Job ID = 6367142 SRX = SRX277100 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:15:17 prefetch.2.10.7: 1) Downloading 'SRR849776'... 2020-06-15T23:15:17 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:15:54 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:15:54 prefetch.2.10.7: 'SRR849776' is valid 2020-06-15T23:15:54 prefetch.2.10.7: 1) 'SRR849776' was downloaded successfully Read 7680929 spots for SRR849776/SRR849776.sra Written 7680929 spots for SRR849776/SRR849776.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: 00:01:11 7680929 reads; of these: 7680929 (100.00%) were unpaired; of these: 504619 (6.57%) aligned 0 times 6148128 (80.04%) aligned exactly 1 time 1028182 (13.39%) aligned >1 times 93.43% overall alignment rate Time searching: 00:01:11 Overall time: 00:01:11 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] 863966 / 7176310 = 0.1204 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 08:19:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX277100/SRX277100.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX277100/SRX277100.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX277100/SRX277100.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX277100/SRX277100.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 08:19:13: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:19:13: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:19:18: 1000000 INFO @ Tue, 16 Jun 2020 08:19:23: 2000000 INFO @ Tue, 16 Jun 2020 08:19:28: 3000000 INFO @ Tue, 16 Jun 2020 08:19:32: 4000000 INFO @ Tue, 16 Jun 2020 08:19:37: 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 08:19:42: 6000000 INFO @ Tue, 16 Jun 2020 08:19:43: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:19:43: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:19:43: #1 total tags in treatment: 6312344 INFO @ Tue, 16 Jun 2020 08:19:43: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:19:43: #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 08:19:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX277100/SRX277100.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX277100/SRX277100.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX277100/SRX277100.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX277100/SRX277100.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 08:19:43: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:19:43: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:19:43: #1 tags after filtering in treatment: 6312344 INFO @ Tue, 16 Jun 2020 08:19:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:19:43: #1 finished! INFO @ Tue, 16 Jun 2020 08:19:43: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:19:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:19:44: #2 number of paired peaks: 497 WARNING @ Tue, 16 Jun 2020 08:19:44: Fewer paired peaks (497) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 497 pairs to build model! INFO @ Tue, 16 Jun 2020 08:19:44: start model_add_line... INFO @ Tue, 16 Jun 2020 08:19:44: start X-correlation... INFO @ Tue, 16 Jun 2020 08:19:44: end of X-cor INFO @ Tue, 16 Jun 2020 08:19:44: #2 finished! INFO @ Tue, 16 Jun 2020 08:19:44: #2 predicted fragment length is 66 bps INFO @ Tue, 16 Jun 2020 08:19:44: #2 alternative fragment length(s) may be 4,66,586 bps INFO @ Tue, 16 Jun 2020 08:19:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX277100/SRX277100.05_model.r INFO @ Tue, 16 Jun 2020 08:19:44: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:19:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:19:49: 1000000 INFO @ Tue, 16 Jun 2020 08:19:55: 2000000 INFO @ Tue, 16 Jun 2020 08:19:57: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:20:01: 3000000 INFO @ Tue, 16 Jun 2020 08:20:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX277100/SRX277100.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:20:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX277100/SRX277100.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:20:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX277100/SRX277100.05_summits.bed INFO @ Tue, 16 Jun 2020 08:20:03: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1232 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:20:07: 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 08:20:13: 5000000 INFO @ Tue, 16 Jun 2020 08:20:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX277100/SRX277100.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX277100/SRX277100.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX277100/SRX277100.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX277100/SRX277100.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 08:20:13: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:20:13: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:20:19: 6000000 INFO @ Tue, 16 Jun 2020 08:20:20: 1000000 INFO @ Tue, 16 Jun 2020 08:20:21: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:20:21: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:20:21: #1 total tags in treatment: 6312344 INFO @ Tue, 16 Jun 2020 08:20:21: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:20:21: #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 08:20:21: #1 tags after filtering in treatment: 6312344 INFO @ Tue, 16 Jun 2020 08:20:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:20:21: #1 finished! INFO @ Tue, 16 Jun 2020 08:20:21: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:20:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:20:22: #2 number of paired peaks: 497 WARNING @ Tue, 16 Jun 2020 08:20:22: Fewer paired peaks (497) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 497 pairs to build model! INFO @ Tue, 16 Jun 2020 08:20:22: start model_add_line... INFO @ Tue, 16 Jun 2020 08:20:22: start X-correlation... INFO @ Tue, 16 Jun 2020 08:20:22: end of X-cor INFO @ Tue, 16 Jun 2020 08:20:22: #2 finished! INFO @ Tue, 16 Jun 2020 08:20:22: #2 predicted fragment length is 66 bps INFO @ Tue, 16 Jun 2020 08:20:22: #2 alternative fragment length(s) may be 4,66,586 bps INFO @ Tue, 16 Jun 2020 08:20:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX277100/SRX277100.10_model.r INFO @ Tue, 16 Jun 2020 08:20:22: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:20:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:20:26: 2000000 INFO @ Tue, 16 Jun 2020 08:20:32: 3000000 INFO @ Tue, 16 Jun 2020 08:20:35: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:20:38: 4000000 INFO @ Tue, 16 Jun 2020 08:20:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX277100/SRX277100.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:20:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX277100/SRX277100.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:20:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX277100/SRX277100.10_summits.bed INFO @ Tue, 16 Jun 2020 08:20:42: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (479 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:20:45: 5000000 INFO @ Tue, 16 Jun 2020 08:20:50: 6000000 INFO @ Tue, 16 Jun 2020 08:20:52: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:20:52: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:20:52: #1 total tags in treatment: 6312344 INFO @ Tue, 16 Jun 2020 08:20:52: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:20:52: #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 08:20:52: #1 tags after filtering in treatment: 6312344 INFO @ Tue, 16 Jun 2020 08:20:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:20:52: #1 finished! INFO @ Tue, 16 Jun 2020 08:20:52: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:20:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:20:53: #2 number of paired peaks: 497 WARNING @ Tue, 16 Jun 2020 08:20:53: Fewer paired peaks (497) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 497 pairs to build model! INFO @ Tue, 16 Jun 2020 08:20:53: start model_add_line... INFO @ Tue, 16 Jun 2020 08:20:53: start X-correlation... INFO @ Tue, 16 Jun 2020 08:20:53: end of X-cor INFO @ Tue, 16 Jun 2020 08:20:53: #2 finished! INFO @ Tue, 16 Jun 2020 08:20:53: #2 predicted fragment length is 66 bps INFO @ Tue, 16 Jun 2020 08:20:53: #2 alternative fragment length(s) may be 4,66,586 bps INFO @ Tue, 16 Jun 2020 08:20:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX277100/SRX277100.20_model.r INFO @ Tue, 16 Jun 2020 08:20:53: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:20:53: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:21:06: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:21:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX277100/SRX277100.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:21:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX277100/SRX277100.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:21:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX277100/SRX277100.20_summits.bed INFO @ Tue, 16 Jun 2020 08:21:13: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (145 records, 4 fields): 1 millis CompletedMACS2peakCalling