Job ID = 6367964 SRX = SRX4456923 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:01:18 prefetch.2.10.7: 1) Downloading 'SRR7591864'... 2020-06-16T00:01:18 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:02:18 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:02:18 prefetch.2.10.7: 'SRR7591864' is valid 2020-06-16T00:02:18 prefetch.2.10.7: 1) 'SRR7591864' was downloaded successfully Read 10540793 spots for SRR7591864/SRR7591864.sra Written 10540793 spots for SRR7591864/SRR7591864.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: 00:01:54 10540793 reads; of these: 10540793 (100.00%) were unpaired; of these: 3474460 (32.96%) aligned 0 times 6094479 (57.82%) aligned exactly 1 time 971854 (9.22%) aligned >1 times 67.04% overall alignment rate Time searching: 00:01:54 Overall time: 00:01:54 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] 1257022 / 7066333 = 0.1779 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 09:07:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4456923/SRX4456923.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4456923/SRX4456923.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4456923/SRX4456923.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4456923/SRX4456923.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 09:07:03: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:07:03: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:07:09: 1000000 INFO @ Tue, 16 Jun 2020 09:07:14: 2000000 INFO @ Tue, 16 Jun 2020 09:07:19: 3000000 INFO @ Tue, 16 Jun 2020 09:07:24: 4000000 INFO @ Tue, 16 Jun 2020 09:07:30: 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 09:07:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4456923/SRX4456923.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4456923/SRX4456923.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4456923/SRX4456923.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4456923/SRX4456923.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 09:07:33: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:07:33: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:07:34: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:07:34: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:07:34: #1 total tags in treatment: 5809311 INFO @ Tue, 16 Jun 2020 09:07:34: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:07:34: #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 09:07:34: #1 tags after filtering in treatment: 5809311 INFO @ Tue, 16 Jun 2020 09:07:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:07:34: #1 finished! INFO @ Tue, 16 Jun 2020 09:07:34: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:07:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:07:35: #2 number of paired peaks: 2650 INFO @ Tue, 16 Jun 2020 09:07:35: start model_add_line... INFO @ Tue, 16 Jun 2020 09:07:35: start X-correlation... INFO @ Tue, 16 Jun 2020 09:07:35: end of X-cor INFO @ Tue, 16 Jun 2020 09:07:35: #2 finished! INFO @ Tue, 16 Jun 2020 09:07:35: #2 predicted fragment length is 145 bps INFO @ Tue, 16 Jun 2020 09:07:35: #2 alternative fragment length(s) may be 145,148 bps INFO @ Tue, 16 Jun 2020 09:07:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4456923/SRX4456923.05_model.r INFO @ Tue, 16 Jun 2020 09:07:35: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:07:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:07:40: 1000000 INFO @ Tue, 16 Jun 2020 09:07:46: 2000000 INFO @ Tue, 16 Jun 2020 09:07:48: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:07:52: 3000000 INFO @ Tue, 16 Jun 2020 09:07:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4456923/SRX4456923.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:07:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4456923/SRX4456923.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:07:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4456923/SRX4456923.05_summits.bed INFO @ Tue, 16 Jun 2020 09:07:55: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3813 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:07:58: 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 09:08:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4456923/SRX4456923.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4456923/SRX4456923.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4456923/SRX4456923.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4456923/SRX4456923.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 09:08:03: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:08:03: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:08:04: 5000000 INFO @ Tue, 16 Jun 2020 09:08:10: 1000000 INFO @ Tue, 16 Jun 2020 09:08:10: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:08:10: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:08:10: #1 total tags in treatment: 5809311 INFO @ Tue, 16 Jun 2020 09:08:10: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:08:10: #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 09:08:10: #1 tags after filtering in treatment: 5809311 INFO @ Tue, 16 Jun 2020 09:08:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:08:10: #1 finished! INFO @ Tue, 16 Jun 2020 09:08:10: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:08:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:08:11: #2 number of paired peaks: 2650 INFO @ Tue, 16 Jun 2020 09:08:11: start model_add_line... INFO @ Tue, 16 Jun 2020 09:08:11: start X-correlation... INFO @ Tue, 16 Jun 2020 09:08:11: end of X-cor INFO @ Tue, 16 Jun 2020 09:08:11: #2 finished! INFO @ Tue, 16 Jun 2020 09:08:11: #2 predicted fragment length is 145 bps INFO @ Tue, 16 Jun 2020 09:08:11: #2 alternative fragment length(s) may be 145,148 bps INFO @ Tue, 16 Jun 2020 09:08:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4456923/SRX4456923.10_model.r INFO @ Tue, 16 Jun 2020 09:08:11: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:08:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:08:15: 2000000 INFO @ Tue, 16 Jun 2020 09:08:21: 3000000 INFO @ Tue, 16 Jun 2020 09:08:25: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:08:26: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:08:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4456923/SRX4456923.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:08:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4456923/SRX4456923.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:08:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4456923/SRX4456923.10_summits.bed INFO @ Tue, 16 Jun 2020 09:08:31: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1959 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:08:32: 5000000 INFO @ Tue, 16 Jun 2020 09:08:36: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:08:36: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:08:36: #1 total tags in treatment: 5809311 INFO @ Tue, 16 Jun 2020 09:08:36: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:08:36: #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 09:08:36: #1 tags after filtering in treatment: 5809311 INFO @ Tue, 16 Jun 2020 09:08:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:08:36: #1 finished! INFO @ Tue, 16 Jun 2020 09:08:36: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:08:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:08:36: #2 number of paired peaks: 2650 INFO @ Tue, 16 Jun 2020 09:08:36: start model_add_line... INFO @ Tue, 16 Jun 2020 09:08:37: start X-correlation... INFO @ Tue, 16 Jun 2020 09:08:37: end of X-cor INFO @ Tue, 16 Jun 2020 09:08:37: #2 finished! INFO @ Tue, 16 Jun 2020 09:08:37: #2 predicted fragment length is 145 bps INFO @ Tue, 16 Jun 2020 09:08:37: #2 alternative fragment length(s) may be 145,148 bps INFO @ Tue, 16 Jun 2020 09:08:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4456923/SRX4456923.20_model.r INFO @ Tue, 16 Jun 2020 09:08:37: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:08:37: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:08:50: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:08:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4456923/SRX4456923.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:08:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4456923/SRX4456923.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:08:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4456923/SRX4456923.20_summits.bed INFO @ Tue, 16 Jun 2020 09:08:56: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (736 records, 4 fields): 2 millis CompletedMACS2peakCalling