Job ID = 6367115 SRX = SRX277072 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:20:46 prefetch.2.10.7: 1) Downloading 'SRR849748'... 2020-06-15T23:20:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:21:21 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:21:22 prefetch.2.10.7: 'SRR849748' is valid 2020-06-15T23:21:22 prefetch.2.10.7: 1) 'SRR849748' was downloaded successfully Read 8370704 spots for SRR849748/SRR849748.sra Written 8370704 spots for SRR849748/SRR849748.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: 00:01:10 8370704 reads; of these: 8370704 (100.00%) were unpaired; of these: 1098922 (13.13%) aligned 0 times 6088987 (72.74%) aligned exactly 1 time 1182795 (14.13%) aligned >1 times 86.87% overall alignment rate Time searching: 00:01:10 Overall time: 00:01:10 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] 823255 / 7271782 = 0.1132 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 08:24:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX277072/SRX277072.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX277072/SRX277072.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX277072/SRX277072.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX277072/SRX277072.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 08:24:42: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:24:42: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:24:48: 1000000 INFO @ Tue, 16 Jun 2020 08:24:53: 2000000 INFO @ Tue, 16 Jun 2020 08:24:59: 3000000 INFO @ Tue, 16 Jun 2020 08:25:04: 4000000 INFO @ Tue, 16 Jun 2020 08:25:10: 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 08:25:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX277072/SRX277072.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX277072/SRX277072.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX277072/SRX277072.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX277072/SRX277072.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 08:25:13: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:25:13: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:25:15: 6000000 INFO @ Tue, 16 Jun 2020 08:25:18: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:25:18: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:25:18: #1 total tags in treatment: 6448527 INFO @ Tue, 16 Jun 2020 08:25:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:25:18: #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 08:25:18: #1 tags after filtering in treatment: 6448527 INFO @ Tue, 16 Jun 2020 08:25:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:25:18: #1 finished! INFO @ Tue, 16 Jun 2020 08:25:18: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:25:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:25:19: 1000000 INFO @ Tue, 16 Jun 2020 08:25:19: #2 number of paired peaks: 990 WARNING @ Tue, 16 Jun 2020 08:25:19: Fewer paired peaks (990) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 990 pairs to build model! INFO @ Tue, 16 Jun 2020 08:25:19: start model_add_line... INFO @ Tue, 16 Jun 2020 08:25:19: start X-correlation... INFO @ Tue, 16 Jun 2020 08:25:19: end of X-cor INFO @ Tue, 16 Jun 2020 08:25:19: #2 finished! INFO @ Tue, 16 Jun 2020 08:25:19: #2 predicted fragment length is 142 bps INFO @ Tue, 16 Jun 2020 08:25:19: #2 alternative fragment length(s) may be 142 bps INFO @ Tue, 16 Jun 2020 08:25:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX277072/SRX277072.05_model.r INFO @ Tue, 16 Jun 2020 08:25:19: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:25:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:25:24: 2000000 INFO @ Tue, 16 Jun 2020 08:25:30: 3000000 INFO @ Tue, 16 Jun 2020 08:25:34: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:25:36: 4000000 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 08:25:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX277072/SRX277072.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:25:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX277072/SRX277072.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:25:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX277072/SRX277072.05_summits.bed INFO @ Tue, 16 Jun 2020 08:25:42: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (3303 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:25:42: 5000000 INFO @ Tue, 16 Jun 2020 08:25:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX277072/SRX277072.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX277072/SRX277072.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX277072/SRX277072.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX277072/SRX277072.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 08:25:43: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:25:43: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:25:48: 6000000 INFO @ Tue, 16 Jun 2020 08:25:49: 1000000 INFO @ Tue, 16 Jun 2020 08:25:51: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:25:51: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:25:51: #1 total tags in treatment: 6448527 INFO @ Tue, 16 Jun 2020 08:25:51: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:25:51: #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 08:25:51: #1 tags after filtering in treatment: 6448527 INFO @ Tue, 16 Jun 2020 08:25:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:25:51: #1 finished! INFO @ Tue, 16 Jun 2020 08:25:51: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:25:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:25:51: #2 number of paired peaks: 990 WARNING @ Tue, 16 Jun 2020 08:25:51: Fewer paired peaks (990) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 990 pairs to build model! INFO @ Tue, 16 Jun 2020 08:25:51: start model_add_line... INFO @ Tue, 16 Jun 2020 08:25:51: start X-correlation... INFO @ Tue, 16 Jun 2020 08:25:51: end of X-cor INFO @ Tue, 16 Jun 2020 08:25:51: #2 finished! INFO @ Tue, 16 Jun 2020 08:25:51: #2 predicted fragment length is 142 bps INFO @ Tue, 16 Jun 2020 08:25:51: #2 alternative fragment length(s) may be 142 bps INFO @ Tue, 16 Jun 2020 08:25:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX277072/SRX277072.10_model.r INFO @ Tue, 16 Jun 2020 08:25:51: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:25:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:25:55: 2000000 INFO @ Tue, 16 Jun 2020 08:26:01: 3000000 INFO @ Tue, 16 Jun 2020 08:26:07: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:26:07: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:26:14: 5000000 INFO @ Tue, 16 Jun 2020 08:26:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX277072/SRX277072.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:26:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX277072/SRX277072.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:26:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX277072/SRX277072.10_summits.bed INFO @ Tue, 16 Jun 2020 08:26:14: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1825 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:26:20: 6000000 INFO @ Tue, 16 Jun 2020 08:26:23: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:26:23: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:26:23: #1 total tags in treatment: 6448527 INFO @ Tue, 16 Jun 2020 08:26:23: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:26:23: #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 08:26:23: #1 tags after filtering in treatment: 6448527 INFO @ Tue, 16 Jun 2020 08:26:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:26:23: #1 finished! INFO @ Tue, 16 Jun 2020 08:26:23: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:26:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:26:23: #2 number of paired peaks: 990 WARNING @ Tue, 16 Jun 2020 08:26:23: Fewer paired peaks (990) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 990 pairs to build model! INFO @ Tue, 16 Jun 2020 08:26:23: start model_add_line... INFO @ Tue, 16 Jun 2020 08:26:23: start X-correlation... INFO @ Tue, 16 Jun 2020 08:26:23: end of X-cor INFO @ Tue, 16 Jun 2020 08:26:23: #2 finished! INFO @ Tue, 16 Jun 2020 08:26:23: #2 predicted fragment length is 142 bps INFO @ Tue, 16 Jun 2020 08:26:23: #2 alternative fragment length(s) may be 142 bps INFO @ Tue, 16 Jun 2020 08:26:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX277072/SRX277072.20_model.r INFO @ Tue, 16 Jun 2020 08:26:23: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:26:23: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:26:39: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:26:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX277072/SRX277072.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:26:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX277072/SRX277072.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:26:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX277072/SRX277072.20_summits.bed INFO @ Tue, 16 Jun 2020 08:26:47: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (952 records, 4 fields): 2 millis CompletedMACS2peakCalling