Job ID = 6366341 SRX = SRX113619 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:35:21 prefetch.2.10.7: 1) Downloading 'SRR393719'... 2020-06-15T22:35:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:36:00 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:36:00 prefetch.2.10.7: 'SRR393719' is valid 2020-06-15T22:36:00 prefetch.2.10.7: 1) 'SRR393719' was downloaded successfully Read 7562954 spots for SRR393719/SRR393719.sra Written 7562954 spots for SRR393719/SRR393719.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: 00:01:46 7562954 reads; of these: 7562954 (100.00%) were unpaired; of these: 424093 (5.61%) aligned 0 times 5087828 (67.27%) aligned exactly 1 time 2051033 (27.12%) aligned >1 times 94.39% overall alignment rate Time searching: 00:01:46 Overall time: 00:01:46 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] 2231518 / 7138861 = 0.3126 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 07:40:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX113619/SRX113619.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX113619/SRX113619.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX113619/SRX113619.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX113619/SRX113619.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 07:40:07: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:40:07: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:40:13: 1000000 INFO @ Tue, 16 Jun 2020 07:40:18: 2000000 INFO @ Tue, 16 Jun 2020 07:40:23: 3000000 INFO @ Tue, 16 Jun 2020 07:40:28: 4000000 INFO @ Tue, 16 Jun 2020 07:40:33: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:40:33: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:40:33: #1 total tags in treatment: 4907343 INFO @ Tue, 16 Jun 2020 07:40:33: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:40:33: #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 07:40:33: #1 tags after filtering in treatment: 4907343 INFO @ Tue, 16 Jun 2020 07:40:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:40:33: #1 finished! INFO @ Tue, 16 Jun 2020 07:40:33: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:40:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:40:34: #2 number of paired peaks: 3447 INFO @ Tue, 16 Jun 2020 07:40:34: start model_add_line... INFO @ Tue, 16 Jun 2020 07:40:34: start X-correlation... INFO @ Tue, 16 Jun 2020 07:40:34: end of X-cor INFO @ Tue, 16 Jun 2020 07:40:34: #2 finished! INFO @ Tue, 16 Jun 2020 07:40:34: #2 predicted fragment length is 163 bps INFO @ Tue, 16 Jun 2020 07:40:34: #2 alternative fragment length(s) may be 1,18,93,121,148,163,179,193,232 bps INFO @ Tue, 16 Jun 2020 07:40:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX113619/SRX113619.05_model.r INFO @ Tue, 16 Jun 2020 07:40:34: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:40:34: #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 07:40:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX113619/SRX113619.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX113619/SRX113619.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX113619/SRX113619.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX113619/SRX113619.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 07:40:37: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:40:37: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:40:42: 1000000 INFO @ Tue, 16 Jun 2020 07:40:46: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:40:47: 2000000 INFO @ Tue, 16 Jun 2020 07:40:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX113619/SRX113619.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:40:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX113619/SRX113619.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:40:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX113619/SRX113619.05_summits.bed INFO @ Tue, 16 Jun 2020 07:40:52: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (699 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:40:53: 3000000 INFO @ Tue, 16 Jun 2020 07:40:58: 4000000 INFO @ Tue, 16 Jun 2020 07:41:02: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:41:02: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:41:02: #1 total tags in treatment: 4907343 INFO @ Tue, 16 Jun 2020 07:41:02: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:41:02: #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 07:41:02: #1 tags after filtering in treatment: 4907343 INFO @ Tue, 16 Jun 2020 07:41:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:41:02: #1 finished! INFO @ Tue, 16 Jun 2020 07:41:02: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:41:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:41:03: #2 number of paired peaks: 3447 INFO @ Tue, 16 Jun 2020 07:41:03: start model_add_line... INFO @ Tue, 16 Jun 2020 07:41:03: start X-correlation... INFO @ Tue, 16 Jun 2020 07:41:03: end of X-cor INFO @ Tue, 16 Jun 2020 07:41:03: #2 finished! INFO @ Tue, 16 Jun 2020 07:41:03: #2 predicted fragment length is 163 bps INFO @ Tue, 16 Jun 2020 07:41:03: #2 alternative fragment length(s) may be 1,18,93,121,148,163,179,193,232 bps INFO @ Tue, 16 Jun 2020 07:41:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX113619/SRX113619.10_model.r INFO @ Tue, 16 Jun 2020 07:41:03: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:41:03: #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 07:41:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX113619/SRX113619.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX113619/SRX113619.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX113619/SRX113619.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX113619/SRX113619.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 07:41:07: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:41:07: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:41:12: 1000000 INFO @ Tue, 16 Jun 2020 07:41:14: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:41:17: 2000000 INFO @ Tue, 16 Jun 2020 07:41:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX113619/SRX113619.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:41:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX113619/SRX113619.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:41:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX113619/SRX113619.10_summits.bed INFO @ Tue, 16 Jun 2020 07:41:21: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (262 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:41:23: 3000000 INFO @ Tue, 16 Jun 2020 07:41:28: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:41:32: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:41:32: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:41:32: #1 total tags in treatment: 4907343 INFO @ Tue, 16 Jun 2020 07:41:32: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:41:32: #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 07:41:32: #1 tags after filtering in treatment: 4907343 INFO @ Tue, 16 Jun 2020 07:41:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:41:32: #1 finished! INFO @ Tue, 16 Jun 2020 07:41:32: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:41:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:41:33: #2 number of paired peaks: 3447 INFO @ Tue, 16 Jun 2020 07:41:33: start model_add_line... INFO @ Tue, 16 Jun 2020 07:41:33: start X-correlation... INFO @ Tue, 16 Jun 2020 07:41:33: end of X-cor INFO @ Tue, 16 Jun 2020 07:41:33: #2 finished! INFO @ Tue, 16 Jun 2020 07:41:33: #2 predicted fragment length is 163 bps INFO @ Tue, 16 Jun 2020 07:41:33: #2 alternative fragment length(s) may be 1,18,93,121,148,163,179,193,232 bps INFO @ Tue, 16 Jun 2020 07:41:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX113619/SRX113619.20_model.r INFO @ Tue, 16 Jun 2020 07:41:33: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:41:33: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:41:45: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:41:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX113619/SRX113619.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:41:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX113619/SRX113619.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:41:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX113619/SRX113619.20_summits.bed INFO @ Tue, 16 Jun 2020 07:41:50: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (72 records, 4 fields): 1 millis CompletedMACS2peakCalling