Job ID = 16435541 SRX = SRX13110352 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T01:47:15 prefetch.2.10.7: 1) Downloading 'SRR16918022'... 2022-08-02T01:47:15 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T01:47:48 prefetch.2.10.7: HTTPS download succeed 2022-08-02T01:47:48 prefetch.2.10.7: 'SRR16918022' is valid 2022-08-02T01:47:48 prefetch.2.10.7: 1) 'SRR16918022' was downloaded successfully 2022-08-02T01:47:48 prefetch.2.10.7: 'SRR16918022' has 0 unresolved dependencies Read 8256086 spots for SRR16918022/SRR16918022.sra Written 8256086 spots for SRR16918022/SRR16918022.sra fastq に変換しました。 bowtie でマッピング中... Your job 16436102 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:37 8256086 reads; of these: 8256086 (100.00%) were unpaired; of these: 921790 (11.16%) aligned 0 times 6408468 (77.62%) aligned exactly 1 time 925828 (11.21%) aligned >1 times 88.84% overall alignment rate Time searching: 00:02:37 Overall time: 00:02:37 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] 1034462 / 7334296 = 0.1410 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 10:53:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13110352/SRX13110352.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13110352/SRX13110352.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13110352/SRX13110352.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13110352/SRX13110352.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, 02 Aug 2022 10:53:05: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:53:05: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:53:12: 1000000 INFO @ Tue, 02 Aug 2022 10:53:19: 2000000 INFO @ Tue, 02 Aug 2022 10:53:26: 3000000 INFO @ Tue, 02 Aug 2022 10:53:32: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 10:53:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13110352/SRX13110352.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13110352/SRX13110352.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13110352/SRX13110352.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13110352/SRX13110352.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, 02 Aug 2022 10:53:35: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:53:35: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:53:38: 5000000 INFO @ Tue, 02 Aug 2022 10:53:43: 1000000 INFO @ Tue, 02 Aug 2022 10:53:45: 6000000 INFO @ Tue, 02 Aug 2022 10:53:47: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:53:47: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:53:47: #1 total tags in treatment: 6299834 INFO @ Tue, 02 Aug 2022 10:53:47: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:53:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 10:53:47: #1 tags after filtering in treatment: 6299834 INFO @ Tue, 02 Aug 2022 10:53:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:53:47: #1 finished! INFO @ Tue, 02 Aug 2022 10:53:47: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:53:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:53:48: #2 number of paired peaks: 2173 INFO @ Tue, 02 Aug 2022 10:53:48: start model_add_line... INFO @ Tue, 02 Aug 2022 10:53:48: start X-correlation... INFO @ Tue, 02 Aug 2022 10:53:48: end of X-cor INFO @ Tue, 02 Aug 2022 10:53:48: #2 finished! INFO @ Tue, 02 Aug 2022 10:53:48: #2 predicted fragment length is 222 bps INFO @ Tue, 02 Aug 2022 10:53:48: #2 alternative fragment length(s) may be 222 bps INFO @ Tue, 02 Aug 2022 10:53:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13110352/SRX13110352.05_model.r INFO @ Tue, 02 Aug 2022 10:53:48: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:53:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:53:51: 2000000 INFO @ Tue, 02 Aug 2022 10:53:57: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 10:54:04: 4000000 INFO @ Tue, 02 Aug 2022 10:54:04: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:54:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13110352/SRX13110352.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13110352/SRX13110352.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13110352/SRX13110352.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13110352/SRX13110352.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, 02 Aug 2022 10:54:05: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:54:05: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:54:11: 5000000 INFO @ Tue, 02 Aug 2022 10:54:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13110352/SRX13110352.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:54:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13110352/SRX13110352.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:54:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13110352/SRX13110352.05_summits.bed INFO @ Tue, 02 Aug 2022 10:54:12: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (7735 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:54:13: 1000000 INFO @ Tue, 02 Aug 2022 10:54:18: 6000000 INFO @ Tue, 02 Aug 2022 10:54:20: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:54:20: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:54:20: #1 total tags in treatment: 6299834 INFO @ Tue, 02 Aug 2022 10:54:20: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:54:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 10:54:20: #1 tags after filtering in treatment: 6299834 INFO @ Tue, 02 Aug 2022 10:54:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:54:20: #1 finished! INFO @ Tue, 02 Aug 2022 10:54:20: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:54:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:54:21: #2 number of paired peaks: 2173 INFO @ Tue, 02 Aug 2022 10:54:21: start model_add_line... INFO @ Tue, 02 Aug 2022 10:54:21: start X-correlation... INFO @ Tue, 02 Aug 2022 10:54:21: end of X-cor INFO @ Tue, 02 Aug 2022 10:54:21: #2 finished! INFO @ Tue, 02 Aug 2022 10:54:21: #2 predicted fragment length is 222 bps INFO @ Tue, 02 Aug 2022 10:54:21: #2 alternative fragment length(s) may be 222 bps INFO @ Tue, 02 Aug 2022 10:54:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13110352/SRX13110352.10_model.r INFO @ Tue, 02 Aug 2022 10:54:21: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:54:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:54:21: 2000000 INFO @ Tue, 02 Aug 2022 10:54:28: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:54:35: 4000000 INFO @ Tue, 02 Aug 2022 10:54:38: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:54:43: 5000000 INFO @ Tue, 02 Aug 2022 10:54:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13110352/SRX13110352.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:54:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13110352/SRX13110352.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:54:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13110352/SRX13110352.10_summits.bed INFO @ Tue, 02 Aug 2022 10:54:46: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5260 records, 4 fields): 35 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 10:54:50: 6000000 INFO @ Tue, 02 Aug 2022 10:54:52: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:54:52: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:54:52: #1 total tags in treatment: 6299834 INFO @ Tue, 02 Aug 2022 10:54:52: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:54:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 10:54:52: #1 tags after filtering in treatment: 6299834 INFO @ Tue, 02 Aug 2022 10:54:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:54:52: #1 finished! INFO @ Tue, 02 Aug 2022 10:54:52: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:54:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:54:52: #2 number of paired peaks: 2173 INFO @ Tue, 02 Aug 2022 10:54:52: start model_add_line... INFO @ Tue, 02 Aug 2022 10:54:52: start X-correlation... INFO @ Tue, 02 Aug 2022 10:54:52: end of X-cor INFO @ Tue, 02 Aug 2022 10:54:52: #2 finished! INFO @ Tue, 02 Aug 2022 10:54:52: #2 predicted fragment length is 222 bps INFO @ Tue, 02 Aug 2022 10:54:52: #2 alternative fragment length(s) may be 222 bps INFO @ Tue, 02 Aug 2022 10:54:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13110352/SRX13110352.20_model.r INFO @ Tue, 02 Aug 2022 10:54:53: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:54:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:55:09: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:55:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13110352/SRX13110352.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:55:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13110352/SRX13110352.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:55:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13110352/SRX13110352.20_summits.bed INFO @ Tue, 02 Aug 2022 10:55:17: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2925 records, 4 fields): 29 millis CompletedMACS2peakCalling