Job ID = 16436154 SRX = SRX13110354 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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: 00:06:10 20710289 reads; of these: 20710289 (100.00%) were unpaired; of these: 494872 (2.39%) aligned 0 times 17805104 (85.97%) aligned exactly 1 time 2410313 (11.64%) aligned >1 times 97.61% overall alignment rate Time searching: 00:06:10 Overall time: 00:06:10 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 12 files... [bam_rmdupse_core] 4384834 / 20215417 = 0.2169 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 11:10:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13110354/SRX13110354.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13110354/SRX13110354.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13110354/SRX13110354.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13110354/SRX13110354.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 11:10:22: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:10:22: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:10:29: 1000000 INFO @ Tue, 02 Aug 2022 11:10:35: 2000000 INFO @ Tue, 02 Aug 2022 11:10:41: 3000000 INFO @ Tue, 02 Aug 2022 11:10:47: 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 11:10:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13110354/SRX13110354.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13110354/SRX13110354.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13110354/SRX13110354.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13110354/SRX13110354.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 11:10:52: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:10:52: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:10:53: 5000000 INFO @ Tue, 02 Aug 2022 11:10:59: 1000000 INFO @ Tue, 02 Aug 2022 11:11:00: 6000000 INFO @ Tue, 02 Aug 2022 11:11:06: 2000000 INFO @ Tue, 02 Aug 2022 11:11:07: 7000000 INFO @ Tue, 02 Aug 2022 11:11:13: 3000000 INFO @ Tue, 02 Aug 2022 11:11:14: 8000000 INFO @ Tue, 02 Aug 2022 11:11:19: 4000000 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 11:11:21: 9000000 INFO @ Tue, 02 Aug 2022 11:11:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13110354/SRX13110354.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13110354/SRX13110354.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13110354/SRX13110354.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13110354/SRX13110354.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 11:11:22: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:11:22: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:11:26: 5000000 INFO @ Tue, 02 Aug 2022 11:11:28: 10000000 INFO @ Tue, 02 Aug 2022 11:11:29: 1000000 INFO @ Tue, 02 Aug 2022 11:11:33: 6000000 INFO @ Tue, 02 Aug 2022 11:11:35: 11000000 INFO @ Tue, 02 Aug 2022 11:11:35: 2000000 INFO @ Tue, 02 Aug 2022 11:11:39: 7000000 INFO @ Tue, 02 Aug 2022 11:11:42: 12000000 INFO @ Tue, 02 Aug 2022 11:11:42: 3000000 INFO @ Tue, 02 Aug 2022 11:11:46: 8000000 INFO @ Tue, 02 Aug 2022 11:11:49: 13000000 INFO @ Tue, 02 Aug 2022 11:11:49: 4000000 INFO @ Tue, 02 Aug 2022 11:11:52: 9000000 INFO @ Tue, 02 Aug 2022 11:11:55: 5000000 INFO @ Tue, 02 Aug 2022 11:11:55: 14000000 INFO @ Tue, 02 Aug 2022 11:11:59: 10000000 INFO @ Tue, 02 Aug 2022 11:12:02: 6000000 INFO @ Tue, 02 Aug 2022 11:12:02: 15000000 INFO @ Tue, 02 Aug 2022 11:12:06: 11000000 INFO @ Tue, 02 Aug 2022 11:12:08: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 11:12:08: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 11:12:08: #1 total tags in treatment: 15830583 INFO @ Tue, 02 Aug 2022 11:12:08: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:12:08: #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 11:12:08: #1 tags after filtering in treatment: 15830583 INFO @ Tue, 02 Aug 2022 11:12:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:12:08: #1 finished! INFO @ Tue, 02 Aug 2022 11:12:08: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:12:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:12:08: 7000000 INFO @ Tue, 02 Aug 2022 11:12:09: #2 number of paired peaks: 1223 INFO @ Tue, 02 Aug 2022 11:12:09: start model_add_line... INFO @ Tue, 02 Aug 2022 11:12:09: start X-correlation... INFO @ Tue, 02 Aug 2022 11:12:09: end of X-cor INFO @ Tue, 02 Aug 2022 11:12:09: #2 finished! INFO @ Tue, 02 Aug 2022 11:12:09: #2 predicted fragment length is 185 bps INFO @ Tue, 02 Aug 2022 11:12:09: #2 alternative fragment length(s) may be 185 bps INFO @ Tue, 02 Aug 2022 11:12:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13110354/SRX13110354.05_model.r INFO @ Tue, 02 Aug 2022 11:12:09: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:12:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:12:13: 12000000 INFO @ Tue, 02 Aug 2022 11:12:15: 8000000 INFO @ Tue, 02 Aug 2022 11:12:19: 13000000 INFO @ Tue, 02 Aug 2022 11:12:21: 9000000 INFO @ Tue, 02 Aug 2022 11:12:26: 14000000 INFO @ Tue, 02 Aug 2022 11:12:28: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 11:12:33: 15000000 INFO @ Tue, 02 Aug 2022 11:12:35: 11000000 INFO @ Tue, 02 Aug 2022 11:12:38: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 11:12:38: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 11:12:38: #1 total tags in treatment: 15830583 INFO @ Tue, 02 Aug 2022 11:12:38: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:12:38: #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 11:12:38: #1 tags after filtering in treatment: 15830583 INFO @ Tue, 02 Aug 2022 11:12:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:12:38: #1 finished! INFO @ Tue, 02 Aug 2022 11:12:38: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:12:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:12:39: #2 number of paired peaks: 1223 INFO @ Tue, 02 Aug 2022 11:12:39: start model_add_line... INFO @ Tue, 02 Aug 2022 11:12:40: start X-correlation... INFO @ Tue, 02 Aug 2022 11:12:40: end of X-cor INFO @ Tue, 02 Aug 2022 11:12:40: #2 finished! INFO @ Tue, 02 Aug 2022 11:12:40: #2 predicted fragment length is 185 bps INFO @ Tue, 02 Aug 2022 11:12:40: #2 alternative fragment length(s) may be 185 bps INFO @ Tue, 02 Aug 2022 11:12:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13110354/SRX13110354.10_model.r INFO @ Tue, 02 Aug 2022 11:12:40: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:12:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:12:41: 12000000 INFO @ Tue, 02 Aug 2022 11:12:46: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:12:48: 13000000 INFO @ Tue, 02 Aug 2022 11:12:54: 14000000 INFO @ Tue, 02 Aug 2022 11:13:00: 15000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 11:13:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13110354/SRX13110354.05_peaks.xls INFO @ Tue, 02 Aug 2022 11:13:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13110354/SRX13110354.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:13:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13110354/SRX13110354.05_summits.bed INFO @ Tue, 02 Aug 2022 11:13:02: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (13660 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:13:05: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 11:13:05: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 11:13:05: #1 total tags in treatment: 15830583 INFO @ Tue, 02 Aug 2022 11:13:05: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:13:05: #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 11:13:05: #1 tags after filtering in treatment: 15830583 INFO @ Tue, 02 Aug 2022 11:13:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:13:05: #1 finished! INFO @ Tue, 02 Aug 2022 11:13:05: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:13:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:13:06: #2 number of paired peaks: 1223 INFO @ Tue, 02 Aug 2022 11:13:06: start model_add_line... INFO @ Tue, 02 Aug 2022 11:13:06: start X-correlation... INFO @ Tue, 02 Aug 2022 11:13:06: end of X-cor INFO @ Tue, 02 Aug 2022 11:13:06: #2 finished! INFO @ Tue, 02 Aug 2022 11:13:06: #2 predicted fragment length is 185 bps INFO @ Tue, 02 Aug 2022 11:13:06: #2 alternative fragment length(s) may be 185 bps INFO @ Tue, 02 Aug 2022 11:13:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13110354/SRX13110354.20_model.r INFO @ Tue, 02 Aug 2022 11:13:06: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:13:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:13:17: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:13:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13110354/SRX13110354.10_peaks.xls INFO @ Tue, 02 Aug 2022 11:13:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13110354/SRX13110354.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:13:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13110354/SRX13110354.10_summits.bed INFO @ Tue, 02 Aug 2022 11:13:34: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (10117 records, 4 fields): 95 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:13:43: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:14:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13110354/SRX13110354.20_peaks.xls INFO @ Tue, 02 Aug 2022 11:14:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13110354/SRX13110354.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:14:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13110354/SRX13110354.20_summits.bed INFO @ Tue, 02 Aug 2022 11:14:01: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (6563 records, 4 fields): 24 millis CompletedMACS2peakCalling