Job ID = 6507928 SRX = SRX495023 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T13:41:00 prefetch.2.10.7: 1) Downloading 'SRR1198555'... 2020-06-26T13:41:00 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:43:20 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:43:21 prefetch.2.10.7: 'SRR1198555' is valid 2020-06-26T13:43:21 prefetch.2.10.7: 1) 'SRR1198555' was downloaded successfully Read 17440591 spots for SRR1198555/SRR1198555.sra Written 17440591 spots for SRR1198555/SRR1198555.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: 00:03:00 17440591 reads; of these: 17440591 (100.00%) were unpaired; of these: 2955605 (16.95%) aligned 0 times 11863375 (68.02%) aligned exactly 1 time 2621611 (15.03%) aligned >1 times 83.05% overall alignment rate Time searching: 00:03:00 Overall time: 00:03:00 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] 9965639 / 14484986 = 0.6880 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 22:49:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495023/SRX495023.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495023/SRX495023.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495023/SRX495023.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495023/SRX495023.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 22:49:57: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:49:57: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:50:02: 1000000 INFO @ Fri, 26 Jun 2020 22:50:07: 2000000 INFO @ Fri, 26 Jun 2020 22:50:12: 3000000 INFO @ Fri, 26 Jun 2020 22:50:17: 4000000 INFO @ Fri, 26 Jun 2020 22:50:19: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 22:50:19: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 22:50:19: #1 total tags in treatment: 4519347 INFO @ Fri, 26 Jun 2020 22:50:19: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:50:19: #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 22:50:19: #1 tags after filtering in treatment: 4519347 INFO @ Fri, 26 Jun 2020 22:50:19: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:50:19: #1 finished! INFO @ Fri, 26 Jun 2020 22:50:19: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:50:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:50:20: #2 number of paired peaks: 858 WARNING @ Fri, 26 Jun 2020 22:50:20: Fewer paired peaks (858) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 858 pairs to build model! INFO @ Fri, 26 Jun 2020 22:50:20: start model_add_line... INFO @ Fri, 26 Jun 2020 22:50:20: start X-correlation... INFO @ Fri, 26 Jun 2020 22:50:20: end of X-cor INFO @ Fri, 26 Jun 2020 22:50:20: #2 finished! INFO @ Fri, 26 Jun 2020 22:50:20: #2 predicted fragment length is 123 bps INFO @ Fri, 26 Jun 2020 22:50:20: #2 alternative fragment length(s) may be 123 bps INFO @ Fri, 26 Jun 2020 22:50:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495023/SRX495023.05_model.r INFO @ Fri, 26 Jun 2020 22:50:20: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:50:20: #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 @ Fri, 26 Jun 2020 22:50:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495023/SRX495023.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495023/SRX495023.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495023/SRX495023.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495023/SRX495023.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 22:50:27: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:50:27: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:50:32: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:50:32: 1000000 INFO @ Fri, 26 Jun 2020 22:50:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495023/SRX495023.05_peaks.xls INFO @ Fri, 26 Jun 2020 22:50:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495023/SRX495023.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:50:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495023/SRX495023.05_summits.bed INFO @ Fri, 26 Jun 2020 22:50:37: 2000000 INFO @ Fri, 26 Jun 2020 22:50:37: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1934 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:50:42: 3000000 INFO @ Fri, 26 Jun 2020 22:50:47: 4000000 INFO @ Fri, 26 Jun 2020 22:50:50: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 22:50:50: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 22:50:50: #1 total tags in treatment: 4519347 INFO @ Fri, 26 Jun 2020 22:50:50: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:50:50: #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 22:50:50: #1 tags after filtering in treatment: 4519347 INFO @ Fri, 26 Jun 2020 22:50:50: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:50:50: #1 finished! INFO @ Fri, 26 Jun 2020 22:50:50: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:50:50: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:50:50: #2 number of paired peaks: 858 WARNING @ Fri, 26 Jun 2020 22:50:50: Fewer paired peaks (858) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 858 pairs to build model! INFO @ Fri, 26 Jun 2020 22:50:50: start model_add_line... INFO @ Fri, 26 Jun 2020 22:50:50: start X-correlation... INFO @ Fri, 26 Jun 2020 22:50:50: end of X-cor INFO @ Fri, 26 Jun 2020 22:50:50: #2 finished! INFO @ Fri, 26 Jun 2020 22:50:50: #2 predicted fragment length is 123 bps INFO @ Fri, 26 Jun 2020 22:50:50: #2 alternative fragment length(s) may be 123 bps INFO @ Fri, 26 Jun 2020 22:50:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495023/SRX495023.10_model.r INFO @ Fri, 26 Jun 2020 22:50:50: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:50:50: #3 Pre-compute pvalue-qvalue table... 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 22:50:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495023/SRX495023.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495023/SRX495023.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495023/SRX495023.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495023/SRX495023.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 22:50:57: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:50:57: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:51:02: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:51:02: 1000000 INFO @ Fri, 26 Jun 2020 22:51:07: 2000000 INFO @ Fri, 26 Jun 2020 22:51:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495023/SRX495023.10_peaks.xls INFO @ Fri, 26 Jun 2020 22:51:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495023/SRX495023.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:51:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495023/SRX495023.10_summits.bed INFO @ Fri, 26 Jun 2020 22:51:07: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (930 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:51:12: 3000000 INFO @ Fri, 26 Jun 2020 22:51:17: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 22:51:19: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 22:51:19: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 22:51:19: #1 total tags in treatment: 4519347 INFO @ Fri, 26 Jun 2020 22:51:19: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:51:19: #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 22:51:19: #1 tags after filtering in treatment: 4519347 INFO @ Fri, 26 Jun 2020 22:51:19: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:51:19: #1 finished! INFO @ Fri, 26 Jun 2020 22:51:19: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:51:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:51:20: #2 number of paired peaks: 858 WARNING @ Fri, 26 Jun 2020 22:51:20: Fewer paired peaks (858) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 858 pairs to build model! INFO @ Fri, 26 Jun 2020 22:51:20: start model_add_line... INFO @ Fri, 26 Jun 2020 22:51:20: start X-correlation... INFO @ Fri, 26 Jun 2020 22:51:20: end of X-cor INFO @ Fri, 26 Jun 2020 22:51:20: #2 finished! INFO @ Fri, 26 Jun 2020 22:51:20: #2 predicted fragment length is 123 bps INFO @ Fri, 26 Jun 2020 22:51:20: #2 alternative fragment length(s) may be 123 bps INFO @ Fri, 26 Jun 2020 22:51:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495023/SRX495023.20_model.r INFO @ Fri, 26 Jun 2020 22:51:20: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:51:20: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 22:51:32: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:51:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495023/SRX495023.20_peaks.xls INFO @ Fri, 26 Jun 2020 22:51:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495023/SRX495023.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:51:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495023/SRX495023.20_summits.bed INFO @ Fri, 26 Jun 2020 22:51:37: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (396 records, 4 fields): 2 millis CompletedMACS2peakCalling