tue, 16 Jun 2020 08:03:29: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2075 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:03:32: 1000000 INFO @ Tue, 16 Jun 2020 08:03:38: 2000000 INFO @ Tue, 16 Jun 2020 08:03:44: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:03:47: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 08:03:47: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 08:03:47: #1 total tags in treatment: 3556659 INFO @ Tue, 16 Jun 2020 08:03:47: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:03:47: #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 08:03:47: #1 tags after filtering in treatment: 3556659 INFO @ Tue, 16 Jun 2020 08:03:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:03:47: #1 finished! INFO @ Tue, 16 Jun 2020 08:03:47: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:03:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:03:47: #2 number of paired peaks: 1051 INFO @ Tue, 16 Jun 2020 08:03:47: start model_add_line... INFO @ Tue, 16 Jun 2020 08:03:47: start X-correlation... INFO @ Tue, 16 Jun 2020 08:03:47: end of X-cor INFO @ Tue, 16 Jun 2020 08:03:47: #2 finished! INFO @ Tue, 16 Jun 2020 08:03:47: #2 predicted fragment length is 106 bps INFO @ Tue, 16 Jun 2020 08:03:47: #2 alternative fragment length(s) may be 106 bps INFO @ Tue, 16 Jun 2020 08:03:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX245916/SRX245916.20_model.r INFO @ Tue, 16 Jun 2020 08:03:47: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:03:47: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:03:56: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:04:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX245916/SRX245916.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:04:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX245916/SRX245916.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:04:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX245916/SRX245916.20_summits.bed INFO @ Tue, 16 Jun 2020 08:04:01: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1090 records, 4 fields): 3 millis CompletedMACS2peakCalling