Job ID = 16435540 SRX = SRX13110351 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T01:46:45 prefetch.2.10.7: 1) Downloading 'SRR16918021'... 2022-08-02T01:46:45 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T01:47:07 prefetch.2.10.7: HTTPS download succeed 2022-08-02T01:47:08 prefetch.2.10.7: 'SRR16918021' is valid 2022-08-02T01:47:08 prefetch.2.10.7: 1) 'SRR16918021' was downloaded successfully 2022-08-02T01:47:08 prefetch.2.10.7: 'SRR16918021' has 0 unresolved dependencies Read 12742419 spots for SRR16918021/SRR16918021.sra Written 12742419 spots for SRR16918021/SRR16918021.sra fastq に変換しました。 bowtie でマッピング中... Your job 16436119 ("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: 00:04:11 12742419 reads; of these: 12742419 (100.00%) were unpaired; of these: 748059 (5.87%) aligned 0 times 10451806 (82.02%) aligned exactly 1 time 1542554 (12.11%) aligned >1 times 94.13% overall alignment rate Time searching: 00:04:12 Overall time: 00:04:12 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_sort_core] merging from 8 files... [bam_rmdupse_core] 2162464 / 11994360 = 0.1803 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 10:55:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13110351/SRX13110351.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13110351/SRX13110351.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13110351/SRX13110351.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13110351/SRX13110351.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 10:55:59: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:55:59: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:56:05: 1000000 INFO @ Tue, 02 Aug 2022 10:56:12: 2000000 INFO @ Tue, 02 Aug 2022 10:56:18: 3000000 INFO @ Tue, 02 Aug 2022 10:56:25: 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 10:56:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13110351/SRX13110351.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13110351/SRX13110351.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13110351/SRX13110351.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13110351/SRX13110351.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 10:56:28: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:56:28: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:56:33: 5000000 INFO @ Tue, 02 Aug 2022 10:56:36: 1000000 INFO @ Tue, 02 Aug 2022 10:56:42: 6000000 INFO @ Tue, 02 Aug 2022 10:56:45: 2000000 INFO @ Tue, 02 Aug 2022 10:56:51: 7000000 INFO @ Tue, 02 Aug 2022 10:56:53: 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 10:56:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13110351/SRX13110351.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13110351/SRX13110351.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13110351/SRX13110351.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13110351/SRX13110351.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 10:56:58: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:56:58: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:57:00: 8000000 INFO @ Tue, 02 Aug 2022 10:57:02: 4000000 INFO @ Tue, 02 Aug 2022 10:57:07: 1000000 INFO @ Tue, 02 Aug 2022 10:57:09: 9000000 INFO @ Tue, 02 Aug 2022 10:57:11: 5000000 INFO @ Tue, 02 Aug 2022 10:57:16: 2000000 INFO @ Tue, 02 Aug 2022 10:57:16: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:57:16: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:57:16: #1 total tags in treatment: 9831896 INFO @ Tue, 02 Aug 2022 10:57:16: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:57:16: #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 10:57:17: #1 tags after filtering in treatment: 9831896 INFO @ Tue, 02 Aug 2022 10:57:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:57:17: #1 finished! INFO @ Tue, 02 Aug 2022 10:57:17: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:57:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:57:17: #2 number of paired peaks: 1896 INFO @ Tue, 02 Aug 2022 10:57:17: start model_add_line... INFO @ Tue, 02 Aug 2022 10:57:17: start X-correlation... INFO @ Tue, 02 Aug 2022 10:57:18: end of X-cor INFO @ Tue, 02 Aug 2022 10:57:18: #2 finished! INFO @ Tue, 02 Aug 2022 10:57:18: #2 predicted fragment length is 236 bps INFO @ Tue, 02 Aug 2022 10:57:18: #2 alternative fragment length(s) may be 236 bps INFO @ Tue, 02 Aug 2022 10:57:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13110351/SRX13110351.05_model.r INFO @ Tue, 02 Aug 2022 10:57:18: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:57:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:57:20: 6000000 INFO @ Tue, 02 Aug 2022 10:57:25: 3000000 INFO @ Tue, 02 Aug 2022 10:57:29: 7000000 INFO @ Tue, 02 Aug 2022 10:57:34: 4000000 INFO @ Tue, 02 Aug 2022 10:57:38: 8000000 INFO @ Tue, 02 Aug 2022 10:57:43: 5000000 INFO @ Tue, 02 Aug 2022 10:57:46: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:57:47: 9000000 INFO @ Tue, 02 Aug 2022 10:57:52: 6000000 INFO @ Tue, 02 Aug 2022 10:57:54: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:57:54: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:57:54: #1 total tags in treatment: 9831896 INFO @ Tue, 02 Aug 2022 10:57:54: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:57:54: #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 10:57:54: #1 tags after filtering in treatment: 9831896 INFO @ Tue, 02 Aug 2022 10:57:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:57:54: #1 finished! INFO @ Tue, 02 Aug 2022 10:57:54: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:57:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:57:55: #2 number of paired peaks: 1896 INFO @ Tue, 02 Aug 2022 10:57:55: start model_add_line... INFO @ Tue, 02 Aug 2022 10:57:55: start X-correlation... INFO @ Tue, 02 Aug 2022 10:57:55: end of X-cor INFO @ Tue, 02 Aug 2022 10:57:55: #2 finished! INFO @ Tue, 02 Aug 2022 10:57:55: #2 predicted fragment length is 236 bps INFO @ Tue, 02 Aug 2022 10:57:55: #2 alternative fragment length(s) may be 236 bps INFO @ Tue, 02 Aug 2022 10:57:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13110351/SRX13110351.10_model.r INFO @ Tue, 02 Aug 2022 10:57:55: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:57:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:57:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13110351/SRX13110351.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:57:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13110351/SRX13110351.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:57:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13110351/SRX13110351.05_summits.bed INFO @ Tue, 02 Aug 2022 10:57:58: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (9352 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:58:01: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:58:10: 8000000 INFO @ Tue, 02 Aug 2022 10:58:18: 9000000 INFO @ Tue, 02 Aug 2022 10:58:23: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:58:24: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:58:24: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:58:24: #1 total tags in treatment: 9831896 INFO @ Tue, 02 Aug 2022 10:58:24: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:58:24: #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 10:58:25: #1 tags after filtering in treatment: 9831896 INFO @ Tue, 02 Aug 2022 10:58:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:58:25: #1 finished! INFO @ Tue, 02 Aug 2022 10:58:25: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:58:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:58:25: #2 number of paired peaks: 1896 INFO @ Tue, 02 Aug 2022 10:58:25: start model_add_line... INFO @ Tue, 02 Aug 2022 10:58:26: start X-correlation... INFO @ Tue, 02 Aug 2022 10:58:26: end of X-cor INFO @ Tue, 02 Aug 2022 10:58:26: #2 finished! INFO @ Tue, 02 Aug 2022 10:58:26: #2 predicted fragment length is 236 bps INFO @ Tue, 02 Aug 2022 10:58:26: #2 alternative fragment length(s) may be 236 bps INFO @ Tue, 02 Aug 2022 10:58:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13110351/SRX13110351.20_model.r INFO @ Tue, 02 Aug 2022 10:58:26: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:58:26: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 10:58:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13110351/SRX13110351.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:58:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13110351/SRX13110351.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:58:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13110351/SRX13110351.10_summits.bed INFO @ Tue, 02 Aug 2022 10:58:35: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (6718 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:58:53: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:59:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13110351/SRX13110351.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:59:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13110351/SRX13110351.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:59:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13110351/SRX13110351.20_summits.bed INFO @ Tue, 02 Aug 2022 10:59:05: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4168 records, 4 fields): 26 millis CompletedMACS2peakCalling