Job ID = 6367532 SRX = SRX331288 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:28:06 prefetch.2.10.7: 1) Downloading 'SRR947524'... 2020-06-15T23:28:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:28:34 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:28:34 prefetch.2.10.7: 'SRR947524' is valid 2020-06-15T23:28:34 prefetch.2.10.7: 1) 'SRR947524' was downloaded successfully Read 2231801 spots for SRR947524/SRR947524.sra Written 2231801 spots for SRR947524/SRR947524.sra 2020-06-15T23:28:51 prefetch.2.10.7: 1) Downloading 'SRR947525'... 2020-06-15T23:28:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:29:41 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:29:41 prefetch.2.10.7: 'SRR947525' is valid 2020-06-15T23:29:41 prefetch.2.10.7: 1) 'SRR947525' was downloaded successfully Read 3988589 spots for SRR947525/SRR947525.sra Written 3988589 spots for SRR947525/SRR947525.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: 00:00:36 6220390 reads; of these: 6220390 (100.00%) were unpaired; of these: 4016585 (64.57%) aligned 0 times 1875562 (30.15%) aligned exactly 1 time 328243 (5.28%) aligned >1 times 35.43% overall alignment rate Time searching: 00:00:36 Overall time: 00:00:36 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] 356296 / 2203805 = 0.1617 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 08:31:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331288/SRX331288.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331288/SRX331288.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331288/SRX331288.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331288/SRX331288.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 08:31:24: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:31:24: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:31:29: 1000000 INFO @ Tue, 16 Jun 2020 08:31:33: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:31:33: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:31:33: #1 total tags in treatment: 1847509 INFO @ Tue, 16 Jun 2020 08:31:33: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:31:33: #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 08:31:33: #1 tags after filtering in treatment: 1847509 INFO @ Tue, 16 Jun 2020 08:31:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:31:33: #1 finished! INFO @ Tue, 16 Jun 2020 08:31:33: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:31:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:31:33: #2 number of paired peaks: 726 WARNING @ Tue, 16 Jun 2020 08:31:33: Fewer paired peaks (726) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 726 pairs to build model! INFO @ Tue, 16 Jun 2020 08:31:33: start model_add_line... INFO @ Tue, 16 Jun 2020 08:31:33: start X-correlation... INFO @ Tue, 16 Jun 2020 08:31:33: end of X-cor INFO @ Tue, 16 Jun 2020 08:31:33: #2 finished! INFO @ Tue, 16 Jun 2020 08:31:33: #2 predicted fragment length is 132 bps INFO @ Tue, 16 Jun 2020 08:31:33: #2 alternative fragment length(s) may be 132 bps INFO @ Tue, 16 Jun 2020 08:31:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331288/SRX331288.05_model.r INFO @ Tue, 16 Jun 2020 08:31:33: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:31:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:31:37: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:31:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331288/SRX331288.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:31:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331288/SRX331288.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:31:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331288/SRX331288.05_summits.bed INFO @ Tue, 16 Jun 2020 08:31:39: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1470 records, 4 fields): 2 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 08:31:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331288/SRX331288.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331288/SRX331288.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331288/SRX331288.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331288/SRX331288.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 08:31:54: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:31:54: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:31:59: 1000000 INFO @ Tue, 16 Jun 2020 08:32:03: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:32:03: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:32:03: #1 total tags in treatment: 1847509 INFO @ Tue, 16 Jun 2020 08:32:03: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:32:03: #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 08:32:03: #1 tags after filtering in treatment: 1847509 INFO @ Tue, 16 Jun 2020 08:32:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:32:03: #1 finished! INFO @ Tue, 16 Jun 2020 08:32:03: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:32:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:32:03: #2 number of paired peaks: 726 WARNING @ Tue, 16 Jun 2020 08:32:03: Fewer paired peaks (726) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 726 pairs to build model! INFO @ Tue, 16 Jun 2020 08:32:03: start model_add_line... INFO @ Tue, 16 Jun 2020 08:32:03: start X-correlation... INFO @ Tue, 16 Jun 2020 08:32:03: end of X-cor INFO @ Tue, 16 Jun 2020 08:32:03: #2 finished! INFO @ Tue, 16 Jun 2020 08:32:03: #2 predicted fragment length is 132 bps INFO @ Tue, 16 Jun 2020 08:32:03: #2 alternative fragment length(s) may be 132 bps INFO @ Tue, 16 Jun 2020 08:32:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331288/SRX331288.10_model.r INFO @ Tue, 16 Jun 2020 08:32:03: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:32:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:32:07: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:32:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331288/SRX331288.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:32:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331288/SRX331288.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:32:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331288/SRX331288.10_summits.bed INFO @ Tue, 16 Jun 2020 08:32:10: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (616 records, 4 fields): 1 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 08:32:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331288/SRX331288.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331288/SRX331288.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331288/SRX331288.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331288/SRX331288.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 08:32:24: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:32:24: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:32:29: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:32:33: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:32:33: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:32:33: #1 total tags in treatment: 1847509 INFO @ Tue, 16 Jun 2020 08:32:33: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:32:33: #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 08:32:33: #1 tags after filtering in treatment: 1847509 INFO @ Tue, 16 Jun 2020 08:32:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:32:33: #1 finished! INFO @ Tue, 16 Jun 2020 08:32:33: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:32:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:32:33: #2 number of paired peaks: 726 WARNING @ Tue, 16 Jun 2020 08:32:33: Fewer paired peaks (726) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 726 pairs to build model! INFO @ Tue, 16 Jun 2020 08:32:33: start model_add_line... INFO @ Tue, 16 Jun 2020 08:32:33: start X-correlation... INFO @ Tue, 16 Jun 2020 08:32:33: end of X-cor INFO @ Tue, 16 Jun 2020 08:32:33: #2 finished! INFO @ Tue, 16 Jun 2020 08:32:33: #2 predicted fragment length is 132 bps INFO @ Tue, 16 Jun 2020 08:32:33: #2 alternative fragment length(s) may be 132 bps INFO @ Tue, 16 Jun 2020 08:32:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331288/SRX331288.20_model.r INFO @ Tue, 16 Jun 2020 08:32:33: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:32:33: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:32:37: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:32:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331288/SRX331288.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:32:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331288/SRX331288.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:32:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331288/SRX331288.20_summits.bed INFO @ Tue, 16 Jun 2020 08:32:39: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (185 records, 4 fields): 1 millis CompletedMACS2peakCalling