Job ID = 14160312 SRX = SRX8832069 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: 00:03:29 14729232 reads; of these: 14729232 (100.00%) were unpaired; of these: 688927 (4.68%) aligned 0 times 11959862 (81.20%) aligned exactly 1 time 2080443 (14.12%) aligned >1 times 95.32% overall alignment rate Time searching: 00:03:29 Overall time: 00:03:29 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] 1740818 / 14040305 = 0.1240 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 01:28:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8832069/SRX8832069.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8832069/SRX8832069.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8832069/SRX8832069.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8832069/SRX8832069.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 @ Thu, 09 Dec 2021 01:28:29: #1 read tag files... INFO @ Thu, 09 Dec 2021 01:28:29: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 01:28:38: 1000000 INFO @ Thu, 09 Dec 2021 01:28:45: 2000000 INFO @ Thu, 09 Dec 2021 01:28:51: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 01:28:58: 4000000 INFO @ Thu, 09 Dec 2021 01:28:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8832069/SRX8832069.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8832069/SRX8832069.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8832069/SRX8832069.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8832069/SRX8832069.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 @ Thu, 09 Dec 2021 01:28:58: #1 read tag files... INFO @ Thu, 09 Dec 2021 01:28:58: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 01:29:05: 5000000 INFO @ Thu, 09 Dec 2021 01:29:05: 1000000 INFO @ Thu, 09 Dec 2021 01:29:12: 6000000 INFO @ Thu, 09 Dec 2021 01:29:12: 2000000 INFO @ Thu, 09 Dec 2021 01:29:19: 7000000 INFO @ Thu, 09 Dec 2021 01:29:19: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 01:29:25: 4000000 INFO @ Thu, 09 Dec 2021 01:29:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8832069/SRX8832069.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8832069/SRX8832069.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8832069/SRX8832069.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8832069/SRX8832069.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 @ Thu, 09 Dec 2021 01:29:28: #1 read tag files... INFO @ Thu, 09 Dec 2021 01:29:28: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 01:29:28: 8000000 INFO @ Thu, 09 Dec 2021 01:29:32: 5000000 INFO @ Thu, 09 Dec 2021 01:29:35: 9000000 INFO @ Thu, 09 Dec 2021 01:29:37: 1000000 INFO @ Thu, 09 Dec 2021 01:29:39: 6000000 INFO @ Thu, 09 Dec 2021 01:29:42: 10000000 INFO @ Thu, 09 Dec 2021 01:29:46: 2000000 INFO @ Thu, 09 Dec 2021 01:29:47: 7000000 INFO @ Thu, 09 Dec 2021 01:29:50: 11000000 INFO @ Thu, 09 Dec 2021 01:29:55: 3000000 INFO @ Thu, 09 Dec 2021 01:29:55: 8000000 INFO @ Thu, 09 Dec 2021 01:29:58: 12000000 INFO @ Thu, 09 Dec 2021 01:30:01: #1 tag size is determined as 50 bps INFO @ Thu, 09 Dec 2021 01:30:01: #1 tag size = 50 INFO @ Thu, 09 Dec 2021 01:30:01: #1 total tags in treatment: 12299487 INFO @ Thu, 09 Dec 2021 01:30:01: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 01:30:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 01:30:01: #1 tags after filtering in treatment: 12299487 INFO @ Thu, 09 Dec 2021 01:30:01: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 01:30:01: #1 finished! INFO @ Thu, 09 Dec 2021 01:30:01: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 01:30:01: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 01:30:02: #2 number of paired peaks: 891 WARNING @ Thu, 09 Dec 2021 01:30:02: Fewer paired peaks (891) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 891 pairs to build model! INFO @ Thu, 09 Dec 2021 01:30:02: start model_add_line... INFO @ Thu, 09 Dec 2021 01:30:02: start X-correlation... INFO @ Thu, 09 Dec 2021 01:30:02: end of X-cor INFO @ Thu, 09 Dec 2021 01:30:02: #2 finished! INFO @ Thu, 09 Dec 2021 01:30:02: #2 predicted fragment length is 163 bps INFO @ Thu, 09 Dec 2021 01:30:02: #2 alternative fragment length(s) may be 163 bps INFO @ Thu, 09 Dec 2021 01:30:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8832069/SRX8832069.05_model.r INFO @ Thu, 09 Dec 2021 01:30:02: #3 Call peaks... INFO @ Thu, 09 Dec 2021 01:30:02: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 01:30:02: 9000000 INFO @ Thu, 09 Dec 2021 01:30:03: 4000000 INFO @ Thu, 09 Dec 2021 01:30:09: 10000000 INFO @ Thu, 09 Dec 2021 01:30:11: 5000000 INFO @ Thu, 09 Dec 2021 01:30:16: 11000000 INFO @ Thu, 09 Dec 2021 01:30:20: 6000000 INFO @ Thu, 09 Dec 2021 01:30:23: 12000000 INFO @ Thu, 09 Dec 2021 01:30:25: #1 tag size is determined as 50 bps INFO @ Thu, 09 Dec 2021 01:30:25: #1 tag size = 50 INFO @ Thu, 09 Dec 2021 01:30:25: #1 total tags in treatment: 12299487 INFO @ Thu, 09 Dec 2021 01:30:25: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 01:30:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 01:30:25: #1 tags after filtering in treatment: 12299487 INFO @ Thu, 09 Dec 2021 01:30:25: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 01:30:25: #1 finished! INFO @ Thu, 09 Dec 2021 01:30:25: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 01:30:25: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 01:30:26: #2 number of paired peaks: 891 WARNING @ Thu, 09 Dec 2021 01:30:26: Fewer paired peaks (891) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 891 pairs to build model! INFO @ Thu, 09 Dec 2021 01:30:26: start model_add_line... INFO @ Thu, 09 Dec 2021 01:30:26: start X-correlation... INFO @ Thu, 09 Dec 2021 01:30:26: end of X-cor INFO @ Thu, 09 Dec 2021 01:30:26: #2 finished! INFO @ Thu, 09 Dec 2021 01:30:26: #2 predicted fragment length is 163 bps INFO @ Thu, 09 Dec 2021 01:30:26: #2 alternative fragment length(s) may be 163 bps INFO @ Thu, 09 Dec 2021 01:30:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8832069/SRX8832069.10_model.r INFO @ Thu, 09 Dec 2021 01:30:26: #3 Call peaks... INFO @ Thu, 09 Dec 2021 01:30:26: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 01:30:28: 7000000 INFO @ Thu, 09 Dec 2021 01:30:32: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 01:30:36: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 01:30:45: 9000000 INFO @ Thu, 09 Dec 2021 01:30:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8832069/SRX8832069.05_peaks.xls INFO @ Thu, 09 Dec 2021 01:30:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8832069/SRX8832069.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 01:30:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8832069/SRX8832069.05_summits.bed INFO @ Thu, 09 Dec 2021 01:30:47: Done! pass1 - making usageList (7 chroms): 4 millis pass2 - checking and writing primary data (7390 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 01:30:52: 10000000 INFO @ Thu, 09 Dec 2021 01:30:55: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 01:30:59: 11000000 INFO @ Thu, 09 Dec 2021 01:31:06: 12000000 INFO @ Thu, 09 Dec 2021 01:31:08: #1 tag size is determined as 50 bps INFO @ Thu, 09 Dec 2021 01:31:08: #1 tag size = 50 INFO @ Thu, 09 Dec 2021 01:31:08: #1 total tags in treatment: 12299487 INFO @ Thu, 09 Dec 2021 01:31:08: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 01:31:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 01:31:08: #1 tags after filtering in treatment: 12299487 INFO @ Thu, 09 Dec 2021 01:31:08: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 01:31:08: #1 finished! INFO @ Thu, 09 Dec 2021 01:31:08: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 01:31:08: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 01:31:09: #2 number of paired peaks: 891 WARNING @ Thu, 09 Dec 2021 01:31:09: Fewer paired peaks (891) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 891 pairs to build model! INFO @ Thu, 09 Dec 2021 01:31:09: start model_add_line... INFO @ Thu, 09 Dec 2021 01:31:09: start X-correlation... INFO @ Thu, 09 Dec 2021 01:31:10: end of X-cor INFO @ Thu, 09 Dec 2021 01:31:10: #2 finished! INFO @ Thu, 09 Dec 2021 01:31:10: #2 predicted fragment length is 163 bps INFO @ Thu, 09 Dec 2021 01:31:10: #2 alternative fragment length(s) may be 163 bps INFO @ Thu, 09 Dec 2021 01:31:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8832069/SRX8832069.20_model.r INFO @ Thu, 09 Dec 2021 01:31:10: #3 Call peaks... INFO @ Thu, 09 Dec 2021 01:31:10: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 01:31:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8832069/SRX8832069.10_peaks.xls INFO @ Thu, 09 Dec 2021 01:31:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8832069/SRX8832069.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 01:31:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8832069/SRX8832069.10_summits.bed INFO @ Thu, 09 Dec 2021 01:31:10: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (4924 records, 4 fields): 9 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 01:31:39: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 01:31:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8832069/SRX8832069.20_peaks.xls INFO @ Thu, 09 Dec 2021 01:31:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8832069/SRX8832069.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 01:31:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8832069/SRX8832069.20_summits.bed INFO @ Thu, 09 Dec 2021 01:31:54: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2379 records, 4 fields): 6 millis CompletedMACS2peakCalling