Job ID = 6367407 SRX = SRX331166 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:18:31 prefetch.2.10.7: 1) Downloading 'SRR947398'... 2020-06-15T23:18:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:18:54 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:18:54 prefetch.2.10.7: 'SRR947398' is valid 2020-06-15T23:18:54 prefetch.2.10.7: 1) 'SRR947398' was downloaded successfully Read 5062929 spots for SRR947398/SRR947398.sra Written 5062929 spots for SRR947398/SRR947398.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: 00:00:40 5062929 reads; of these: 5062929 (100.00%) were unpaired; of these: 1686044 (33.30%) aligned 0 times 2938898 (58.05%) aligned exactly 1 time 437987 (8.65%) aligned >1 times 66.70% overall alignment rate Time searching: 00:00:40 Overall time: 00:00:40 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] 854389 / 3376885 = 0.2530 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 08:20:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331166/SRX331166.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331166/SRX331166.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331166/SRX331166.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331166/SRX331166.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 08:20:50: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:20:50: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:20:56: 1000000 INFO @ Tue, 16 Jun 2020 08:21:01: 2000000 INFO @ Tue, 16 Jun 2020 08:21:04: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:21:04: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:21:04: #1 total tags in treatment: 2522496 INFO @ Tue, 16 Jun 2020 08:21:04: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:21:04: #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 08:21:04: #1 tags after filtering in treatment: 2522496 INFO @ Tue, 16 Jun 2020 08:21:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:21:04: #1 finished! INFO @ Tue, 16 Jun 2020 08:21:04: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:21:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:21:04: #2 number of paired peaks: 2171 INFO @ Tue, 16 Jun 2020 08:21:04: start model_add_line... INFO @ Tue, 16 Jun 2020 08:21:04: start X-correlation... INFO @ Tue, 16 Jun 2020 08:21:04: end of X-cor INFO @ Tue, 16 Jun 2020 08:21:04: #2 finished! INFO @ Tue, 16 Jun 2020 08:21:04: #2 predicted fragment length is 158 bps INFO @ Tue, 16 Jun 2020 08:21:04: #2 alternative fragment length(s) may be 158 bps INFO @ Tue, 16 Jun 2020 08:21:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331166/SRX331166.05_model.r INFO @ Tue, 16 Jun 2020 08:21:04: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:21:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:21:11: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:21:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331166/SRX331166.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:21:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331166/SRX331166.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:21:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331166/SRX331166.05_summits.bed INFO @ Tue, 16 Jun 2020 08:21:14: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3996 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 08:21:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331166/SRX331166.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331166/SRX331166.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331166/SRX331166.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331166/SRX331166.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 08:21:20: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:21:20: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:21:26: 1000000 INFO @ Tue, 16 Jun 2020 08:21:31: 2000000 INFO @ Tue, 16 Jun 2020 08:21:34: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:21:34: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:21:34: #1 total tags in treatment: 2522496 INFO @ Tue, 16 Jun 2020 08:21:34: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:21:34: #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 08:21:34: #1 tags after filtering in treatment: 2522496 INFO @ Tue, 16 Jun 2020 08:21:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:21:34: #1 finished! INFO @ Tue, 16 Jun 2020 08:21:34: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:21:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:21:34: #2 number of paired peaks: 2171 INFO @ Tue, 16 Jun 2020 08:21:34: start model_add_line... INFO @ Tue, 16 Jun 2020 08:21:34: start X-correlation... INFO @ Tue, 16 Jun 2020 08:21:34: end of X-cor INFO @ Tue, 16 Jun 2020 08:21:34: #2 finished! INFO @ Tue, 16 Jun 2020 08:21:34: #2 predicted fragment length is 158 bps INFO @ Tue, 16 Jun 2020 08:21:34: #2 alternative fragment length(s) may be 158 bps INFO @ Tue, 16 Jun 2020 08:21:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331166/SRX331166.10_model.r INFO @ Tue, 16 Jun 2020 08:21:34: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:21:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:21:41: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:21:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331166/SRX331166.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:21:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331166/SRX331166.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:21:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331166/SRX331166.10_summits.bed INFO @ Tue, 16 Jun 2020 08:21:44: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (2549 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 08:21:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331166/SRX331166.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331166/SRX331166.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331166/SRX331166.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331166/SRX331166.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 08:21:50: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:21:50: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:21:56: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:22:01: 2000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:22:04: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:22:04: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:22:04: #1 total tags in treatment: 2522496 INFO @ Tue, 16 Jun 2020 08:22:04: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:22:04: #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 08:22:04: #1 tags after filtering in treatment: 2522496 INFO @ Tue, 16 Jun 2020 08:22:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:22:04: #1 finished! INFO @ Tue, 16 Jun 2020 08:22:04: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:22:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:22:04: #2 number of paired peaks: 2171 INFO @ Tue, 16 Jun 2020 08:22:04: start model_add_line... INFO @ Tue, 16 Jun 2020 08:22:04: start X-correlation... INFO @ Tue, 16 Jun 2020 08:22:04: end of X-cor INFO @ Tue, 16 Jun 2020 08:22:04: #2 finished! INFO @ Tue, 16 Jun 2020 08:22:04: #2 predicted fragment length is 158 bps INFO @ Tue, 16 Jun 2020 08:22:04: #2 alternative fragment length(s) may be 158 bps INFO @ Tue, 16 Jun 2020 08:22:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331166/SRX331166.20_model.r INFO @ Tue, 16 Jun 2020 08:22:04: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:22:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:22:11: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:22:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331166/SRX331166.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:22:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331166/SRX331166.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:22:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331166/SRX331166.20_summits.bed INFO @ Tue, 16 Jun 2020 08:22:14: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (1424 records, 4 fields): 3 millis CompletedMACS2peakCalling