Job ID = 6367518 SRX = SRX331274 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:37:29 prefetch.2.10.7: 1) Downloading 'SRR947509'... 2020-06-15T23:37:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:38:10 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:38:10 prefetch.2.10.7: 'SRR947509' is valid 2020-06-15T23:38:10 prefetch.2.10.7: 1) 'SRR947509' was downloaded successfully Read 4872531 spots for SRR947509/SRR947509.sra Written 4872531 spots for SRR947509/SRR947509.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: 00:00:39 4872531 reads; of these: 4872531 (100.00%) were unpaired; of these: 1582232 (32.47%) aligned 0 times 2872393 (58.95%) aligned exactly 1 time 417906 (8.58%) aligned >1 times 67.53% overall alignment rate Time searching: 00:00:39 Overall time: 00:00:39 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] 1023990 / 3290299 = 0.3112 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 08:40:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331274/SRX331274.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331274/SRX331274.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331274/SRX331274.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331274/SRX331274.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 08:40:10: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:40:10: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:40:16: 1000000 INFO @ Tue, 16 Jun 2020 08:40:22: 2000000 INFO @ Tue, 16 Jun 2020 08:40:23: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:40:23: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:40:23: #1 total tags in treatment: 2266309 INFO @ Tue, 16 Jun 2020 08:40:23: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:40:23: #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 08:40:23: #1 tags after filtering in treatment: 2266309 INFO @ Tue, 16 Jun 2020 08:40:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:40:23: #1 finished! INFO @ Tue, 16 Jun 2020 08:40:23: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:40:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:40:23: #2 number of paired peaks: 1817 INFO @ Tue, 16 Jun 2020 08:40:23: start model_add_line... INFO @ Tue, 16 Jun 2020 08:40:23: start X-correlation... INFO @ Tue, 16 Jun 2020 08:40:23: end of X-cor INFO @ Tue, 16 Jun 2020 08:40:23: #2 finished! INFO @ Tue, 16 Jun 2020 08:40:23: #2 predicted fragment length is 141 bps INFO @ Tue, 16 Jun 2020 08:40:23: #2 alternative fragment length(s) may be 141 bps INFO @ Tue, 16 Jun 2020 08:40:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331274/SRX331274.05_model.r INFO @ Tue, 16 Jun 2020 08:40:23: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:40:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:40:29: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:40:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331274/SRX331274.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:40:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331274/SRX331274.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:40:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331274/SRX331274.05_summits.bed INFO @ Tue, 16 Jun 2020 08:40:32: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4281 records, 4 fields): 5 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 08:40:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331274/SRX331274.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331274/SRX331274.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331274/SRX331274.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331274/SRX331274.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 08:40:40: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:40:40: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:40:47: 1000000 INFO @ Tue, 16 Jun 2020 08:40:54: 2000000 INFO @ Tue, 16 Jun 2020 08:40:56: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:40:56: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:40:56: #1 total tags in treatment: 2266309 INFO @ Tue, 16 Jun 2020 08:40:56: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:40:56: #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 08:40:56: #1 tags after filtering in treatment: 2266309 INFO @ Tue, 16 Jun 2020 08:40:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:40:56: #1 finished! INFO @ Tue, 16 Jun 2020 08:40:56: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:40:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:40:56: #2 number of paired peaks: 1817 INFO @ Tue, 16 Jun 2020 08:40:56: start model_add_line... INFO @ Tue, 16 Jun 2020 08:40:56: start X-correlation... INFO @ Tue, 16 Jun 2020 08:40:56: end of X-cor INFO @ Tue, 16 Jun 2020 08:40:56: #2 finished! INFO @ Tue, 16 Jun 2020 08:40:56: #2 predicted fragment length is 141 bps INFO @ Tue, 16 Jun 2020 08:40:56: #2 alternative fragment length(s) may be 141 bps INFO @ Tue, 16 Jun 2020 08:40:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331274/SRX331274.10_model.r INFO @ Tue, 16 Jun 2020 08:40:56: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:40:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:41:02: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:41:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331274/SRX331274.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:41:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331274/SRX331274.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:41:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331274/SRX331274.10_summits.bed INFO @ Tue, 16 Jun 2020 08:41:05: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2610 records, 4 fields): 4 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 08:41:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331274/SRX331274.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331274/SRX331274.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331274/SRX331274.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331274/SRX331274.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 08:41:10: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:41:10: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:41:16: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:41:22: 2000000 INFO @ Tue, 16 Jun 2020 08:41:23: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:41:23: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:41:23: #1 total tags in treatment: 2266309 INFO @ Tue, 16 Jun 2020 08:41:23: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:41:23: #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 08:41:23: #1 tags after filtering in treatment: 2266309 INFO @ Tue, 16 Jun 2020 08:41:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:41:23: #1 finished! INFO @ Tue, 16 Jun 2020 08:41:23: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:41:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:41:24: #2 number of paired peaks: 1817 INFO @ Tue, 16 Jun 2020 08:41:24: start model_add_line... INFO @ Tue, 16 Jun 2020 08:41:24: start X-correlation... INFO @ Tue, 16 Jun 2020 08:41:24: end of X-cor INFO @ Tue, 16 Jun 2020 08:41:24: #2 finished! INFO @ Tue, 16 Jun 2020 08:41:24: #2 predicted fragment length is 141 bps INFO @ Tue, 16 Jun 2020 08:41:24: #2 alternative fragment length(s) may be 141 bps INFO @ Tue, 16 Jun 2020 08:41:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331274/SRX331274.20_model.r INFO @ Tue, 16 Jun 2020 08:41:24: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:41:24: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:41:29: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:41:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331274/SRX331274.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:41:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331274/SRX331274.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:41:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331274/SRX331274.20_summits.bed INFO @ Tue, 16 Jun 2020 08:41:32: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1093 records, 4 fields): 2 millis CompletedMACS2peakCalling