Job ID = 16435533 SRX = SRX13110345 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T01:46:30 prefetch.2.10.7: 1) Downloading 'SRR16918015'... 2022-08-02T01:46:30 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T01:46:36 prefetch.2.10.7: HTTPS download succeed 2022-08-02T01:46:36 prefetch.2.10.7: 'SRR16918015' is valid 2022-08-02T01:46:36 prefetch.2.10.7: 1) 'SRR16918015' was downloaded successfully 2022-08-02T01:46:36 prefetch.2.10.7: 'SRR16918015' has 0 unresolved dependencies Read 13003194 spots for SRR16918015/SRR16918015.sra Written 13003194 spots for SRR16918015/SRR16918015.sra fastq に変換しました。 bowtie でマッピング中... Your job 16436011 ("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: 00:02:44 13003194 reads; of these: 13003194 (100.00%) were unpaired; of these: 6945104 (53.41%) aligned 0 times 5299637 (40.76%) aligned exactly 1 time 758453 (5.83%) aligned >1 times 46.59% overall alignment rate Time searching: 00:02:44 Overall time: 00:02:44 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] 1360388 / 6058090 = 0.2246 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 10:51:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13110345/SRX13110345.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13110345/SRX13110345.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13110345/SRX13110345.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13110345/SRX13110345.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 10:51:55: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:51:55: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:52:03: 1000000 INFO @ Tue, 02 Aug 2022 10:52:11: 2000000 INFO @ Tue, 02 Aug 2022 10:52:18: 3000000 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 10:52:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13110345/SRX13110345.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13110345/SRX13110345.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13110345/SRX13110345.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13110345/SRX13110345.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 10:52:24: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:52:24: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:52:26: 4000000 INFO @ Tue, 02 Aug 2022 10:52:32: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:52:32: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:52:32: #1 total tags in treatment: 4697702 INFO @ Tue, 02 Aug 2022 10:52:32: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:52:32: #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 10:52:32: #1 tags after filtering in treatment: 4697702 INFO @ Tue, 02 Aug 2022 10:52:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:52:32: #1 finished! INFO @ Tue, 02 Aug 2022 10:52:32: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:52:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:52:32: #2 number of paired peaks: 2058 INFO @ Tue, 02 Aug 2022 10:52:32: start model_add_line... INFO @ Tue, 02 Aug 2022 10:52:32: start X-correlation... INFO @ Tue, 02 Aug 2022 10:52:33: end of X-cor INFO @ Tue, 02 Aug 2022 10:52:33: #2 finished! INFO @ Tue, 02 Aug 2022 10:52:33: #2 predicted fragment length is 206 bps INFO @ Tue, 02 Aug 2022 10:52:33: #2 alternative fragment length(s) may be 206 bps INFO @ Tue, 02 Aug 2022 10:52:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13110345/SRX13110345.05_model.r INFO @ Tue, 02 Aug 2022 10:52:33: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:52:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:52:33: 1000000 INFO @ Tue, 02 Aug 2022 10:52:41: 2000000 INFO @ Tue, 02 Aug 2022 10:52:44: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:52:49: 3000000 INFO @ Tue, 02 Aug 2022 10:52:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13110345/SRX13110345.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:52:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13110345/SRX13110345.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:52:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13110345/SRX13110345.05_summits.bed INFO @ Tue, 02 Aug 2022 10:52:49: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5736 records, 4 fields): 26 millis CompletedMACS2peakCalling 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 10:52:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13110345/SRX13110345.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13110345/SRX13110345.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13110345/SRX13110345.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13110345/SRX13110345.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 10:52:54: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:52:54: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:52:56: 4000000 INFO @ Tue, 02 Aug 2022 10:53:02: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:53:02: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:53:02: #1 total tags in treatment: 4697702 INFO @ Tue, 02 Aug 2022 10:53:02: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:53:02: #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 10:53:02: #1 tags after filtering in treatment: 4697702 INFO @ Tue, 02 Aug 2022 10:53:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:53:02: #1 finished! INFO @ Tue, 02 Aug 2022 10:53:02: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:53:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:53:02: #2 number of paired peaks: 2058 INFO @ Tue, 02 Aug 2022 10:53:02: start model_add_line... INFO @ Tue, 02 Aug 2022 10:53:03: start X-correlation... INFO @ Tue, 02 Aug 2022 10:53:03: end of X-cor INFO @ Tue, 02 Aug 2022 10:53:03: #2 finished! INFO @ Tue, 02 Aug 2022 10:53:03: #2 predicted fragment length is 206 bps INFO @ Tue, 02 Aug 2022 10:53:03: #2 alternative fragment length(s) may be 206 bps INFO @ Tue, 02 Aug 2022 10:53:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13110345/SRX13110345.10_model.r INFO @ Tue, 02 Aug 2022 10:53:03: 1000000 INFO @ Tue, 02 Aug 2022 10:53:03: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:53:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:53:10: 2000000 INFO @ Tue, 02 Aug 2022 10:53:15: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:53:19: 3000000 INFO @ Tue, 02 Aug 2022 10:53:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13110345/SRX13110345.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:53:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13110345/SRX13110345.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:53:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13110345/SRX13110345.10_summits.bed INFO @ Tue, 02 Aug 2022 10:53:21: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3675 records, 4 fields): 6 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 10:53:27: 4000000 INFO @ Tue, 02 Aug 2022 10:53:32: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:53:32: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:53:32: #1 total tags in treatment: 4697702 INFO @ Tue, 02 Aug 2022 10:53:32: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:53:32: #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 10:53:32: #1 tags after filtering in treatment: 4697702 INFO @ Tue, 02 Aug 2022 10:53:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:53:32: #1 finished! INFO @ Tue, 02 Aug 2022 10:53:32: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:53:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:53:33: #2 number of paired peaks: 2058 INFO @ Tue, 02 Aug 2022 10:53:33: start model_add_line... INFO @ Tue, 02 Aug 2022 10:53:33: start X-correlation... INFO @ Tue, 02 Aug 2022 10:53:33: end of X-cor INFO @ Tue, 02 Aug 2022 10:53:33: #2 finished! INFO @ Tue, 02 Aug 2022 10:53:33: #2 predicted fragment length is 206 bps INFO @ Tue, 02 Aug 2022 10:53:33: #2 alternative fragment length(s) may be 206 bps INFO @ Tue, 02 Aug 2022 10:53:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13110345/SRX13110345.20_model.r INFO @ Tue, 02 Aug 2022 10:53:33: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:53:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:53:45: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:53:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13110345/SRX13110345.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:53:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13110345/SRX13110345.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:53:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13110345/SRX13110345.20_summits.bed INFO @ Tue, 02 Aug 2022 10:53:51: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1881 records, 4 fields): 34 millis CompletedMACS2peakCalling