Job ID = 6366659 SRX = SRX216759 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:51:11 prefetch.2.10.7: 1) Downloading 'SRR648394'... 2020-06-15T22:51:11 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:51:53 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:51:54 prefetch.2.10.7: 'SRR648394' is valid 2020-06-15T22:51:54 prefetch.2.10.7: 1) 'SRR648394' was downloaded successfully Read 7514426 spots for SRR648394/SRR648394.sra Written 7514426 spots for SRR648394/SRR648394.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: 00:01:24 7514426 reads; of these: 7514426 (100.00%) were unpaired; of these: 1118973 (14.89%) aligned 0 times 5633337 (74.97%) aligned exactly 1 time 762116 (10.14%) aligned >1 times 85.11% overall alignment rate Time searching: 00:01:24 Overall time: 00:01:24 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] 892595 / 6395453 = 0.1396 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 07:55:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX216759/SRX216759.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX216759/SRX216759.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX216759/SRX216759.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX216759/SRX216759.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 07:55:54: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:55:54: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:55:59: 1000000 INFO @ Tue, 16 Jun 2020 07:56:05: 2000000 INFO @ Tue, 16 Jun 2020 07:56:10: 3000000 INFO @ Tue, 16 Jun 2020 07:56:15: 4000000 INFO @ Tue, 16 Jun 2020 07:56:21: 5000000 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 07:56:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX216759/SRX216759.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX216759/SRX216759.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX216759/SRX216759.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX216759/SRX216759.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 07:56:24: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:56:24: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:56:24: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 07:56:24: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 07:56:24: #1 total tags in treatment: 5502858 INFO @ Tue, 16 Jun 2020 07:56:24: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:56:24: #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 07:56:24: #1 tags after filtering in treatment: 5502858 INFO @ Tue, 16 Jun 2020 07:56:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:56:24: #1 finished! INFO @ Tue, 16 Jun 2020 07:56:24: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:56:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:56:25: #2 number of paired peaks: 890 WARNING @ Tue, 16 Jun 2020 07:56:25: Fewer paired peaks (890) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 890 pairs to build model! INFO @ Tue, 16 Jun 2020 07:56:25: start model_add_line... INFO @ Tue, 16 Jun 2020 07:56:25: start X-correlation... INFO @ Tue, 16 Jun 2020 07:56:25: end of X-cor INFO @ Tue, 16 Jun 2020 07:56:25: #2 finished! INFO @ Tue, 16 Jun 2020 07:56:25: #2 predicted fragment length is 181 bps INFO @ Tue, 16 Jun 2020 07:56:25: #2 alternative fragment length(s) may be 181 bps INFO @ Tue, 16 Jun 2020 07:56:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX216759/SRX216759.05_model.r INFO @ Tue, 16 Jun 2020 07:56:25: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:56:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:56:29: 1000000 INFO @ Tue, 16 Jun 2020 07:56:35: 2000000 INFO @ Tue, 16 Jun 2020 07:56:40: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:56:41: 3000000 INFO @ Tue, 16 Jun 2020 07:56:47: 4000000 INFO @ Tue, 16 Jun 2020 07:56:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX216759/SRX216759.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:56:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX216759/SRX216759.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:56:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX216759/SRX216759.05_summits.bed INFO @ Tue, 16 Jun 2020 07:56:47: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2959 records, 4 fields): 7 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 07:56:52: 5000000 INFO @ Tue, 16 Jun 2020 07:56:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX216759/SRX216759.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX216759/SRX216759.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX216759/SRX216759.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX216759/SRX216759.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 07:56:54: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:56:54: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:56:55: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 07:56:55: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 07:56:55: #1 total tags in treatment: 5502858 INFO @ Tue, 16 Jun 2020 07:56:55: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:56:55: #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 07:56:56: #1 tags after filtering in treatment: 5502858 INFO @ Tue, 16 Jun 2020 07:56:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:56:56: #1 finished! INFO @ Tue, 16 Jun 2020 07:56:56: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:56:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:56:56: #2 number of paired peaks: 890 WARNING @ Tue, 16 Jun 2020 07:56:56: Fewer paired peaks (890) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 890 pairs to build model! INFO @ Tue, 16 Jun 2020 07:56:56: start model_add_line... INFO @ Tue, 16 Jun 2020 07:56:56: start X-correlation... INFO @ Tue, 16 Jun 2020 07:56:56: end of X-cor INFO @ Tue, 16 Jun 2020 07:56:56: #2 finished! INFO @ Tue, 16 Jun 2020 07:56:56: #2 predicted fragment length is 181 bps INFO @ Tue, 16 Jun 2020 07:56:56: #2 alternative fragment length(s) may be 181 bps INFO @ Tue, 16 Jun 2020 07:56:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX216759/SRX216759.10_model.r INFO @ Tue, 16 Jun 2020 07:56:56: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:56:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:56:59: 1000000 INFO @ Tue, 16 Jun 2020 07:57:05: 2000000 INFO @ Tue, 16 Jun 2020 07:57:11: 3000000 INFO @ Tue, 16 Jun 2020 07:57:11: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:57:17: 4000000 INFO @ Tue, 16 Jun 2020 07:57:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX216759/SRX216759.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:57:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX216759/SRX216759.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:57:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX216759/SRX216759.10_summits.bed INFO @ Tue, 16 Jun 2020 07:57:19: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1538 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:57:22: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:57:25: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 07:57:25: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 07:57:25: #1 total tags in treatment: 5502858 INFO @ Tue, 16 Jun 2020 07:57:25: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:57:25: #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 07:57:25: #1 tags after filtering in treatment: 5502858 INFO @ Tue, 16 Jun 2020 07:57:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:57:25: #1 finished! INFO @ Tue, 16 Jun 2020 07:57:25: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:57:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:57:26: #2 number of paired peaks: 890 WARNING @ Tue, 16 Jun 2020 07:57:26: Fewer paired peaks (890) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 890 pairs to build model! INFO @ Tue, 16 Jun 2020 07:57:26: start model_add_line... INFO @ Tue, 16 Jun 2020 07:57:26: start X-correlation... INFO @ Tue, 16 Jun 2020 07:57:26: end of X-cor INFO @ Tue, 16 Jun 2020 07:57:26: #2 finished! INFO @ Tue, 16 Jun 2020 07:57:26: #2 predicted fragment length is 181 bps INFO @ Tue, 16 Jun 2020 07:57:26: #2 alternative fragment length(s) may be 181 bps INFO @ Tue, 16 Jun 2020 07:57:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX216759/SRX216759.20_model.r INFO @ Tue, 16 Jun 2020 07:57:26: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:57:26: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:57:40: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:57:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX216759/SRX216759.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:57:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX216759/SRX216759.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:57:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX216759/SRX216759.20_summits.bed INFO @ Tue, 16 Jun 2020 07:57:46: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (577 records, 4 fields): 1 millis CompletedMACS2peakCalling