Job ID = 16435113 SRX = SRX13110326 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T01:34:47 prefetch.2.10.7: 1) Downloading 'SRR16917996'... 2022-08-02T01:34:47 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T01:35:14 prefetch.2.10.7: HTTPS download succeed 2022-08-02T01:35:15 prefetch.2.10.7: 'SRR16917996' is valid 2022-08-02T01:35:15 prefetch.2.10.7: 1) 'SRR16917996' was downloaded successfully 2022-08-02T01:35:15 prefetch.2.10.7: 'SRR16917996' has 0 unresolved dependencies Read 13613036 spots for SRR16917996/SRR16917996.sra Written 13613036 spots for SRR16917996/SRR16917996.sra fastq に変換しました。 bowtie でマッピング中... Your job 16435503 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:43 13613036 reads; of these: 13613036 (100.00%) were unpaired; of these: 8464286 (62.18%) aligned 0 times 4436308 (32.59%) aligned exactly 1 time 712442 (5.23%) aligned >1 times 37.82% 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] 1011055 / 5148750 = 0.1964 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 10:40:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13110326/SRX13110326.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13110326/SRX13110326.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13110326/SRX13110326.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13110326/SRX13110326.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 10:40:28: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:40:28: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:40:34: 1000000 INFO @ Tue, 02 Aug 2022 10:40:40: 2000000 INFO @ Tue, 02 Aug 2022 10:40:47: 3000000 INFO @ Tue, 02 Aug 2022 10:40:53: 4000000 INFO @ Tue, 02 Aug 2022 10:40:53: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:40:53: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:40:53: #1 total tags in treatment: 4137695 INFO @ Tue, 02 Aug 2022 10:40:53: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:40:53: #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 10:40:53: #1 tags after filtering in treatment: 4137695 INFO @ Tue, 02 Aug 2022 10:40:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:40:53: #1 finished! INFO @ Tue, 02 Aug 2022 10:40:53: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:40:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:40:54: #2 number of paired peaks: 1221 INFO @ Tue, 02 Aug 2022 10:40:54: start model_add_line... INFO @ Tue, 02 Aug 2022 10:40:54: start X-correlation... INFO @ Tue, 02 Aug 2022 10:40:54: end of X-cor INFO @ Tue, 02 Aug 2022 10:40:54: #2 finished! INFO @ Tue, 02 Aug 2022 10:40:54: #2 predicted fragment length is 168 bps INFO @ Tue, 02 Aug 2022 10:40:54: #2 alternative fragment length(s) may be 168 bps INFO @ Tue, 02 Aug 2022 10:40:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13110326/SRX13110326.05_model.r INFO @ Tue, 02 Aug 2022 10:40:54: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:40:54: #3 Pre-compute pvalue-qvalue table... 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 10:40:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13110326/SRX13110326.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13110326/SRX13110326.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13110326/SRX13110326.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13110326/SRX13110326.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 10:40:57: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:40:57: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:41:03: 1000000 INFO @ Tue, 02 Aug 2022 10:41:04: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:41:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13110326/SRX13110326.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:41:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13110326/SRX13110326.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:41:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13110326/SRX13110326.05_summits.bed INFO @ Tue, 02 Aug 2022 10:41:09: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1342 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:41:10: 2000000 INFO @ Tue, 02 Aug 2022 10:41:16: 3000000 INFO @ Tue, 02 Aug 2022 10:41:22: 4000000 INFO @ Tue, 02 Aug 2022 10:41:22: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:41:22: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:41:22: #1 total tags in treatment: 4137695 INFO @ Tue, 02 Aug 2022 10:41:22: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:41:22: #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 10:41:22: #1 tags after filtering in treatment: 4137695 INFO @ Tue, 02 Aug 2022 10:41:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:41:22: #1 finished! INFO @ Tue, 02 Aug 2022 10:41:22: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:41:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:41:23: #2 number of paired peaks: 1221 INFO @ Tue, 02 Aug 2022 10:41:23: start model_add_line... INFO @ Tue, 02 Aug 2022 10:41:23: start X-correlation... INFO @ Tue, 02 Aug 2022 10:41:23: end of X-cor INFO @ Tue, 02 Aug 2022 10:41:23: #2 finished! INFO @ Tue, 02 Aug 2022 10:41:23: #2 predicted fragment length is 168 bps INFO @ Tue, 02 Aug 2022 10:41:23: #2 alternative fragment length(s) may be 168 bps INFO @ Tue, 02 Aug 2022 10:41:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13110326/SRX13110326.10_model.r INFO @ Tue, 02 Aug 2022 10:41:23: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:41:23: #3 Pre-compute pvalue-qvalue table... 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 10:41:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13110326/SRX13110326.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13110326/SRX13110326.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13110326/SRX13110326.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13110326/SRX13110326.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 10:41:28: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:41:28: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:41:33: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:41:34: 1000000 INFO @ Tue, 02 Aug 2022 10:41:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13110326/SRX13110326.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:41:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13110326/SRX13110326.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:41:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13110326/SRX13110326.10_summits.bed INFO @ Tue, 02 Aug 2022 10:41:38: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (910 records, 4 fields): 63 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:41:40: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:41:46: 3000000 INFO @ Tue, 02 Aug 2022 10:41:52: 4000000 INFO @ Tue, 02 Aug 2022 10:41:53: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:41:53: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:41:53: #1 total tags in treatment: 4137695 INFO @ Tue, 02 Aug 2022 10:41:53: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:41:53: #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 10:41:53: #1 tags after filtering in treatment: 4137695 INFO @ Tue, 02 Aug 2022 10:41:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:41:53: #1 finished! INFO @ Tue, 02 Aug 2022 10:41:53: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:41:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:41:53: #2 number of paired peaks: 1221 INFO @ Tue, 02 Aug 2022 10:41:53: start model_add_line... INFO @ Tue, 02 Aug 2022 10:41:53: start X-correlation... INFO @ Tue, 02 Aug 2022 10:41:53: end of X-cor INFO @ Tue, 02 Aug 2022 10:41:53: #2 finished! INFO @ Tue, 02 Aug 2022 10:41:53: #2 predicted fragment length is 168 bps INFO @ Tue, 02 Aug 2022 10:41:53: #2 alternative fragment length(s) may be 168 bps INFO @ Tue, 02 Aug 2022 10:41:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13110326/SRX13110326.20_model.r INFO @ Tue, 02 Aug 2022 10:41:53: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:41:53: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 10:42:03: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:42:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13110326/SRX13110326.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:42:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13110326/SRX13110326.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:42:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13110326/SRX13110326.20_summits.bed INFO @ Tue, 02 Aug 2022 10:42:08: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (595 records, 4 fields): 20 millis CompletedMACS2peakCalling