Job ID = 6366616 SRX = SRX212235 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:53:26 prefetch.2.10.7: 1) Downloading 'SRR639150'... 2020-06-15T22:53:26 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:53:52 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:53:53 prefetch.2.10.7: 'SRR639150' is valid 2020-06-15T22:53:53 prefetch.2.10.7: 1) 'SRR639150' was downloaded successfully Read 4734806 spots for SRR639150/SRR639150.sra Written 4734806 spots for SRR639150/SRR639150.sra 2020-06-15T22:54:17 prefetch.2.10.7: 1) Downloading 'SRR639151'... 2020-06-15T22:54:17 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:54:48 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:54:48 prefetch.2.10.7: 'SRR639151' is valid 2020-06-15T22:54:48 prefetch.2.10.7: 1) 'SRR639151' was downloaded successfully Read 7817443 spots for SRR639151/SRR639151.sra Written 7817443 spots for SRR639151/SRR639151.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: 00:02:03 12552249 reads; of these: 12552249 (100.00%) were unpaired; of these: 217711 (1.73%) aligned 0 times 10108321 (80.53%) aligned exactly 1 time 2226217 (17.74%) aligned >1 times 98.27% overall alignment rate Time searching: 00:02:03 Overall time: 00:02:03 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] 1776395 / 12334538 = 0.1440 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 08:00:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX212235/SRX212235.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX212235/SRX212235.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX212235/SRX212235.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX212235/SRX212235.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 08:00:12: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:00:12: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:00:18: 1000000 INFO @ Tue, 16 Jun 2020 08:00:23: 2000000 INFO @ Tue, 16 Jun 2020 08:00:28: 3000000 INFO @ Tue, 16 Jun 2020 08:00:34: 4000000 INFO @ Tue, 16 Jun 2020 08:00:39: 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 08:00:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX212235/SRX212235.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX212235/SRX212235.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX212235/SRX212235.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX212235/SRX212235.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 08:00:42: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:00:42: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:00:45: 6000000 INFO @ Tue, 16 Jun 2020 08:00:49: 1000000 INFO @ Tue, 16 Jun 2020 08:00:51: 7000000 INFO @ Tue, 16 Jun 2020 08:00:56: 2000000 INFO @ Tue, 16 Jun 2020 08:00:57: 8000000 INFO @ Tue, 16 Jun 2020 08:01:03: 3000000 INFO @ Tue, 16 Jun 2020 08:01:03: 9000000 INFO @ Tue, 16 Jun 2020 08:01:10: 10000000 INFO @ Tue, 16 Jun 2020 08:01:10: 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 08:01:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX212235/SRX212235.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX212235/SRX212235.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX212235/SRX212235.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX212235/SRX212235.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 08:01:12: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:01:12: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:01:13: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:01:13: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:01:13: #1 total tags in treatment: 10558143 INFO @ Tue, 16 Jun 2020 08:01:13: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:01:13: #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 08:01:14: #1 tags after filtering in treatment: 10558143 INFO @ Tue, 16 Jun 2020 08:01:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:01:14: #1 finished! INFO @ Tue, 16 Jun 2020 08:01:14: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:01:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:01:14: #2 number of paired peaks: 788 WARNING @ Tue, 16 Jun 2020 08:01:14: Fewer paired peaks (788) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 788 pairs to build model! INFO @ Tue, 16 Jun 2020 08:01:14: start model_add_line... INFO @ Tue, 16 Jun 2020 08:01:15: start X-correlation... INFO @ Tue, 16 Jun 2020 08:01:15: end of X-cor INFO @ Tue, 16 Jun 2020 08:01:15: #2 finished! INFO @ Tue, 16 Jun 2020 08:01:15: #2 predicted fragment length is 105 bps INFO @ Tue, 16 Jun 2020 08:01:15: #2 alternative fragment length(s) may be 105 bps INFO @ Tue, 16 Jun 2020 08:01:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX212235/SRX212235.05_model.r INFO @ Tue, 16 Jun 2020 08:01:15: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:01:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:01:17: 5000000 INFO @ Tue, 16 Jun 2020 08:01:19: 1000000 INFO @ Tue, 16 Jun 2020 08:01:25: 6000000 INFO @ Tue, 16 Jun 2020 08:01:25: 2000000 INFO @ Tue, 16 Jun 2020 08:01:32: 7000000 INFO @ Tue, 16 Jun 2020 08:01:32: 3000000 INFO @ Tue, 16 Jun 2020 08:01:37: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:01:38: 4000000 INFO @ Tue, 16 Jun 2020 08:01:39: 8000000 INFO @ Tue, 16 Jun 2020 08:01:45: 5000000 INFO @ Tue, 16 Jun 2020 08:01:46: 9000000 INFO @ Tue, 16 Jun 2020 08:01:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX212235/SRX212235.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:01:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX212235/SRX212235.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:01:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX212235/SRX212235.05_summits.bed INFO @ Tue, 16 Jun 2020 08:01:50: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (9590 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:01:52: 6000000 INFO @ Tue, 16 Jun 2020 08:01:54: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:01:57: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:01:57: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:01:57: #1 total tags in treatment: 10558143 INFO @ Tue, 16 Jun 2020 08:01:57: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:01:57: #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 08:01:58: #1 tags after filtering in treatment: 10558143 INFO @ Tue, 16 Jun 2020 08:01:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:01:58: #1 finished! INFO @ Tue, 16 Jun 2020 08:01:58: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:01:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:01:58: #2 number of paired peaks: 788 WARNING @ Tue, 16 Jun 2020 08:01:58: Fewer paired peaks (788) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 788 pairs to build model! INFO @ Tue, 16 Jun 2020 08:01:58: start model_add_line... INFO @ Tue, 16 Jun 2020 08:01:58: start X-correlation... INFO @ Tue, 16 Jun 2020 08:01:59: end of X-cor INFO @ Tue, 16 Jun 2020 08:01:59: #2 finished! INFO @ Tue, 16 Jun 2020 08:01:59: #2 predicted fragment length is 105 bps INFO @ Tue, 16 Jun 2020 08:01:59: #2 alternative fragment length(s) may be 105 bps INFO @ Tue, 16 Jun 2020 08:01:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX212235/SRX212235.10_model.r INFO @ Tue, 16 Jun 2020 08:01:59: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:01:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:01:59: 7000000 INFO @ Tue, 16 Jun 2020 08:02:05: 8000000 INFO @ Tue, 16 Jun 2020 08:02:11: 9000000 INFO @ Tue, 16 Jun 2020 08:02:17: 10000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:02:20: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:02:20: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:02:20: #1 total tags in treatment: 10558143 INFO @ Tue, 16 Jun 2020 08:02:20: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:02:20: #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 08:02:20: #1 tags after filtering in treatment: 10558143 INFO @ Tue, 16 Jun 2020 08:02:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:02:20: #1 finished! INFO @ Tue, 16 Jun 2020 08:02:20: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:02:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:02:21: #2 number of paired peaks: 788 WARNING @ Tue, 16 Jun 2020 08:02:21: Fewer paired peaks (788) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 788 pairs to build model! INFO @ Tue, 16 Jun 2020 08:02:21: start model_add_line... INFO @ Tue, 16 Jun 2020 08:02:21: start X-correlation... INFO @ Tue, 16 Jun 2020 08:02:21: end of X-cor INFO @ Tue, 16 Jun 2020 08:02:21: #2 finished! INFO @ Tue, 16 Jun 2020 08:02:21: #2 predicted fragment length is 105 bps INFO @ Tue, 16 Jun 2020 08:02:21: #2 alternative fragment length(s) may be 105 bps INFO @ Tue, 16 Jun 2020 08:02:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX212235/SRX212235.20_model.r INFO @ Tue, 16 Jun 2020 08:02:21: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:02:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:02:23: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:02:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX212235/SRX212235.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:02:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX212235/SRX212235.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:02:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX212235/SRX212235.10_summits.bed INFO @ Tue, 16 Jun 2020 08:02:37: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4194 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:02:46: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:02:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX212235/SRX212235.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:02:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX212235/SRX212235.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:02:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX212235/SRX212235.20_summits.bed INFO @ Tue, 16 Jun 2020 08:02:59: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1810 records, 4 fields): 4 millis CompletedMACS2peakCalling