Job ID = 6366908 SRX = SRX257653 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:05:53 prefetch.2.10.7: 1) Downloading 'SRR800664'... 2020-06-15T23:05:53 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:06:45 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:06:46 prefetch.2.10.7: 'SRR800664' is valid 2020-06-15T23:06:46 prefetch.2.10.7: 1) 'SRR800664' was downloaded successfully Read 12762765 spots for SRR800664/SRR800664.sra Written 12762765 spots for SRR800664/SRR800664.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: 00:02:17 12762765 reads; of these: 12762765 (100.00%) were unpaired; of these: 981019 (7.69%) aligned 0 times 9881884 (77.43%) aligned exactly 1 time 1899862 (14.89%) aligned >1 times 92.31% overall alignment rate Time searching: 00:02:17 Overall time: 00:02:17 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] 3868690 / 11781746 = 0.3284 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 08:12:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257653/SRX257653.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257653/SRX257653.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257653/SRX257653.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257653/SRX257653.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 08:12:29: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:12:29: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:12:36: 1000000 INFO @ Tue, 16 Jun 2020 08:12:43: 2000000 INFO @ Tue, 16 Jun 2020 08:12:50: 3000000 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 08:12:57: 4000000 INFO @ Tue, 16 Jun 2020 08:12:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257653/SRX257653.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257653/SRX257653.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257653/SRX257653.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257653/SRX257653.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 08:12:59: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:12:59: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:13:04: 5000000 INFO @ Tue, 16 Jun 2020 08:13:07: 1000000 INFO @ Tue, 16 Jun 2020 08:13:12: 6000000 INFO @ Tue, 16 Jun 2020 08:13:14: 2000000 INFO @ Tue, 16 Jun 2020 08:13:20: 7000000 INFO @ Tue, 16 Jun 2020 08:13:22: 3000000 INFO @ Tue, 16 Jun 2020 08:13:26: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 08:13:26: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 08:13:26: #1 total tags in treatment: 7913056 INFO @ Tue, 16 Jun 2020 08:13:26: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:13:26: #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 08:13:26: #1 tags after filtering in treatment: 7913056 INFO @ Tue, 16 Jun 2020 08:13:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:13:26: #1 finished! INFO @ Tue, 16 Jun 2020 08:13:26: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:13:26: #2 looking for paired plus/minus strand peaks... 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 08:13:27: #2 number of paired peaks: 529 WARNING @ Tue, 16 Jun 2020 08:13:27: Fewer paired peaks (529) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 529 pairs to build model! INFO @ Tue, 16 Jun 2020 08:13:27: start model_add_line... INFO @ Tue, 16 Jun 2020 08:13:27: start X-correlation... INFO @ Tue, 16 Jun 2020 08:13:27: end of X-cor INFO @ Tue, 16 Jun 2020 08:13:27: #2 finished! INFO @ Tue, 16 Jun 2020 08:13:27: #2 predicted fragment length is 136 bps INFO @ Tue, 16 Jun 2020 08:13:27: #2 alternative fragment length(s) may be 136 bps INFO @ Tue, 16 Jun 2020 08:13:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257653/SRX257653.05_model.r INFO @ Tue, 16 Jun 2020 08:13:27: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:13:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:13:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257653/SRX257653.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257653/SRX257653.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257653/SRX257653.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257653/SRX257653.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 08:13:29: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:13:29: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:13:29: 4000000 INFO @ Tue, 16 Jun 2020 08:13:35: 1000000 INFO @ Tue, 16 Jun 2020 08:13:37: 5000000 INFO @ Tue, 16 Jun 2020 08:13:42: 2000000 INFO @ Tue, 16 Jun 2020 08:13:44: 6000000 INFO @ Tue, 16 Jun 2020 08:13:45: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:13:49: 3000000 INFO @ Tue, 16 Jun 2020 08:13:52: 7000000 INFO @ Tue, 16 Jun 2020 08:13:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257653/SRX257653.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:13:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257653/SRX257653.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:13:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257653/SRX257653.05_summits.bed INFO @ Tue, 16 Jun 2020 08:13:54: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1611 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:13:55: 4000000 INFO @ Tue, 16 Jun 2020 08:13:59: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 08:13:59: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 08:13:59: #1 total tags in treatment: 7913056 INFO @ Tue, 16 Jun 2020 08:13:59: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:13:59: #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 08:13:59: #1 tags after filtering in treatment: 7913056 INFO @ Tue, 16 Jun 2020 08:13:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:13:59: #1 finished! INFO @ Tue, 16 Jun 2020 08:13:59: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:13:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:13:59: #2 number of paired peaks: 529 WARNING @ Tue, 16 Jun 2020 08:13:59: Fewer paired peaks (529) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 529 pairs to build model! INFO @ Tue, 16 Jun 2020 08:13:59: start model_add_line... INFO @ Tue, 16 Jun 2020 08:13:59: start X-correlation... INFO @ Tue, 16 Jun 2020 08:13:59: end of X-cor INFO @ Tue, 16 Jun 2020 08:13:59: #2 finished! INFO @ Tue, 16 Jun 2020 08:13:59: #2 predicted fragment length is 136 bps INFO @ Tue, 16 Jun 2020 08:13:59: #2 alternative fragment length(s) may be 136 bps INFO @ Tue, 16 Jun 2020 08:13:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257653/SRX257653.10_model.r INFO @ Tue, 16 Jun 2020 08:13:59: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:13:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:14:01: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:14:07: 6000000 INFO @ Tue, 16 Jun 2020 08:14:13: 7000000 INFO @ Tue, 16 Jun 2020 08:14:17: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:14:18: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 08:14:18: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 08:14:18: #1 total tags in treatment: 7913056 INFO @ Tue, 16 Jun 2020 08:14:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:14:18: #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 08:14:18: #1 tags after filtering in treatment: 7913056 INFO @ Tue, 16 Jun 2020 08:14:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:14:18: #1 finished! INFO @ Tue, 16 Jun 2020 08:14:18: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:14:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:14:18: #2 number of paired peaks: 529 WARNING @ Tue, 16 Jun 2020 08:14:18: Fewer paired peaks (529) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 529 pairs to build model! INFO @ Tue, 16 Jun 2020 08:14:18: start model_add_line... INFO @ Tue, 16 Jun 2020 08:14:18: start X-correlation... INFO @ Tue, 16 Jun 2020 08:14:18: end of X-cor INFO @ Tue, 16 Jun 2020 08:14:18: #2 finished! INFO @ Tue, 16 Jun 2020 08:14:18: #2 predicted fragment length is 136 bps INFO @ Tue, 16 Jun 2020 08:14:18: #2 alternative fragment length(s) may be 136 bps INFO @ Tue, 16 Jun 2020 08:14:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257653/SRX257653.20_model.r INFO @ Tue, 16 Jun 2020 08:14:18: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:14:18: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:14:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257653/SRX257653.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:14:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257653/SRX257653.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:14:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257653/SRX257653.10_summits.bed INFO @ Tue, 16 Jun 2020 08:14:26: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (861 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:14:35: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:14:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257653/SRX257653.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:14:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257653/SRX257653.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:14:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257653/SRX257653.20_summits.bed INFO @ Tue, 16 Jun 2020 08:14:43: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (433 records, 4 fields): 6 millis CompletedMACS2peakCalling