Job ID = 6367609 SRX = SRX335101 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:32:50 prefetch.2.10.7: 1) Downloading 'SRR952379'... 2020-06-15T23:32:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:35:19 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:35:19 prefetch.2.10.7: 'SRR952379' is valid 2020-06-15T23:35:19 prefetch.2.10.7: 1) 'SRR952379' was downloaded successfully Read 13765284 spots for SRR952379/SRR952379.sra Written 13765284 spots for SRR952379/SRR952379.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: 00:02:10 13765284 reads; of these: 13765284 (100.00%) were unpaired; of these: 1746027 (12.68%) aligned 0 times 10019788 (72.79%) aligned exactly 1 time 1999469 (14.53%) aligned >1 times 87.32% overall alignment rate Time searching: 00:02:10 Overall time: 00:02:10 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] 2639457 / 12019257 = 0.2196 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 08:40:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX335101/SRX335101.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX335101/SRX335101.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX335101/SRX335101.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX335101/SRX335101.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 08:40:46: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:40:46: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:40:52: 1000000 INFO @ Tue, 16 Jun 2020 08:40:57: 2000000 INFO @ Tue, 16 Jun 2020 08:41:02: 3000000 INFO @ Tue, 16 Jun 2020 08:41:07: 4000000 INFO @ Tue, 16 Jun 2020 08:41:12: 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 08:41:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX335101/SRX335101.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX335101/SRX335101.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX335101/SRX335101.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX335101/SRX335101.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 08:41:16: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:41:16: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:41:17: 6000000 INFO @ Tue, 16 Jun 2020 08:41:22: 1000000 INFO @ Tue, 16 Jun 2020 08:41:23: 7000000 INFO @ Tue, 16 Jun 2020 08:41:28: 2000000 INFO @ Tue, 16 Jun 2020 08:41:29: 8000000 INFO @ Tue, 16 Jun 2020 08:41:34: 3000000 INFO @ Tue, 16 Jun 2020 08:41:35: 9000000 INFO @ Tue, 16 Jun 2020 08:41:37: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 08:41:37: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 08:41:37: #1 total tags in treatment: 9379800 INFO @ Tue, 16 Jun 2020 08:41:37: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:41:37: #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 08:41:37: #1 tags after filtering in treatment: 9379800 INFO @ Tue, 16 Jun 2020 08:41:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:41:37: #1 finished! INFO @ Tue, 16 Jun 2020 08:41:37: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:41:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:41:37: #2 number of paired peaks: 977 WARNING @ Tue, 16 Jun 2020 08:41:37: Fewer paired peaks (977) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 977 pairs to build model! INFO @ Tue, 16 Jun 2020 08:41:37: start model_add_line... INFO @ Tue, 16 Jun 2020 08:41:38: start X-correlation... INFO @ Tue, 16 Jun 2020 08:41:38: end of X-cor INFO @ Tue, 16 Jun 2020 08:41:38: #2 finished! INFO @ Tue, 16 Jun 2020 08:41:38: #2 predicted fragment length is 146 bps INFO @ Tue, 16 Jun 2020 08:41:38: #2 alternative fragment length(s) may be 146 bps INFO @ Tue, 16 Jun 2020 08:41:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX335101/SRX335101.05_model.r INFO @ Tue, 16 Jun 2020 08:41:38: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:41:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:41:39: 4000000 INFO @ Tue, 16 Jun 2020 08:41:44: 5000000 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 08:41:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX335101/SRX335101.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX335101/SRX335101.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX335101/SRX335101.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX335101/SRX335101.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 08:41:46: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:41:46: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:41:50: 6000000 INFO @ Tue, 16 Jun 2020 08:41:53: 1000000 INFO @ Tue, 16 Jun 2020 08:41:56: 7000000 INFO @ Tue, 16 Jun 2020 08:41:59: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:41:59: 2000000 INFO @ Tue, 16 Jun 2020 08:42:02: 8000000 INFO @ Tue, 16 Jun 2020 08:42:05: 3000000 INFO @ Tue, 16 Jun 2020 08:42:08: 9000000 INFO @ Tue, 16 Jun 2020 08:42:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX335101/SRX335101.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:42:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX335101/SRX335101.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:42:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX335101/SRX335101.05_summits.bed INFO @ Tue, 16 Jun 2020 08:42:10: Done! INFO @ Tue, 16 Jun 2020 08:42:10: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 08:42:10: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 08:42:10: #1 total tags in treatment: 9379800 INFO @ Tue, 16 Jun 2020 08:42:10: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:42:10: #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 08:42:11: #1 tags after filtering in treatment: 9379800 INFO @ Tue, 16 Jun 2020 08:42:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:42:11: #1 finished! INFO @ Tue, 16 Jun 2020 08:42:11: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:42:11: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (5266 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:42:11: 4000000 INFO @ Tue, 16 Jun 2020 08:42:11: #2 number of paired peaks: 977 WARNING @ Tue, 16 Jun 2020 08:42:11: Fewer paired peaks (977) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 977 pairs to build model! INFO @ Tue, 16 Jun 2020 08:42:11: start model_add_line... INFO @ Tue, 16 Jun 2020 08:42:11: start X-correlation... INFO @ Tue, 16 Jun 2020 08:42:11: end of X-cor INFO @ Tue, 16 Jun 2020 08:42:11: #2 finished! INFO @ Tue, 16 Jun 2020 08:42:11: #2 predicted fragment length is 146 bps INFO @ Tue, 16 Jun 2020 08:42:11: #2 alternative fragment length(s) may be 146 bps INFO @ Tue, 16 Jun 2020 08:42:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX335101/SRX335101.10_model.r INFO @ Tue, 16 Jun 2020 08:42:11: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:42:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:42:17: 5000000 INFO @ Tue, 16 Jun 2020 08:42:22: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:42:28: 7000000 INFO @ Tue, 16 Jun 2020 08:42:33: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:42:34: 8000000 INFO @ Tue, 16 Jun 2020 08:42:39: 9000000 INFO @ Tue, 16 Jun 2020 08:42:41: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 08:42:41: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 08:42:41: #1 total tags in treatment: 9379800 INFO @ Tue, 16 Jun 2020 08:42:41: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:42:41: #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 08:42:41: #1 tags after filtering in treatment: 9379800 INFO @ Tue, 16 Jun 2020 08:42:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:42:41: #1 finished! INFO @ Tue, 16 Jun 2020 08:42:41: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:42:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:42:42: #2 number of paired peaks: 977 WARNING @ Tue, 16 Jun 2020 08:42:42: Fewer paired peaks (977) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 977 pairs to build model! INFO @ Tue, 16 Jun 2020 08:42:42: start model_add_line... INFO @ Tue, 16 Jun 2020 08:42:42: start X-correlation... INFO @ Tue, 16 Jun 2020 08:42:42: end of X-cor INFO @ Tue, 16 Jun 2020 08:42:42: #2 finished! INFO @ Tue, 16 Jun 2020 08:42:42: #2 predicted fragment length is 146 bps INFO @ Tue, 16 Jun 2020 08:42:42: #2 alternative fragment length(s) may be 146 bps INFO @ Tue, 16 Jun 2020 08:42:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX335101/SRX335101.20_model.r INFO @ Tue, 16 Jun 2020 08:42:42: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:42:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:42:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX335101/SRX335101.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:42:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX335101/SRX335101.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:42:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX335101/SRX335101.10_summits.bed INFO @ Tue, 16 Jun 2020 08:42:44: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3853 records, 4 fields): 5 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:43:03: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:43:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX335101/SRX335101.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:43:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX335101/SRX335101.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:43:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX335101/SRX335101.20_summits.bed INFO @ Tue, 16 Jun 2020 08:43:14: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2561 records, 4 fields): 3 millis CompletedMACS2peakCalling