Job ID = 6507920 SRX = SRX495016 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T13:28:18 prefetch.2.10.7: 1) Downloading 'SRR1198548'... 2020-06-26T13:28:18 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:29:22 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:29:23 prefetch.2.10.7: 'SRR1198548' is valid 2020-06-26T13:29:23 prefetch.2.10.7: 1) 'SRR1198548' was downloaded successfully Read 10976216 spots for SRR1198548/SRR1198548.sra Written 10976216 spots for SRR1198548/SRR1198548.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: 00:00:46 10976216 reads; of these: 10976216 (100.00%) were unpaired; of these: 9295974 (84.69%) aligned 0 times 1373800 (12.52%) aligned exactly 1 time 306442 (2.79%) aligned >1 times 15.31% overall alignment rate Time searching: 00:00:46 Overall time: 00:00:46 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] 305770 / 1680242 = 0.1820 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 @ Fri, 26 Jun 2020 22:31:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495016/SRX495016.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495016/SRX495016.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495016/SRX495016.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495016/SRX495016.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 @ Fri, 26 Jun 2020 22:31:35: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:31:35: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:31:41: 1000000 INFO @ Fri, 26 Jun 2020 22:31:43: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 22:31:43: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 22:31:43: #1 total tags in treatment: 1374472 INFO @ Fri, 26 Jun 2020 22:31:43: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:31:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:31:43: #1 tags after filtering in treatment: 1374472 INFO @ Fri, 26 Jun 2020 22:31:43: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:31:43: #1 finished! INFO @ Fri, 26 Jun 2020 22:31:43: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:31:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:31:43: #2 number of paired peaks: 662 WARNING @ Fri, 26 Jun 2020 22:31:43: Fewer paired peaks (662) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 662 pairs to build model! INFO @ Fri, 26 Jun 2020 22:31:43: start model_add_line... INFO @ Fri, 26 Jun 2020 22:31:43: start X-correlation... INFO @ Fri, 26 Jun 2020 22:31:43: end of X-cor INFO @ Fri, 26 Jun 2020 22:31:43: #2 finished! INFO @ Fri, 26 Jun 2020 22:31:43: #2 predicted fragment length is 93 bps INFO @ Fri, 26 Jun 2020 22:31:43: #2 alternative fragment length(s) may be 93 bps INFO @ Fri, 26 Jun 2020 22:31:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495016/SRX495016.05_model.r INFO @ Fri, 26 Jun 2020 22:31:43: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:31:43: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:31:46: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:31:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495016/SRX495016.05_peaks.xls INFO @ Fri, 26 Jun 2020 22:31:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495016/SRX495016.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:31:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495016/SRX495016.05_summits.bed INFO @ Fri, 26 Jun 2020 22:31:48: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (697 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 @ Fri, 26 Jun 2020 22:32:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495016/SRX495016.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495016/SRX495016.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495016/SRX495016.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495016/SRX495016.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 @ Fri, 26 Jun 2020 22:32:05: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:32:05: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:32:11: 1000000 INFO @ Fri, 26 Jun 2020 22:32:13: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 22:32:13: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 22:32:13: #1 total tags in treatment: 1374472 INFO @ Fri, 26 Jun 2020 22:32:13: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:32:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:32:13: #1 tags after filtering in treatment: 1374472 INFO @ Fri, 26 Jun 2020 22:32:13: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:32:13: #1 finished! INFO @ Fri, 26 Jun 2020 22:32:13: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:32:13: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:32:13: #2 number of paired peaks: 662 WARNING @ Fri, 26 Jun 2020 22:32:13: Fewer paired peaks (662) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 662 pairs to build model! INFO @ Fri, 26 Jun 2020 22:32:13: start model_add_line... INFO @ Fri, 26 Jun 2020 22:32:13: start X-correlation... INFO @ Fri, 26 Jun 2020 22:32:13: end of X-cor INFO @ Fri, 26 Jun 2020 22:32:13: #2 finished! INFO @ Fri, 26 Jun 2020 22:32:13: #2 predicted fragment length is 93 bps INFO @ Fri, 26 Jun 2020 22:32:13: #2 alternative fragment length(s) may be 93 bps INFO @ Fri, 26 Jun 2020 22:32:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495016/SRX495016.10_model.r INFO @ Fri, 26 Jun 2020 22:32:13: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:32:13: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:32:16: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:32:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495016/SRX495016.10_peaks.xls INFO @ Fri, 26 Jun 2020 22:32:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495016/SRX495016.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:32:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495016/SRX495016.10_summits.bed INFO @ Fri, 26 Jun 2020 22:32:18: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (290 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 @ Fri, 26 Jun 2020 22:32:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495016/SRX495016.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495016/SRX495016.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495016/SRX495016.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495016/SRX495016.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 @ Fri, 26 Jun 2020 22:32:35: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:32:35: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:32:41: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 22:32:43: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 22:32:43: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 22:32:43: #1 total tags in treatment: 1374472 INFO @ Fri, 26 Jun 2020 22:32:43: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:32:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:32:43: #1 tags after filtering in treatment: 1374472 INFO @ Fri, 26 Jun 2020 22:32:43: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:32:43: #1 finished! INFO @ Fri, 26 Jun 2020 22:32:43: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:32:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:32:43: #2 number of paired peaks: 662 WARNING @ Fri, 26 Jun 2020 22:32:43: Fewer paired peaks (662) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 662 pairs to build model! INFO @ Fri, 26 Jun 2020 22:32:43: start model_add_line... INFO @ Fri, 26 Jun 2020 22:32:43: start X-correlation... INFO @ Fri, 26 Jun 2020 22:32:43: end of X-cor INFO @ Fri, 26 Jun 2020 22:32:43: #2 finished! INFO @ Fri, 26 Jun 2020 22:32:43: #2 predicted fragment length is 93 bps INFO @ Fri, 26 Jun 2020 22:32:43: #2 alternative fragment length(s) may be 93 bps INFO @ Fri, 26 Jun 2020 22:32:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495016/SRX495016.20_model.r INFO @ Fri, 26 Jun 2020 22:32:43: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:32:43: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 22:32:46: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:32:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495016/SRX495016.20_peaks.xls INFO @ Fri, 26 Jun 2020 22:32:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495016/SRX495016.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:32:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495016/SRX495016.20_summits.bed INFO @ Fri, 26 Jun 2020 22:32:48: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (88 records, 4 fields): 1 millis CompletedMACS2peakCalling