Job ID = 6368488 SRX = SRX5020718 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:24:48 prefetch.2.10.7: 1) Downloading 'SRR8201341'... 2020-06-16T00:24:48 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:26:50 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:26:51 prefetch.2.10.7: 'SRR8201341' is valid 2020-06-16T00:26:51 prefetch.2.10.7: 1) 'SRR8201341' was downloaded successfully Read 8528916 spots for SRR8201341/SRR8201341.sra Written 8528916 spots for SRR8201341/SRR8201341.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:01:49 8528916 reads; of these: 8528916 (100.00%) were unpaired; of these: 1032108 (12.10%) aligned 0 times 6319628 (74.10%) aligned exactly 1 time 1177180 (13.80%) aligned >1 times 87.90% overall alignment rate Time searching: 00:01:50 Overall time: 00:01:50 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] 542609 / 7496808 = 0.0724 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 09:31:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020718/SRX5020718.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020718/SRX5020718.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020718/SRX5020718.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020718/SRX5020718.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 09:31:34: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:31:34: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:31:40: 1000000 INFO @ Tue, 16 Jun 2020 09:31:46: 2000000 INFO @ Tue, 16 Jun 2020 09:31:52: 3000000 INFO @ Tue, 16 Jun 2020 09:31:58: 4000000 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 09:32:04: 5000000 INFO @ Tue, 16 Jun 2020 09:32:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020718/SRX5020718.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020718/SRX5020718.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020718/SRX5020718.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020718/SRX5020718.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 09:32:04: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:32:04: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:32:10: 1000000 INFO @ Tue, 16 Jun 2020 09:32:10: 6000000 INFO @ Tue, 16 Jun 2020 09:32:16: 2000000 INFO @ Tue, 16 Jun 2020 09:32:17: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:32:17: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:32:17: #1 total tags in treatment: 6954199 INFO @ Tue, 16 Jun 2020 09:32:17: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:32:17: #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 09:32:17: #1 tags after filtering in treatment: 6954199 INFO @ Tue, 16 Jun 2020 09:32:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:32:17: #1 finished! INFO @ Tue, 16 Jun 2020 09:32:17: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:32:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:32:17: #2 number of paired peaks: 842 WARNING @ Tue, 16 Jun 2020 09:32:17: Fewer paired peaks (842) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 842 pairs to build model! INFO @ Tue, 16 Jun 2020 09:32:17: start model_add_line... INFO @ Tue, 16 Jun 2020 09:32:17: start X-correlation... INFO @ Tue, 16 Jun 2020 09:32:17: end of X-cor INFO @ Tue, 16 Jun 2020 09:32:17: #2 finished! INFO @ Tue, 16 Jun 2020 09:32:17: #2 predicted fragment length is 194 bps INFO @ Tue, 16 Jun 2020 09:32:17: #2 alternative fragment length(s) may be 194 bps INFO @ Tue, 16 Jun 2020 09:32:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020718/SRX5020718.05_model.r INFO @ Tue, 16 Jun 2020 09:32:17: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:32:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:32:21: 3000000 INFO @ Tue, 16 Jun 2020 09:32:26: 4000000 INFO @ Tue, 16 Jun 2020 09:32:32: 5000000 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 09:32:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020718/SRX5020718.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020718/SRX5020718.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020718/SRX5020718.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020718/SRX5020718.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 09:32:34: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:32:34: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:32:35: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:32:37: 6000000 INFO @ Tue, 16 Jun 2020 09:32:40: 1000000 INFO @ Tue, 16 Jun 2020 09:32:42: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:32:42: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:32:42: #1 total tags in treatment: 6954199 INFO @ Tue, 16 Jun 2020 09:32:42: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:32:42: #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 09:32:42: #1 tags after filtering in treatment: 6954199 INFO @ Tue, 16 Jun 2020 09:32:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:32:42: #1 finished! INFO @ Tue, 16 Jun 2020 09:32:42: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:32:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:32:43: #2 number of paired peaks: 842 WARNING @ Tue, 16 Jun 2020 09:32:43: Fewer paired peaks (842) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 842 pairs to build model! INFO @ Tue, 16 Jun 2020 09:32:43: start model_add_line... INFO @ Tue, 16 Jun 2020 09:32:43: start X-correlation... INFO @ Tue, 16 Jun 2020 09:32:43: end of X-cor INFO @ Tue, 16 Jun 2020 09:32:43: #2 finished! INFO @ Tue, 16 Jun 2020 09:32:43: #2 predicted fragment length is 194 bps INFO @ Tue, 16 Jun 2020 09:32:43: #2 alternative fragment length(s) may be 194 bps INFO @ Tue, 16 Jun 2020 09:32:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020718/SRX5020718.10_model.r INFO @ Tue, 16 Jun 2020 09:32:43: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:32:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:32:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020718/SRX5020718.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:32:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020718/SRX5020718.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:32:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020718/SRX5020718.05_summits.bed INFO @ Tue, 16 Jun 2020 09:32:44: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3168 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:32:45: 2000000 INFO @ Tue, 16 Jun 2020 09:32:50: 3000000 INFO @ Tue, 16 Jun 2020 09:32:55: 4000000 INFO @ Tue, 16 Jun 2020 09:33:00: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:33:01: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:33:06: 6000000 INFO @ Tue, 16 Jun 2020 09:33:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020718/SRX5020718.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:33:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020718/SRX5020718.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:33:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020718/SRX5020718.10_summits.bed INFO @ Tue, 16 Jun 2020 09:33:09: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1658 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:33:11: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:33:11: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:33:11: #1 total tags in treatment: 6954199 INFO @ Tue, 16 Jun 2020 09:33:11: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:33:11: #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 09:33:11: #1 tags after filtering in treatment: 6954199 INFO @ Tue, 16 Jun 2020 09:33:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:33:11: #1 finished! INFO @ Tue, 16 Jun 2020 09:33:11: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:33:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:33:12: #2 number of paired peaks: 842 WARNING @ Tue, 16 Jun 2020 09:33:12: Fewer paired peaks (842) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 842 pairs to build model! INFO @ Tue, 16 Jun 2020 09:33:12: start model_add_line... INFO @ Tue, 16 Jun 2020 09:33:12: start X-correlation... INFO @ Tue, 16 Jun 2020 09:33:12: end of X-cor INFO @ Tue, 16 Jun 2020 09:33:12: #2 finished! INFO @ Tue, 16 Jun 2020 09:33:12: #2 predicted fragment length is 194 bps INFO @ Tue, 16 Jun 2020 09:33:12: #2 alternative fragment length(s) may be 194 bps INFO @ Tue, 16 Jun 2020 09:33:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020718/SRX5020718.20_model.r INFO @ Tue, 16 Jun 2020 09:33:12: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:33:12: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:33:30: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:33:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020718/SRX5020718.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:33:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020718/SRX5020718.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:33:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020718/SRX5020718.20_summits.bed INFO @ Tue, 16 Jun 2020 09:33:38: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (669 records, 4 fields): 2 millis CompletedMACS2peakCalling