Job ID = 6365986 SRX = SRX043997 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:30:14 prefetch.2.10.7: 1) Downloading 'SRR107576'... 2020-06-15T22:30:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:30:41 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:30:42 prefetch.2.10.7: 'SRR107576' is valid 2020-06-15T22:30:42 prefetch.2.10.7: 1) 'SRR107576' was downloaded successfully Read 2977962 spots for SRR107576/SRR107576.sra Written 2977962 spots for SRR107576/SRR107576.sra 2020-06-15T22:31:00 prefetch.2.10.7: 1) Downloading 'SRR107577'... 2020-06-15T22:31:00 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:31:30 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:31:30 prefetch.2.10.7: 'SRR107577' is valid 2020-06-15T22:31:30 prefetch.2.10.7: 1) 'SRR107577' was downloaded successfully Read 3364196 spots for SRR107577/SRR107577.sra Written 3364196 spots for SRR107577/SRR107577.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: 00:00:51 6342158 reads; of these: 6342158 (100.00%) were unpaired; of these: 132296 (2.09%) aligned 0 times 5236057 (82.56%) aligned exactly 1 time 973805 (15.35%) aligned >1 times 97.91% overall alignment rate Time searching: 00:00:51 Overall time: 00:00:51 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] 367729 / 6209862 = 0.0592 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 07:34:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX043997/SRX043997.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX043997/SRX043997.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX043997/SRX043997.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX043997/SRX043997.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 07:34:22: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:34:22: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:34:27: 1000000 INFO @ Tue, 16 Jun 2020 07:34:32: 2000000 INFO @ Tue, 16 Jun 2020 07:34:38: 3000000 INFO @ Tue, 16 Jun 2020 07:34:43: 4000000 INFO @ Tue, 16 Jun 2020 07:34:48: 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 07:34:52: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:34:52: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:34:52: #1 total tags in treatment: 5842133 INFO @ Tue, 16 Jun 2020 07:34:52: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:34:52: #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 07:34:52: #1 tags after filtering in treatment: 5842133 INFO @ Tue, 16 Jun 2020 07:34:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:34:52: #1 finished! INFO @ Tue, 16 Jun 2020 07:34:52: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:34:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:34:52: #2 number of paired peaks: 331 WARNING @ Tue, 16 Jun 2020 07:34:52: Fewer paired peaks (331) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 331 pairs to build model! INFO @ Tue, 16 Jun 2020 07:34:52: start model_add_line... INFO @ Tue, 16 Jun 2020 07:34:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX043997/SRX043997.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX043997/SRX043997.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX043997/SRX043997.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX043997/SRX043997.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 07:34:52: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:34:52: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:34:52: start X-correlation... INFO @ Tue, 16 Jun 2020 07:34:52: end of X-cor INFO @ Tue, 16 Jun 2020 07:34:52: #2 finished! INFO @ Tue, 16 Jun 2020 07:34:52: #2 predicted fragment length is 76 bps INFO @ Tue, 16 Jun 2020 07:34:52: #2 alternative fragment length(s) may be 3,36,76,97,109,458,561 bps INFO @ Tue, 16 Jun 2020 07:34:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX043997/SRX043997.05_model.r INFO @ Tue, 16 Jun 2020 07:34:52: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:34:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:34:58: 1000000 INFO @ Tue, 16 Jun 2020 07:35:03: 2000000 INFO @ Tue, 16 Jun 2020 07:35:05: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:35:08: 3000000 INFO @ Tue, 16 Jun 2020 07:35:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX043997/SRX043997.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:35:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX043997/SRX043997.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:35:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX043997/SRX043997.05_summits.bed INFO @ Tue, 16 Jun 2020 07:35:11: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (302 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:35:13: 4000000 INFO @ Tue, 16 Jun 2020 07:35:18: 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 07:35:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX043997/SRX043997.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX043997/SRX043997.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX043997/SRX043997.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX043997/SRX043997.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 07:35:23: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:35:23: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:35:23: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:35:23: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:35:23: #1 total tags in treatment: 5842133 INFO @ Tue, 16 Jun 2020 07:35:23: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:35:23: #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 07:35:23: #1 tags after filtering in treatment: 5842133 INFO @ Tue, 16 Jun 2020 07:35:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:35:23: #1 finished! INFO @ Tue, 16 Jun 2020 07:35:23: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:35:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:35:23: #2 number of paired peaks: 331 WARNING @ Tue, 16 Jun 2020 07:35:23: Fewer paired peaks (331) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 331 pairs to build model! INFO @ Tue, 16 Jun 2020 07:35:23: start model_add_line... INFO @ Tue, 16 Jun 2020 07:35:23: start X-correlation... INFO @ Tue, 16 Jun 2020 07:35:23: end of X-cor INFO @ Tue, 16 Jun 2020 07:35:23: #2 finished! INFO @ Tue, 16 Jun 2020 07:35:23: #2 predicted fragment length is 76 bps INFO @ Tue, 16 Jun 2020 07:35:23: #2 alternative fragment length(s) may be 3,36,76,97,109,458,561 bps INFO @ Tue, 16 Jun 2020 07:35:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX043997/SRX043997.10_model.r INFO @ Tue, 16 Jun 2020 07:35:23: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:35:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:35:28: 1000000 INFO @ Tue, 16 Jun 2020 07:35:33: 2000000 INFO @ Tue, 16 Jun 2020 07:35:36: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:35:39: 3000000 INFO @ Tue, 16 Jun 2020 07:35:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX043997/SRX043997.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:35:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX043997/SRX043997.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:35:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX043997/SRX043997.10_summits.bed INFO @ Tue, 16 Jun 2020 07:35:42: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (174 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:35:44: 4000000 INFO @ Tue, 16 Jun 2020 07:35:50: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:35:55: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:35:55: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:35:55: #1 total tags in treatment: 5842133 INFO @ Tue, 16 Jun 2020 07:35:55: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:35:55: #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 07:35:55: #1 tags after filtering in treatment: 5842133 INFO @ Tue, 16 Jun 2020 07:35:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:35:55: #1 finished! INFO @ Tue, 16 Jun 2020 07:35:55: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:35:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:35:55: #2 number of paired peaks: 331 WARNING @ Tue, 16 Jun 2020 07:35:55: Fewer paired peaks (331) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 331 pairs to build model! INFO @ Tue, 16 Jun 2020 07:35:55: start model_add_line... INFO @ Tue, 16 Jun 2020 07:35:55: start X-correlation... INFO @ Tue, 16 Jun 2020 07:35:55: end of X-cor INFO @ Tue, 16 Jun 2020 07:35:55: #2 finished! INFO @ Tue, 16 Jun 2020 07:35:55: #2 predicted fragment length is 76 bps INFO @ Tue, 16 Jun 2020 07:35:55: #2 alternative fragment length(s) may be 3,36,76,97,109,458,561 bps INFO @ Tue, 16 Jun 2020 07:35:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX043997/SRX043997.20_model.r INFO @ Tue, 16 Jun 2020 07:35:55: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:35:55: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:36:08: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:36:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX043997/SRX043997.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:36:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX043997/SRX043997.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:36:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX043997/SRX043997.20_summits.bed INFO @ Tue, 16 Jun 2020 07:36:14: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (68 records, 4 fields): 1 millis CompletedMACS2peakCalling