Job ID = 6368911 SRX = SRX6720188 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:29:35 prefetch.2.10.7: 1) Downloading 'SRR9972842'... 2020-06-16T00:29:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:30:58 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:30:59 prefetch.2.10.7: 'SRR9972842' is valid 2020-06-16T00:30:59 prefetch.2.10.7: 1) 'SRR9972842' was downloaded successfully Read 10745046 spots for SRR9972842/SRR9972842.sra Written 10745046 spots for SRR9972842/SRR9972842.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: 00:02:29 10745046 reads; of these: 10745046 (100.00%) were unpaired; of these: 568527 (5.29%) aligned 0 times 8770245 (81.62%) aligned exactly 1 time 1406274 (13.09%) aligned >1 times 94.71% overall alignment rate Time searching: 00:02:29 Overall time: 00:02:29 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_sort_core] merging from 8 files... [bam_rmdupse_core] 1562271 / 10176519 = 0.1535 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 09:37:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6720188/SRX6720188.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6720188/SRX6720188.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6720188/SRX6720188.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6720188/SRX6720188.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 09:37:16: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:37:16: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:37:22: 1000000 INFO @ Tue, 16 Jun 2020 09:37:28: 2000000 INFO @ Tue, 16 Jun 2020 09:37:34: 3000000 INFO @ Tue, 16 Jun 2020 09:37:40: 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 09:37:46: 5000000 INFO @ Tue, 16 Jun 2020 09:37:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6720188/SRX6720188.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6720188/SRX6720188.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6720188/SRX6720188.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6720188/SRX6720188.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 09:37:47: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:37:47: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:37:53: 6000000 INFO @ Tue, 16 Jun 2020 09:37:54: 1000000 INFO @ Tue, 16 Jun 2020 09:37:59: 7000000 INFO @ Tue, 16 Jun 2020 09:38:00: 2000000 INFO @ Tue, 16 Jun 2020 09:38:06: 8000000 INFO @ Tue, 16 Jun 2020 09:38:07: 3000000 INFO @ Tue, 16 Jun 2020 09:38:10: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:38:10: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:38:10: #1 total tags in treatment: 8614248 INFO @ Tue, 16 Jun 2020 09:38:10: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:38:10: #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 09:38:10: #1 tags after filtering in treatment: 8614248 INFO @ Tue, 16 Jun 2020 09:38:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:38:10: #1 finished! INFO @ Tue, 16 Jun 2020 09:38:10: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:38:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:38:11: #2 number of paired peaks: 656 WARNING @ Tue, 16 Jun 2020 09:38:11: Fewer paired peaks (656) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 656 pairs to build model! INFO @ Tue, 16 Jun 2020 09:38:11: start model_add_line... INFO @ Tue, 16 Jun 2020 09:38:11: start X-correlation... INFO @ Tue, 16 Jun 2020 09:38:11: end of X-cor INFO @ Tue, 16 Jun 2020 09:38:11: #2 finished! INFO @ Tue, 16 Jun 2020 09:38:11: #2 predicted fragment length is 131 bps INFO @ Tue, 16 Jun 2020 09:38:11: #2 alternative fragment length(s) may be 131 bps INFO @ Tue, 16 Jun 2020 09:38:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6720188/SRX6720188.05_model.r INFO @ Tue, 16 Jun 2020 09:38:11: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:38:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:38:14: 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 09:38:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6720188/SRX6720188.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6720188/SRX6720188.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6720188/SRX6720188.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6720188/SRX6720188.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 09:38:16: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:38:16: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:38:20: 5000000 INFO @ Tue, 16 Jun 2020 09:38:23: 1000000 INFO @ Tue, 16 Jun 2020 09:38:27: 6000000 INFO @ Tue, 16 Jun 2020 09:38:31: 2000000 INFO @ Tue, 16 Jun 2020 09:38:32: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:38:34: 7000000 INFO @ Tue, 16 Jun 2020 09:38:38: 3000000 INFO @ Tue, 16 Jun 2020 09:38:41: 8000000 INFO @ Tue, 16 Jun 2020 09:38:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6720188/SRX6720188.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:38:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6720188/SRX6720188.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:38:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6720188/SRX6720188.05_summits.bed INFO @ Tue, 16 Jun 2020 09:38:43: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3812 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:38:46: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:38:46: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:38:46: #1 total tags in treatment: 8614248 INFO @ Tue, 16 Jun 2020 09:38:46: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:38:46: #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 09:38:46: #1 tags after filtering in treatment: 8614248 INFO @ Tue, 16 Jun 2020 09:38:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:38:46: #1 finished! INFO @ Tue, 16 Jun 2020 09:38:46: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:38:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:38:46: 4000000 INFO @ Tue, 16 Jun 2020 09:38:47: #2 number of paired peaks: 656 WARNING @ Tue, 16 Jun 2020 09:38:47: Fewer paired peaks (656) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 656 pairs to build model! INFO @ Tue, 16 Jun 2020 09:38:47: start model_add_line... INFO @ Tue, 16 Jun 2020 09:38:47: start X-correlation... INFO @ Tue, 16 Jun 2020 09:38:47: end of X-cor INFO @ Tue, 16 Jun 2020 09:38:47: #2 finished! INFO @ Tue, 16 Jun 2020 09:38:47: #2 predicted fragment length is 131 bps INFO @ Tue, 16 Jun 2020 09:38:47: #2 alternative fragment length(s) may be 131 bps INFO @ Tue, 16 Jun 2020 09:38:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6720188/SRX6720188.10_model.r INFO @ Tue, 16 Jun 2020 09:38:47: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:38:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:38:53: 5000000 INFO @ Tue, 16 Jun 2020 09:39:00: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:39:07: 7000000 INFO @ Tue, 16 Jun 2020 09:39:08: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:39:14: 8000000 INFO @ Tue, 16 Jun 2020 09:39:19: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:39:19: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:39:19: #1 total tags in treatment: 8614248 INFO @ Tue, 16 Jun 2020 09:39:19: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:39:19: #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 09:39:19: #1 tags after filtering in treatment: 8614248 INFO @ Tue, 16 Jun 2020 09:39:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:39:19: #1 finished! INFO @ Tue, 16 Jun 2020 09:39:19: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:39:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:39:20: #2 number of paired peaks: 656 WARNING @ Tue, 16 Jun 2020 09:39:20: Fewer paired peaks (656) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 656 pairs to build model! INFO @ Tue, 16 Jun 2020 09:39:20: start model_add_line... INFO @ Tue, 16 Jun 2020 09:39:20: start X-correlation... INFO @ Tue, 16 Jun 2020 09:39:20: end of X-cor INFO @ Tue, 16 Jun 2020 09:39:20: #2 finished! INFO @ Tue, 16 Jun 2020 09:39:20: #2 predicted fragment length is 131 bps INFO @ Tue, 16 Jun 2020 09:39:20: #2 alternative fragment length(s) may be 131 bps INFO @ Tue, 16 Jun 2020 09:39:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6720188/SRX6720188.20_model.r INFO @ Tue, 16 Jun 2020 09:39:20: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:39:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:39:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6720188/SRX6720188.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:39:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6720188/SRX6720188.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:39:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6720188/SRX6720188.10_summits.bed INFO @ Tue, 16 Jun 2020 09:39:20: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1722 records, 4 fields): 4 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:39:41: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:39:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6720188/SRX6720188.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:39:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6720188/SRX6720188.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:39:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6720188/SRX6720188.20_summits.bed INFO @ Tue, 16 Jun 2020 09:39:52: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (564 records, 4 fields): 2 millis CompletedMACS2peakCalling