Job ID = 6367119 SRX = SRX277076 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:28:21 prefetch.2.10.7: 1) Downloading 'SRR849752'... 2020-06-15T23:28:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:29:19 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:29:19 prefetch.2.10.7: 'SRR849752' is valid 2020-06-15T23:29:19 prefetch.2.10.7: 1) 'SRR849752' was downloaded successfully Read 7572162 spots for SRR849752/SRR849752.sra Written 7572162 spots for SRR849752/SRR849752.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:00:49 7572162 reads; of these: 7572162 (100.00%) were unpaired; of these: 3205379 (42.33%) aligned 0 times 3685915 (48.68%) aligned exactly 1 time 680868 (8.99%) aligned >1 times 57.67% overall alignment rate Time searching: 00:00:50 Overall time: 00:00:50 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] 400910 / 4366783 = 0.0918 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 08:31:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX277076/SRX277076.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX277076/SRX277076.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX277076/SRX277076.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX277076/SRX277076.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 08:31:47: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:31:47: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:31:51: 1000000 INFO @ Tue, 16 Jun 2020 08:31:56: 2000000 INFO @ Tue, 16 Jun 2020 08:32:00: 3000000 INFO @ Tue, 16 Jun 2020 08:32:04: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:32:04: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:32:04: #1 total tags in treatment: 3965873 INFO @ Tue, 16 Jun 2020 08:32:04: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:32:04: #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 08:32:04: #1 tags after filtering in treatment: 3965873 INFO @ Tue, 16 Jun 2020 08:32:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:32:04: #1 finished! INFO @ Tue, 16 Jun 2020 08:32:04: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:32:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:32:04: #2 number of paired peaks: 785 WARNING @ Tue, 16 Jun 2020 08:32:04: Fewer paired peaks (785) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 785 pairs to build model! INFO @ Tue, 16 Jun 2020 08:32:04: start model_add_line... INFO @ Tue, 16 Jun 2020 08:32:04: start X-correlation... INFO @ Tue, 16 Jun 2020 08:32:04: end of X-cor INFO @ Tue, 16 Jun 2020 08:32:04: #2 finished! INFO @ Tue, 16 Jun 2020 08:32:04: #2 predicted fragment length is 133 bps INFO @ Tue, 16 Jun 2020 08:32:04: #2 alternative fragment length(s) may be 133 bps INFO @ Tue, 16 Jun 2020 08:32:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX277076/SRX277076.05_model.r INFO @ Tue, 16 Jun 2020 08:32:04: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:32:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:32:13: #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 08:32:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX277076/SRX277076.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX277076/SRX277076.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX277076/SRX277076.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX277076/SRX277076.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 08:32:17: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:32:17: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:32:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX277076/SRX277076.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:32:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX277076/SRX277076.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:32:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX277076/SRX277076.05_summits.bed INFO @ Tue, 16 Jun 2020 08:32:18: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1936 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:32:21: 1000000 INFO @ Tue, 16 Jun 2020 08:32:26: 2000000 INFO @ Tue, 16 Jun 2020 08:32:30: 3000000 INFO @ Tue, 16 Jun 2020 08:32:34: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:32:34: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:32:34: #1 total tags in treatment: 3965873 INFO @ Tue, 16 Jun 2020 08:32:34: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:32:34: #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 08:32:34: #1 tags after filtering in treatment: 3965873 INFO @ Tue, 16 Jun 2020 08:32:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:32:34: #1 finished! INFO @ Tue, 16 Jun 2020 08:32:34: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:32:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:32:35: #2 number of paired peaks: 785 WARNING @ Tue, 16 Jun 2020 08:32:35: Fewer paired peaks (785) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 785 pairs to build model! INFO @ Tue, 16 Jun 2020 08:32:35: start model_add_line... INFO @ Tue, 16 Jun 2020 08:32:35: start X-correlation... INFO @ Tue, 16 Jun 2020 08:32:35: end of X-cor INFO @ Tue, 16 Jun 2020 08:32:35: #2 finished! INFO @ Tue, 16 Jun 2020 08:32:35: #2 predicted fragment length is 133 bps INFO @ Tue, 16 Jun 2020 08:32:35: #2 alternative fragment length(s) may be 133 bps INFO @ Tue, 16 Jun 2020 08:32:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX277076/SRX277076.10_model.r INFO @ Tue, 16 Jun 2020 08:32:35: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:32:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:32:43: #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 08:32:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX277076/SRX277076.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX277076/SRX277076.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX277076/SRX277076.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX277076/SRX277076.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 08:32:47: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:32:47: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:32:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX277076/SRX277076.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:32:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX277076/SRX277076.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:32:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX277076/SRX277076.10_summits.bed INFO @ Tue, 16 Jun 2020 08:32:48: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1161 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:32:51: 1000000 INFO @ Tue, 16 Jun 2020 08:32:56: 2000000 INFO @ Tue, 16 Jun 2020 08:33:00: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:33:04: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:33:04: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:33:04: #1 total tags in treatment: 3965873 INFO @ Tue, 16 Jun 2020 08:33:04: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:33:04: #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 08:33:04: #1 tags after filtering in treatment: 3965873 INFO @ Tue, 16 Jun 2020 08:33:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:33:04: #1 finished! INFO @ Tue, 16 Jun 2020 08:33:04: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:33:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:33:05: #2 number of paired peaks: 785 WARNING @ Tue, 16 Jun 2020 08:33:05: Fewer paired peaks (785) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 785 pairs to build model! INFO @ Tue, 16 Jun 2020 08:33:05: start model_add_line... INFO @ Tue, 16 Jun 2020 08:33:05: start X-correlation... INFO @ Tue, 16 Jun 2020 08:33:05: end of X-cor INFO @ Tue, 16 Jun 2020 08:33:05: #2 finished! INFO @ Tue, 16 Jun 2020 08:33:05: #2 predicted fragment length is 133 bps INFO @ Tue, 16 Jun 2020 08:33:05: #2 alternative fragment length(s) may be 133 bps INFO @ Tue, 16 Jun 2020 08:33:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX277076/SRX277076.20_model.r INFO @ Tue, 16 Jun 2020 08:33:05: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:33:05: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:33:13: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:33:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX277076/SRX277076.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:33:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX277076/SRX277076.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:33:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX277076/SRX277076.20_summits.bed INFO @ Tue, 16 Jun 2020 08:33:18: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (580 records, 4 fields): 1 millis CompletedMACS2peakCalling