Job ID = 6366355 SRX = SRX120287 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:51:26 prefetch.2.10.7: 1) Downloading 'SRR408773'... 2020-06-15T22:51:26 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:51:51 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:51:51 prefetch.2.10.7: 'SRR408773' is valid 2020-06-15T22:51:51 prefetch.2.10.7: 1) 'SRR408773' was downloaded successfully Read 6005290 spots for SRR408773/SRR408773.sra Written 6005290 spots for SRR408773/SRR408773.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: 00:00:43 6005290 reads; of these: 6005290 (100.00%) were unpaired; of these: 2474278 (41.20%) aligned 0 times 2972171 (49.49%) aligned exactly 1 time 558841 (9.31%) aligned >1 times 58.80% overall alignment rate Time searching: 00:00:43 Overall time: 00:00:43 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] 177174 / 3531012 = 0.0502 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 07:54:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX120287/SRX120287.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX120287/SRX120287.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX120287/SRX120287.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX120287/SRX120287.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 07:54:14: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:54:14: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:54:20: 1000000 INFO @ Tue, 16 Jun 2020 07:54:27: 2000000 INFO @ Tue, 16 Jun 2020 07:54:33: 3000000 INFO @ Tue, 16 Jun 2020 07:54:35: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:54:35: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:54:35: #1 total tags in treatment: 3353838 INFO @ Tue, 16 Jun 2020 07:54:35: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:54:35: #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 07:54:35: #1 tags after filtering in treatment: 3353838 INFO @ Tue, 16 Jun 2020 07:54:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:54:35: #1 finished! INFO @ Tue, 16 Jun 2020 07:54:35: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:54:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:54:36: #2 number of paired peaks: 509 WARNING @ Tue, 16 Jun 2020 07:54:36: Fewer paired peaks (509) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 509 pairs to build model! INFO @ Tue, 16 Jun 2020 07:54:36: start model_add_line... INFO @ Tue, 16 Jun 2020 07:54:36: start X-correlation... INFO @ Tue, 16 Jun 2020 07:54:36: end of X-cor INFO @ Tue, 16 Jun 2020 07:54:36: #2 finished! INFO @ Tue, 16 Jun 2020 07:54:36: #2 predicted fragment length is 96 bps INFO @ Tue, 16 Jun 2020 07:54:36: #2 alternative fragment length(s) may be 96 bps INFO @ Tue, 16 Jun 2020 07:54:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX120287/SRX120287.05_model.r INFO @ Tue, 16 Jun 2020 07:54:36: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:54:36: #3 Pre-compute pvalue-qvalue table... 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 07:54:43: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:54:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX120287/SRX120287.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX120287/SRX120287.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX120287/SRX120287.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX120287/SRX120287.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 07:54:44: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:54:44: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:54:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX120287/SRX120287.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:54:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX120287/SRX120287.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:54:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX120287/SRX120287.05_summits.bed INFO @ Tue, 16 Jun 2020 07:54:47: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1251 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:54:49: 1000000 INFO @ Tue, 16 Jun 2020 07:54:55: 2000000 INFO @ Tue, 16 Jun 2020 07:55:00: 3000000 INFO @ Tue, 16 Jun 2020 07:55:02: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:55:02: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:55:02: #1 total tags in treatment: 3353838 INFO @ Tue, 16 Jun 2020 07:55:02: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:55:02: #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 07:55:02: #1 tags after filtering in treatment: 3353838 INFO @ Tue, 16 Jun 2020 07:55:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:55:02: #1 finished! INFO @ Tue, 16 Jun 2020 07:55:02: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:55:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:55:02: #2 number of paired peaks: 509 WARNING @ Tue, 16 Jun 2020 07:55:02: Fewer paired peaks (509) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 509 pairs to build model! INFO @ Tue, 16 Jun 2020 07:55:02: start model_add_line... INFO @ Tue, 16 Jun 2020 07:55:02: start X-correlation... INFO @ Tue, 16 Jun 2020 07:55:02: end of X-cor INFO @ Tue, 16 Jun 2020 07:55:02: #2 finished! INFO @ Tue, 16 Jun 2020 07:55:02: #2 predicted fragment length is 96 bps INFO @ Tue, 16 Jun 2020 07:55:02: #2 alternative fragment length(s) may be 96 bps INFO @ Tue, 16 Jun 2020 07:55:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX120287/SRX120287.10_model.r INFO @ Tue, 16 Jun 2020 07:55:02: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:55:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:55:10: #3 Call peaks for each chromosome... 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 07:55:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX120287/SRX120287.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX120287/SRX120287.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX120287/SRX120287.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX120287/SRX120287.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 07:55:14: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:55:14: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:55:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX120287/SRX120287.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:55:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX120287/SRX120287.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:55:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX120287/SRX120287.10_summits.bed INFO @ Tue, 16 Jun 2020 07:55:14: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (530 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:55:20: 1000000 INFO @ Tue, 16 Jun 2020 07:55:26: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:55:33: 3000000 INFO @ Tue, 16 Jun 2020 07:55:35: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:55:35: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:55:35: #1 total tags in treatment: 3353838 INFO @ Tue, 16 Jun 2020 07:55:35: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:55:35: #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 07:55:35: #1 tags after filtering in treatment: 3353838 INFO @ Tue, 16 Jun 2020 07:55:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:55:35: #1 finished! INFO @ Tue, 16 Jun 2020 07:55:35: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:55:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:55:35: #2 number of paired peaks: 509 WARNING @ Tue, 16 Jun 2020 07:55:35: Fewer paired peaks (509) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 509 pairs to build model! INFO @ Tue, 16 Jun 2020 07:55:35: start model_add_line... INFO @ Tue, 16 Jun 2020 07:55:35: start X-correlation... INFO @ Tue, 16 Jun 2020 07:55:35: end of X-cor INFO @ Tue, 16 Jun 2020 07:55:35: #2 finished! INFO @ Tue, 16 Jun 2020 07:55:35: #2 predicted fragment length is 96 bps INFO @ Tue, 16 Jun 2020 07:55:35: #2 alternative fragment length(s) may be 96 bps INFO @ Tue, 16 Jun 2020 07:55:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX120287/SRX120287.20_model.r INFO @ Tue, 16 Jun 2020 07:55:35: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:55:35: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:55:43: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:55:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX120287/SRX120287.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:55:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX120287/SRX120287.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:55:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX120287/SRX120287.20_summits.bed INFO @ Tue, 16 Jun 2020 07:55:47: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (155 records, 4 fields): 1 millis CompletedMACS2peakCalling