Job ID = 6367564 SRX = SRX331320 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:30:05 prefetch.2.10.7: 1) Downloading 'SRR947557'... 2020-06-15T23:30:05 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:30:35 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:30:35 prefetch.2.10.7: 'SRR947557' is valid 2020-06-15T23:30:35 prefetch.2.10.7: 1) 'SRR947557' was downloaded successfully Read 4321007 spots for SRR947557/SRR947557.sra Written 4321007 spots for SRR947557/SRR947557.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: 00:00:37 4321007 reads; of these: 4321007 (100.00%) were unpaired; of these: 740976 (17.15%) aligned 0 times 2949258 (68.25%) aligned exactly 1 time 630773 (14.60%) aligned >1 times 82.85% overall alignment rate Time searching: 00:00:37 Overall time: 00:00:37 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] 563954 / 3580031 = 0.1575 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 08:32:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331320/SRX331320.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331320/SRX331320.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331320/SRX331320.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331320/SRX331320.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 08:32:33: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:32:33: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:32:40: 1000000 INFO @ Tue, 16 Jun 2020 08:32:46: 2000000 INFO @ Tue, 16 Jun 2020 08:32:53: 3000000 INFO @ Tue, 16 Jun 2020 08:32:53: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:32:53: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:32:53: #1 total tags in treatment: 3016077 INFO @ Tue, 16 Jun 2020 08:32:53: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:32:53: #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 08:32:53: #1 tags after filtering in treatment: 3016077 INFO @ Tue, 16 Jun 2020 08:32:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:32:53: #1 finished! INFO @ Tue, 16 Jun 2020 08:32:53: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:32:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:32:53: #2 number of paired peaks: 438 WARNING @ Tue, 16 Jun 2020 08:32:53: Fewer paired peaks (438) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 438 pairs to build model! INFO @ Tue, 16 Jun 2020 08:32:53: start model_add_line... INFO @ Tue, 16 Jun 2020 08:32:53: start X-correlation... INFO @ Tue, 16 Jun 2020 08:32:53: end of X-cor INFO @ Tue, 16 Jun 2020 08:32:53: #2 finished! INFO @ Tue, 16 Jun 2020 08:32:53: #2 predicted fragment length is 95 bps INFO @ Tue, 16 Jun 2020 08:32:53: #2 alternative fragment length(s) may be 39,95,572 bps INFO @ Tue, 16 Jun 2020 08:32:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331320/SRX331320.05_model.r INFO @ Tue, 16 Jun 2020 08:32:53: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:32:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:33:00: #3 Call peaks for each chromosome... 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 08:33:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331320/SRX331320.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331320/SRX331320.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331320/SRX331320.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331320/SRX331320.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 08:33:03: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:33:03: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:33:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331320/SRX331320.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:33:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331320/SRX331320.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:33:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331320/SRX331320.05_summits.bed INFO @ Tue, 16 Jun 2020 08:33:04: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (583 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:33:08: 1000000 INFO @ Tue, 16 Jun 2020 08:33:14: 2000000 INFO @ Tue, 16 Jun 2020 08:33:19: 3000000 INFO @ Tue, 16 Jun 2020 08:33:19: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:33:19: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:33:19: #1 total tags in treatment: 3016077 INFO @ Tue, 16 Jun 2020 08:33:19: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:33:19: #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 08:33:19: #1 tags after filtering in treatment: 3016077 INFO @ Tue, 16 Jun 2020 08:33:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:33:19: #1 finished! INFO @ Tue, 16 Jun 2020 08:33:19: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:33:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:33:20: #2 number of paired peaks: 438 WARNING @ Tue, 16 Jun 2020 08:33:20: Fewer paired peaks (438) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 438 pairs to build model! INFO @ Tue, 16 Jun 2020 08:33:20: start model_add_line... INFO @ Tue, 16 Jun 2020 08:33:20: start X-correlation... INFO @ Tue, 16 Jun 2020 08:33:20: end of X-cor INFO @ Tue, 16 Jun 2020 08:33:20: #2 finished! INFO @ Tue, 16 Jun 2020 08:33:20: #2 predicted fragment length is 95 bps INFO @ Tue, 16 Jun 2020 08:33:20: #2 alternative fragment length(s) may be 39,95,572 bps INFO @ Tue, 16 Jun 2020 08:33:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331320/SRX331320.10_model.r INFO @ Tue, 16 Jun 2020 08:33:20: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:33:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:33:27: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:33:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331320/SRX331320.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:33:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331320/SRX331320.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:33:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331320/SRX331320.10_summits.bed INFO @ Tue, 16 Jun 2020 08:33:30: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (321 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 @ Tue, 16 Jun 2020 08:33:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331320/SRX331320.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331320/SRX331320.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331320/SRX331320.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331320/SRX331320.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 08:33:33: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:33:33: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:33:38: 1000000 INFO @ Tue, 16 Jun 2020 08:33:44: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:33:49: 3000000 INFO @ Tue, 16 Jun 2020 08:33:49: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:33:49: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:33:49: #1 total tags in treatment: 3016077 INFO @ Tue, 16 Jun 2020 08:33:49: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:33:49: #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 08:33:49: #1 tags after filtering in treatment: 3016077 INFO @ Tue, 16 Jun 2020 08:33:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:33:49: #1 finished! INFO @ Tue, 16 Jun 2020 08:33:49: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:33:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:33:49: #2 number of paired peaks: 438 WARNING @ Tue, 16 Jun 2020 08:33:49: Fewer paired peaks (438) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 438 pairs to build model! INFO @ Tue, 16 Jun 2020 08:33:49: start model_add_line... INFO @ Tue, 16 Jun 2020 08:33:49: start X-correlation... INFO @ Tue, 16 Jun 2020 08:33:49: end of X-cor INFO @ Tue, 16 Jun 2020 08:33:49: #2 finished! INFO @ Tue, 16 Jun 2020 08:33:49: #2 predicted fragment length is 95 bps INFO @ Tue, 16 Jun 2020 08:33:49: #2 alternative fragment length(s) may be 39,95,572 bps INFO @ Tue, 16 Jun 2020 08:33:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331320/SRX331320.20_model.r INFO @ Tue, 16 Jun 2020 08:33:49: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:33:49: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:33:56: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:34:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331320/SRX331320.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:34:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331320/SRX331320.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:34:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331320/SRX331320.20_summits.bed INFO @ Tue, 16 Jun 2020 08:34:00: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (128 records, 4 fields): 1 millis CompletedMACS2peakCalling