Job ID = 6366058 SRX = SRX059230 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:23:14 prefetch.2.10.7: 1) Downloading 'SRR190670'... 2020-06-15T22:23:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:23:44 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:23:44 prefetch.2.10.7: 'SRR190670' is valid 2020-06-15T22:23:44 prefetch.2.10.7: 1) 'SRR190670' was downloaded successfully Read 4429111 spots for SRR190670/SRR190670.sra Written 4429111 spots for SRR190670/SRR190670.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: 00:00:39 4429111 reads; of these: 4429111 (100.00%) were unpaired; of these: 1143491 (25.82%) aligned 0 times 2626377 (59.30%) aligned exactly 1 time 659243 (14.88%) aligned >1 times 74.18% overall alignment rate Time searching: 00:00:39 Overall time: 00:00:39 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] 336610 / 3285620 = 0.1024 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 07:25:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059230/SRX059230.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059230/SRX059230.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059230/SRX059230.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059230/SRX059230.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 07:25:56: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:25:56: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:26:02: 1000000 INFO @ Tue, 16 Jun 2020 07:26:08: 2000000 INFO @ Tue, 16 Jun 2020 07:26:14: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:26:14: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:26:14: #1 total tags in treatment: 2949010 INFO @ Tue, 16 Jun 2020 07:26:14: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:26:14: #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 07:26:14: #1 tags after filtering in treatment: 2949010 INFO @ Tue, 16 Jun 2020 07:26:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:26:14: #1 finished! INFO @ Tue, 16 Jun 2020 07:26:14: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:26:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:26:14: #2 number of paired peaks: 854 WARNING @ Tue, 16 Jun 2020 07:26:14: Fewer paired peaks (854) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 854 pairs to build model! INFO @ Tue, 16 Jun 2020 07:26:14: start model_add_line... INFO @ Tue, 16 Jun 2020 07:26:14: start X-correlation... INFO @ Tue, 16 Jun 2020 07:26:14: end of X-cor INFO @ Tue, 16 Jun 2020 07:26:14: #2 finished! INFO @ Tue, 16 Jun 2020 07:26:14: #2 predicted fragment length is 96 bps INFO @ Tue, 16 Jun 2020 07:26:14: #2 alternative fragment length(s) may be 96 bps INFO @ Tue, 16 Jun 2020 07:26:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059230/SRX059230.05_model.r INFO @ Tue, 16 Jun 2020 07:26:14: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:26:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:26:21: #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 07:26:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059230/SRX059230.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:26:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059230/SRX059230.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:26:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059230/SRX059230.05_summits.bed INFO @ Tue, 16 Jun 2020 07:26:24: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2015 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:26:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059230/SRX059230.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059230/SRX059230.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059230/SRX059230.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059230/SRX059230.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 07:26:26: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:26:26: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:26:32: 1000000 INFO @ Tue, 16 Jun 2020 07:26:38: 2000000 INFO @ Tue, 16 Jun 2020 07:26:44: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:26:44: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:26:44: #1 total tags in treatment: 2949010 INFO @ Tue, 16 Jun 2020 07:26:44: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:26:44: #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 07:26:44: #1 tags after filtering in treatment: 2949010 INFO @ Tue, 16 Jun 2020 07:26:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:26:44: #1 finished! INFO @ Tue, 16 Jun 2020 07:26:44: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:26:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:26:44: #2 number of paired peaks: 854 WARNING @ Tue, 16 Jun 2020 07:26:44: Fewer paired peaks (854) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 854 pairs to build model! INFO @ Tue, 16 Jun 2020 07:26:44: start model_add_line... INFO @ Tue, 16 Jun 2020 07:26:44: start X-correlation... INFO @ Tue, 16 Jun 2020 07:26:44: end of X-cor INFO @ Tue, 16 Jun 2020 07:26:44: #2 finished! INFO @ Tue, 16 Jun 2020 07:26:44: #2 predicted fragment length is 96 bps INFO @ Tue, 16 Jun 2020 07:26:44: #2 alternative fragment length(s) may be 96 bps INFO @ Tue, 16 Jun 2020 07:26:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059230/SRX059230.10_model.r INFO @ Tue, 16 Jun 2020 07:26:44: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:26:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:26:51: #3 Call peaks for each chromosome... 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 07:26:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059230/SRX059230.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:26:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059230/SRX059230.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:26:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059230/SRX059230.10_summits.bed INFO @ Tue, 16 Jun 2020 07:26:55: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (1135 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:26:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059230/SRX059230.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059230/SRX059230.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059230/SRX059230.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059230/SRX059230.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 07:26:56: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:26:56: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:27:02: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:27:09: 2000000 INFO @ Tue, 16 Jun 2020 07:27:15: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:27:15: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:27:15: #1 total tags in treatment: 2949010 INFO @ Tue, 16 Jun 2020 07:27:15: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:27:15: #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 07:27:16: #1 tags after filtering in treatment: 2949010 INFO @ Tue, 16 Jun 2020 07:27:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:27:16: #1 finished! INFO @ Tue, 16 Jun 2020 07:27:16: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:27:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:27:16: #2 number of paired peaks: 854 WARNING @ Tue, 16 Jun 2020 07:27:16: Fewer paired peaks (854) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 854 pairs to build model! INFO @ Tue, 16 Jun 2020 07:27:16: start model_add_line... INFO @ Tue, 16 Jun 2020 07:27:16: start X-correlation... INFO @ Tue, 16 Jun 2020 07:27:16: end of X-cor INFO @ Tue, 16 Jun 2020 07:27:16: #2 finished! INFO @ Tue, 16 Jun 2020 07:27:16: #2 predicted fragment length is 96 bps INFO @ Tue, 16 Jun 2020 07:27:16: #2 alternative fragment length(s) may be 96 bps INFO @ Tue, 16 Jun 2020 07:27:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059230/SRX059230.20_model.r INFO @ Tue, 16 Jun 2020 07:27:16: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:27:16: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:27:23: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:27:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059230/SRX059230.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:27:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059230/SRX059230.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:27:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059230/SRX059230.20_summits.bed INFO @ Tue, 16 Jun 2020 07:27:27: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (710 records, 4 fields): 1 millis CompletedMACS2peakCalling