Job ID = 6366537 SRX = SRX1769992 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:46:37 prefetch.2.10.7: 1) Downloading 'SRR3535771'... 2020-06-15T22:46:37 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:47:28 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:47:29 prefetch.2.10.7: 'SRR3535771' is valid 2020-06-15T22:47:29 prefetch.2.10.7: 1) 'SRR3535771' was downloaded successfully Read 6174995 spots for SRR3535771/SRR3535771.sra Written 6174995 spots for SRR3535771/SRR3535771.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: 00:01:20 6174995 reads; of these: 6174995 (100.00%) were unpaired; of these: 1827901 (29.60%) aligned 0 times 2023896 (32.78%) aligned exactly 1 time 2323198 (37.62%) aligned >1 times 70.40% overall alignment rate Time searching: 00:01:20 Overall time: 00:01:20 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] 2221331 / 4347094 = 0.5110 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 07:50:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1769992/SRX1769992.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1769992/SRX1769992.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1769992/SRX1769992.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1769992/SRX1769992.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 07:50:31: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:50:31: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:50:37: 1000000 INFO @ Tue, 16 Jun 2020 07:50:43: 2000000 INFO @ Tue, 16 Jun 2020 07:50:43: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 07:50:43: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 07:50:43: #1 total tags in treatment: 2125763 INFO @ Tue, 16 Jun 2020 07:50:43: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:50:43: #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 07:50:43: #1 tags after filtering in treatment: 2125763 INFO @ Tue, 16 Jun 2020 07:50:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:50:43: #1 finished! INFO @ Tue, 16 Jun 2020 07:50:43: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:50:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:50:44: #2 number of paired peaks: 988 WARNING @ Tue, 16 Jun 2020 07:50:44: Fewer paired peaks (988) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 988 pairs to build model! INFO @ Tue, 16 Jun 2020 07:50:44: start model_add_line... INFO @ Tue, 16 Jun 2020 07:50:44: start X-correlation... INFO @ Tue, 16 Jun 2020 07:50:44: end of X-cor INFO @ Tue, 16 Jun 2020 07:50:44: #2 finished! INFO @ Tue, 16 Jun 2020 07:50:44: #2 predicted fragment length is 208 bps INFO @ Tue, 16 Jun 2020 07:50:44: #2 alternative fragment length(s) may be 208 bps INFO @ Tue, 16 Jun 2020 07:50:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1769992/SRX1769992.05_model.r INFO @ Tue, 16 Jun 2020 07:50:44: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:50:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:50:49: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:50:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1769992/SRX1769992.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:50:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1769992/SRX1769992.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:50:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1769992/SRX1769992.05_summits.bed INFO @ Tue, 16 Jun 2020 07:50:52: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (860 records, 4 fields): 2 millis CompletedMACS2peakCalling 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 07:51:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1769992/SRX1769992.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1769992/SRX1769992.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1769992/SRX1769992.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1769992/SRX1769992.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 07:51:01: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:51:01: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:51:06: 1000000 INFO @ Tue, 16 Jun 2020 07:51:12: 2000000 INFO @ Tue, 16 Jun 2020 07:51:13: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 07:51:13: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 07:51:13: #1 total tags in treatment: 2125763 INFO @ Tue, 16 Jun 2020 07:51:13: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:51:13: #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 07:51:13: #1 tags after filtering in treatment: 2125763 INFO @ Tue, 16 Jun 2020 07:51:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:51:13: #1 finished! INFO @ Tue, 16 Jun 2020 07:51:13: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:51:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:51:13: #2 number of paired peaks: 988 WARNING @ Tue, 16 Jun 2020 07:51:13: Fewer paired peaks (988) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 988 pairs to build model! INFO @ Tue, 16 Jun 2020 07:51:13: start model_add_line... INFO @ Tue, 16 Jun 2020 07:51:13: start X-correlation... INFO @ Tue, 16 Jun 2020 07:51:13: end of X-cor INFO @ Tue, 16 Jun 2020 07:51:13: #2 finished! INFO @ Tue, 16 Jun 2020 07:51:13: #2 predicted fragment length is 208 bps INFO @ Tue, 16 Jun 2020 07:51:13: #2 alternative fragment length(s) may be 208 bps INFO @ Tue, 16 Jun 2020 07:51:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1769992/SRX1769992.10_model.r INFO @ Tue, 16 Jun 2020 07:51:13: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:51:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:51:19: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:51:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1769992/SRX1769992.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:51:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1769992/SRX1769992.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:51:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1769992/SRX1769992.10_summits.bed INFO @ Tue, 16 Jun 2020 07:51:21: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (664 records, 4 fields): 2 millis CompletedMACS2peakCalling 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 07:51:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1769992/SRX1769992.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1769992/SRX1769992.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1769992/SRX1769992.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1769992/SRX1769992.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 07:51:31: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:51:31: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:51:36: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:51:42: 2000000 INFO @ Tue, 16 Jun 2020 07:51:43: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 07:51:43: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 07:51:43: #1 total tags in treatment: 2125763 INFO @ Tue, 16 Jun 2020 07:51:43: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:51:43: #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 07:51:43: #1 tags after filtering in treatment: 2125763 INFO @ Tue, 16 Jun 2020 07:51:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:51:43: #1 finished! INFO @ Tue, 16 Jun 2020 07:51:43: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:51:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:51:43: #2 number of paired peaks: 988 WARNING @ Tue, 16 Jun 2020 07:51:43: Fewer paired peaks (988) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 988 pairs to build model! INFO @ Tue, 16 Jun 2020 07:51:43: start model_add_line... INFO @ Tue, 16 Jun 2020 07:51:43: start X-correlation... INFO @ Tue, 16 Jun 2020 07:51:43: end of X-cor INFO @ Tue, 16 Jun 2020 07:51:43: #2 finished! INFO @ Tue, 16 Jun 2020 07:51:43: #2 predicted fragment length is 208 bps INFO @ Tue, 16 Jun 2020 07:51:43: #2 alternative fragment length(s) may be 208 bps INFO @ Tue, 16 Jun 2020 07:51:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1769992/SRX1769992.20_model.r INFO @ Tue, 16 Jun 2020 07:51:43: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:51:43: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:51:49: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:51:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1769992/SRX1769992.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:51:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1769992/SRX1769992.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:51:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1769992/SRX1769992.20_summits.bed INFO @ Tue, 16 Jun 2020 07:51:51: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (478 records, 4 fields): 2 millis CompletedMACS2peakCalling