Job ID = 6368569 SRX = SRX5020795 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:20:51 prefetch.2.10.7: 1) Downloading 'SRR8201418'... 2020-06-16T00:20:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:21:42 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:21:42 prefetch.2.10.7: 'SRR8201418' is valid 2020-06-16T00:21:42 prefetch.2.10.7: 1) 'SRR8201418' was downloaded successfully 2020-06-16T00:21:42 prefetch.2.10.7: 'SRR8201418' has 0 unresolved dependencies Read 10236006 spots for SRR8201418/SRR8201418.sra Written 10236006 spots for SRR8201418/SRR8201418.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: 00:02:17 10236006 reads; of these: 10236006 (100.00%) were unpaired; of these: 560615 (5.48%) aligned 0 times 8356331 (81.64%) aligned exactly 1 time 1319060 (12.89%) aligned >1 times 94.52% overall alignment rate Time searching: 00:02:17 Overall time: 00:02:17 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] 586009 / 9675391 = 0.0606 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 09:27:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020795/SRX5020795.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020795/SRX5020795.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020795/SRX5020795.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020795/SRX5020795.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 09:27:18: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:27:18: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:27:23: 1000000 INFO @ Tue, 16 Jun 2020 09:27:27: 2000000 INFO @ Tue, 16 Jun 2020 09:27:31: 3000000 INFO @ Tue, 16 Jun 2020 09:27:36: 4000000 INFO @ Tue, 16 Jun 2020 09:27:40: 5000000 INFO @ Tue, 16 Jun 2020 09:27:45: 6000000 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 09:27:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020795/SRX5020795.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020795/SRX5020795.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020795/SRX5020795.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020795/SRX5020795.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 09:27:48: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:27:48: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:27:49: 7000000 INFO @ Tue, 16 Jun 2020 09:27:53: 1000000 INFO @ Tue, 16 Jun 2020 09:27:54: 8000000 INFO @ Tue, 16 Jun 2020 09:27:58: 2000000 INFO @ Tue, 16 Jun 2020 09:27:58: 9000000 INFO @ Tue, 16 Jun 2020 09:27:59: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:27:59: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:27:59: #1 total tags in treatment: 9089382 INFO @ Tue, 16 Jun 2020 09:27:59: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:27:59: #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 09:27:59: #1 tags after filtering in treatment: 9089382 INFO @ Tue, 16 Jun 2020 09:27:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:27:59: #1 finished! INFO @ Tue, 16 Jun 2020 09:27:59: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:27:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:27:59: #2 number of paired peaks: 487 WARNING @ Tue, 16 Jun 2020 09:27:59: Fewer paired peaks (487) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 487 pairs to build model! INFO @ Tue, 16 Jun 2020 09:27:59: start model_add_line... INFO @ Tue, 16 Jun 2020 09:28:00: start X-correlation... INFO @ Tue, 16 Jun 2020 09:28:00: end of X-cor INFO @ Tue, 16 Jun 2020 09:28:00: #2 finished! INFO @ Tue, 16 Jun 2020 09:28:00: #2 predicted fragment length is 186 bps INFO @ Tue, 16 Jun 2020 09:28:00: #2 alternative fragment length(s) may be 4,186,598 bps INFO @ Tue, 16 Jun 2020 09:28:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020795/SRX5020795.05_model.r INFO @ Tue, 16 Jun 2020 09:28:00: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:28:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:28:02: 3000000 INFO @ Tue, 16 Jun 2020 09:28:07: 4000000 INFO @ Tue, 16 Jun 2020 09:28:11: 5000000 INFO @ Tue, 16 Jun 2020 09:28:16: 6000000 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 09:28:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020795/SRX5020795.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020795/SRX5020795.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020795/SRX5020795.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020795/SRX5020795.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 09:28:18: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:28:18: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:28:18: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:28:20: 7000000 INFO @ Tue, 16 Jun 2020 09:28:23: 1000000 INFO @ Tue, 16 Jun 2020 09:28:25: 8000000 INFO @ Tue, 16 Jun 2020 09:28:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020795/SRX5020795.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:28:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020795/SRX5020795.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:28:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020795/SRX5020795.05_summits.bed INFO @ Tue, 16 Jun 2020 09:28:27: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2081 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:28:28: 2000000 INFO @ Tue, 16 Jun 2020 09:28:30: 9000000 INFO @ Tue, 16 Jun 2020 09:28:31: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:28:31: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:28:31: #1 total tags in treatment: 9089382 INFO @ Tue, 16 Jun 2020 09:28:31: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:28:31: #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 09:28:31: #1 tags after filtering in treatment: 9089382 INFO @ Tue, 16 Jun 2020 09:28:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:28:31: #1 finished! INFO @ Tue, 16 Jun 2020 09:28:31: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:28:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:28:31: #2 number of paired peaks: 487 WARNING @ Tue, 16 Jun 2020 09:28:31: Fewer paired peaks (487) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 487 pairs to build model! INFO @ Tue, 16 Jun 2020 09:28:31: start model_add_line... INFO @ Tue, 16 Jun 2020 09:28:31: start X-correlation... INFO @ Tue, 16 Jun 2020 09:28:31: end of X-cor INFO @ Tue, 16 Jun 2020 09:28:31: #2 finished! INFO @ Tue, 16 Jun 2020 09:28:31: #2 predicted fragment length is 186 bps INFO @ Tue, 16 Jun 2020 09:28:31: #2 alternative fragment length(s) may be 4,186,598 bps INFO @ Tue, 16 Jun 2020 09:28:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020795/SRX5020795.10_model.r INFO @ Tue, 16 Jun 2020 09:28:32: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:28:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:28:34: 3000000 INFO @ Tue, 16 Jun 2020 09:28:39: 4000000 INFO @ Tue, 16 Jun 2020 09:28:44: 5000000 INFO @ Tue, 16 Jun 2020 09:28:49: 6000000 INFO @ Tue, 16 Jun 2020 09:28:51: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:28:55: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:29:00: 8000000 INFO @ Tue, 16 Jun 2020 09:29:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020795/SRX5020795.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:29:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020795/SRX5020795.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:29:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020795/SRX5020795.10_summits.bed INFO @ Tue, 16 Jun 2020 09:29:01: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (942 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:29:05: 9000000 INFO @ Tue, 16 Jun 2020 09:29:05: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:29:05: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:29:05: #1 total tags in treatment: 9089382 INFO @ Tue, 16 Jun 2020 09:29:05: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:29:05: #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 09:29:05: #1 tags after filtering in treatment: 9089382 INFO @ Tue, 16 Jun 2020 09:29:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:29:05: #1 finished! INFO @ Tue, 16 Jun 2020 09:29:05: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:29:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:29:06: #2 number of paired peaks: 487 WARNING @ Tue, 16 Jun 2020 09:29:06: Fewer paired peaks (487) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 487 pairs to build model! INFO @ Tue, 16 Jun 2020 09:29:06: start model_add_line... INFO @ Tue, 16 Jun 2020 09:29:06: start X-correlation... INFO @ Tue, 16 Jun 2020 09:29:06: end of X-cor INFO @ Tue, 16 Jun 2020 09:29:06: #2 finished! INFO @ Tue, 16 Jun 2020 09:29:06: #2 predicted fragment length is 186 bps INFO @ Tue, 16 Jun 2020 09:29:06: #2 alternative fragment length(s) may be 4,186,598 bps INFO @ Tue, 16 Jun 2020 09:29:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020795/SRX5020795.20_model.r INFO @ Tue, 16 Jun 2020 09:29:06: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:29:06: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:29:25: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:29:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020795/SRX5020795.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:29:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020795/SRX5020795.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:29:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020795/SRX5020795.20_summits.bed INFO @ Tue, 16 Jun 2020 09:29:35: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (338 records, 4 fields): 1 millis CompletedMACS2peakCalling