Job ID = 16434332 SRX = SRX10925650 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: 00:04:31 23421007 reads; of these: 23421007 (100.00%) were unpaired; of these: 13531637 (57.78%) aligned 0 times 8803819 (37.59%) aligned exactly 1 time 1085551 (4.63%) aligned >1 times 42.22% overall alignment rate Time searching: 00:04:31 Overall time: 00:04:31 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] 2085396 / 9889370 = 0.2109 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 09:58:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10925650/SRX10925650.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10925650/SRX10925650.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10925650/SRX10925650.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10925650/SRX10925650.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 09:58:55: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:58:55: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:59:00: 1000000 INFO @ Tue, 02 Aug 2022 09:59:06: 2000000 INFO @ Tue, 02 Aug 2022 09:59:11: 3000000 INFO @ Tue, 02 Aug 2022 09:59:16: 4000000 INFO @ Tue, 02 Aug 2022 09:59:21: 5000000 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 09:59:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10925650/SRX10925650.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10925650/SRX10925650.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10925650/SRX10925650.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10925650/SRX10925650.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 09:59:24: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:59:24: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:59:26: 6000000 INFO @ Tue, 02 Aug 2022 09:59:30: 1000000 INFO @ Tue, 02 Aug 2022 09:59:31: 7000000 INFO @ Tue, 02 Aug 2022 09:59:35: 2000000 INFO @ Tue, 02 Aug 2022 09:59:35: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 09:59:35: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 09:59:35: #1 total tags in treatment: 7803974 INFO @ Tue, 02 Aug 2022 09:59:35: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 09:59:35: #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 09:59:36: #1 tags after filtering in treatment: 7803974 INFO @ Tue, 02 Aug 2022 09:59:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 09:59:36: #1 finished! INFO @ Tue, 02 Aug 2022 09:59:36: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 09:59:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 09:59:37: #2 number of paired peaks: 7523 INFO @ Tue, 02 Aug 2022 09:59:37: start model_add_line... INFO @ Tue, 02 Aug 2022 09:59:37: start X-correlation... INFO @ Tue, 02 Aug 2022 09:59:37: end of X-cor INFO @ Tue, 02 Aug 2022 09:59:37: #2 finished! INFO @ Tue, 02 Aug 2022 09:59:37: #2 predicted fragment length is 234 bps INFO @ Tue, 02 Aug 2022 09:59:37: #2 alternative fragment length(s) may be 234 bps INFO @ Tue, 02 Aug 2022 09:59:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10925650/SRX10925650.05_model.r INFO @ Tue, 02 Aug 2022 09:59:37: #3 Call peaks... INFO @ Tue, 02 Aug 2022 09:59:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 09:59:41: 3000000 INFO @ Tue, 02 Aug 2022 09:59:46: 4000000 INFO @ Tue, 02 Aug 2022 09:59:51: 5000000 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 09:59:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10925650/SRX10925650.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10925650/SRX10925650.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10925650/SRX10925650.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10925650/SRX10925650.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 09:59:54: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:59:54: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:59:56: 6000000 INFO @ Tue, 02 Aug 2022 10:00:00: 1000000 INFO @ Tue, 02 Aug 2022 10:00:01: 7000000 INFO @ Tue, 02 Aug 2022 10:00:02: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:00:05: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 10:00:05: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 10:00:05: #1 total tags in treatment: 7803974 INFO @ Tue, 02 Aug 2022 10:00:05: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:00:05: #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 10:00:05: #1 tags after filtering in treatment: 7803974 INFO @ Tue, 02 Aug 2022 10:00:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:00:05: #1 finished! INFO @ Tue, 02 Aug 2022 10:00:05: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:00:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:00:06: 2000000 INFO @ Tue, 02 Aug 2022 10:00:06: #2 number of paired peaks: 7523 INFO @ Tue, 02 Aug 2022 10:00:06: start model_add_line... INFO @ Tue, 02 Aug 2022 10:00:07: start X-correlation... INFO @ Tue, 02 Aug 2022 10:00:07: end of X-cor INFO @ Tue, 02 Aug 2022 10:00:07: #2 finished! INFO @ Tue, 02 Aug 2022 10:00:07: #2 predicted fragment length is 234 bps INFO @ Tue, 02 Aug 2022 10:00:07: #2 alternative fragment length(s) may be 234 bps INFO @ Tue, 02 Aug 2022 10:00:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10925650/SRX10925650.10_model.r INFO @ Tue, 02 Aug 2022 10:00:07: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:00:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:00:11: 3000000 INFO @ Tue, 02 Aug 2022 10:00:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10925650/SRX10925650.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:00:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10925650/SRX10925650.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:00:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10925650/SRX10925650.05_summits.bed INFO @ Tue, 02 Aug 2022 10:00:13: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (12156 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:00:16: 4000000 INFO @ Tue, 02 Aug 2022 10:00:21: 5000000 INFO @ Tue, 02 Aug 2022 10:00:26: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:00:31: 7000000 INFO @ Tue, 02 Aug 2022 10:00:32: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:00:35: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 10:00:35: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 10:00:35: #1 total tags in treatment: 7803974 INFO @ Tue, 02 Aug 2022 10:00:35: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:00:35: #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 10:00:35: #1 tags after filtering in treatment: 7803974 INFO @ Tue, 02 Aug 2022 10:00:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:00:35: #1 finished! INFO @ Tue, 02 Aug 2022 10:00:35: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:00:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:00:36: #2 number of paired peaks: 7523 INFO @ Tue, 02 Aug 2022 10:00:36: start model_add_line... INFO @ Tue, 02 Aug 2022 10:00:36: start X-correlation... INFO @ Tue, 02 Aug 2022 10:00:36: end of X-cor INFO @ Tue, 02 Aug 2022 10:00:36: #2 finished! INFO @ Tue, 02 Aug 2022 10:00:36: #2 predicted fragment length is 234 bps INFO @ Tue, 02 Aug 2022 10:00:36: #2 alternative fragment length(s) may be 234 bps INFO @ Tue, 02 Aug 2022 10:00:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10925650/SRX10925650.20_model.r INFO @ Tue, 02 Aug 2022 10:00:36: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:00:36: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 10:00:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10925650/SRX10925650.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:00:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10925650/SRX10925650.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:00:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10925650/SRX10925650.10_summits.bed INFO @ Tue, 02 Aug 2022 10:00:42: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (9443 records, 4 fields): 46 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:01:01: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:01:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10925650/SRX10925650.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:01:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10925650/SRX10925650.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:01:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10925650/SRX10925650.20_summits.bed INFO @ Tue, 02 Aug 2022 10:01:11: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (6219 records, 4 fields): 34 millis CompletedMACS2peakCalling