Job ID = 14158818 SRX = SRX7665448 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: 00:04:22 18104969 reads; of these: 18104969 (100.00%) were unpaired; of these: 1434402 (7.92%) aligned 0 times 14195812 (78.41%) aligned exactly 1 time 2474755 (13.67%) aligned >1 times 92.08% overall alignment rate Time searching: 00:04:22 Overall time: 00:04:22 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] 3105980 / 16670567 = 0.1863 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 @ Wed, 08 Dec 2021 18:12:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7665448/SRX7665448.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7665448/SRX7665448.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7665448/SRX7665448.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7665448/SRX7665448.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 @ Wed, 08 Dec 2021 18:12:08: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:12:08: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:12:16: 1000000 INFO @ Wed, 08 Dec 2021 18:12:23: 2000000 INFO @ Wed, 08 Dec 2021 18:12:31: 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 @ Wed, 08 Dec 2021 18:12:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7665448/SRX7665448.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7665448/SRX7665448.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7665448/SRX7665448.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7665448/SRX7665448.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 @ Wed, 08 Dec 2021 18:12:38: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:12:38: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:12:38: 4000000 INFO @ Wed, 08 Dec 2021 18:12:46: 1000000 INFO @ Wed, 08 Dec 2021 18:12:46: 5000000 INFO @ Wed, 08 Dec 2021 18:12:54: 2000000 INFO @ Wed, 08 Dec 2021 18:12:54: 6000000 INFO @ Wed, 08 Dec 2021 18:13:02: 7000000 INFO @ Wed, 08 Dec 2021 18:13:02: 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 @ Wed, 08 Dec 2021 18:13:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7665448/SRX7665448.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7665448/SRX7665448.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7665448/SRX7665448.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7665448/SRX7665448.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 @ Wed, 08 Dec 2021 18:13:08: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:13:08: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:13:10: 8000000 INFO @ Wed, 08 Dec 2021 18:13:10: 4000000 INFO @ Wed, 08 Dec 2021 18:13:15: 1000000 INFO @ Wed, 08 Dec 2021 18:13:18: 9000000 INFO @ Wed, 08 Dec 2021 18:13:18: 5000000 INFO @ Wed, 08 Dec 2021 18:13:22: 2000000 INFO @ Wed, 08 Dec 2021 18:13:25: 10000000 INFO @ Wed, 08 Dec 2021 18:13:26: 6000000 INFO @ Wed, 08 Dec 2021 18:13:29: 3000000 INFO @ Wed, 08 Dec 2021 18:13:33: 11000000 INFO @ Wed, 08 Dec 2021 18:13:34: 7000000 INFO @ Wed, 08 Dec 2021 18:13:36: 4000000 INFO @ Wed, 08 Dec 2021 18:13:41: 12000000 INFO @ Wed, 08 Dec 2021 18:13:42: 8000000 INFO @ Wed, 08 Dec 2021 18:13:43: 5000000 INFO @ Wed, 08 Dec 2021 18:13:48: 13000000 INFO @ Wed, 08 Dec 2021 18:13:50: 9000000 INFO @ Wed, 08 Dec 2021 18:13:50: 6000000 INFO @ Wed, 08 Dec 2021 18:13:53: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 18:13:53: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 18:13:53: #1 total tags in treatment: 13564587 INFO @ Wed, 08 Dec 2021 18:13:53: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:13:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 18:13:53: #1 tags after filtering in treatment: 13564587 INFO @ Wed, 08 Dec 2021 18:13:53: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 18:13:53: #1 finished! INFO @ Wed, 08 Dec 2021 18:13:53: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:13:53: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:13:55: #2 number of paired peaks: 919 WARNING @ Wed, 08 Dec 2021 18:13:55: Fewer paired peaks (919) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 919 pairs to build model! INFO @ Wed, 08 Dec 2021 18:13:55: start model_add_line... INFO @ Wed, 08 Dec 2021 18:13:55: start X-correlation... INFO @ Wed, 08 Dec 2021 18:13:55: end of X-cor INFO @ Wed, 08 Dec 2021 18:13:55: #2 finished! INFO @ Wed, 08 Dec 2021 18:13:55: #2 predicted fragment length is 123 bps INFO @ Wed, 08 Dec 2021 18:13:55: #2 alternative fragment length(s) may be 123 bps INFO @ Wed, 08 Dec 2021 18:13:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7665448/SRX7665448.05_model.r INFO @ Wed, 08 Dec 2021 18:13:55: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:13:55: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:13:57: 7000000 INFO @ Wed, 08 Dec 2021 18:13:57: 10000000 INFO @ Wed, 08 Dec 2021 18:14:04: 8000000 INFO @ Wed, 08 Dec 2021 18:14:05: 11000000 INFO @ Wed, 08 Dec 2021 18:14:11: 9000000 INFO @ Wed, 08 Dec 2021 18:14:12: 12000000 INFO @ Wed, 08 Dec 2021 18:14:18: 10000000 INFO @ Wed, 08 Dec 2021 18:14:20: 13000000 INFO @ Wed, 08 Dec 2021 18:14:24: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 18:14:24: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 18:14:24: #1 total tags in treatment: 13564587 INFO @ Wed, 08 Dec 2021 18:14:24: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:14:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 18:14:24: #1 tags after filtering in treatment: 13564587 INFO @ Wed, 08 Dec 2021 18:14:24: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 18:14:24: #1 finished! INFO @ Wed, 08 Dec 2021 18:14:24: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:14:24: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:14:25: 11000000 INFO @ Wed, 08 Dec 2021 18:14:26: #2 number of paired peaks: 919 WARNING @ Wed, 08 Dec 2021 18:14:26: Fewer paired peaks (919) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 919 pairs to build model! INFO @ Wed, 08 Dec 2021 18:14:26: start model_add_line... INFO @ Wed, 08 Dec 2021 18:14:26: start X-correlation... INFO @ Wed, 08 Dec 2021 18:14:26: end of X-cor INFO @ Wed, 08 Dec 2021 18:14:26: #2 finished! INFO @ Wed, 08 Dec 2021 18:14:26: #2 predicted fragment length is 123 bps INFO @ Wed, 08 Dec 2021 18:14:26: #2 alternative fragment length(s) may be 123 bps INFO @ Wed, 08 Dec 2021 18:14:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7665448/SRX7665448.10_model.r INFO @ Wed, 08 Dec 2021 18:14:26: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:14:26: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:14:31: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 18:14:33: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:14:38: 13000000 INFO @ Wed, 08 Dec 2021 18:14:42: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 18:14:42: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 18:14:42: #1 total tags in treatment: 13564587 INFO @ Wed, 08 Dec 2021 18:14:42: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:14:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 18:14:42: #1 tags after filtering in treatment: 13564587 INFO @ Wed, 08 Dec 2021 18:14:42: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 18:14:42: #1 finished! INFO @ Wed, 08 Dec 2021 18:14:42: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:14:42: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:14:44: #2 number of paired peaks: 919 WARNING @ Wed, 08 Dec 2021 18:14:44: Fewer paired peaks (919) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 919 pairs to build model! INFO @ Wed, 08 Dec 2021 18:14:44: start model_add_line... INFO @ Wed, 08 Dec 2021 18:14:44: start X-correlation... INFO @ Wed, 08 Dec 2021 18:14:44: end of X-cor INFO @ Wed, 08 Dec 2021 18:14:44: #2 finished! INFO @ Wed, 08 Dec 2021 18:14:44: #2 predicted fragment length is 123 bps INFO @ Wed, 08 Dec 2021 18:14:44: #2 alternative fragment length(s) may be 123 bps INFO @ Wed, 08 Dec 2021 18:14:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7665448/SRX7665448.20_model.r INFO @ Wed, 08 Dec 2021 18:14:44: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:14:44: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:14:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7665448/SRX7665448.05_peaks.xls INFO @ Wed, 08 Dec 2021 18:14:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7665448/SRX7665448.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:14:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7665448/SRX7665448.05_summits.bed INFO @ Wed, 08 Dec 2021 18:14:51: Done! pass1 - making usageList (7 chroms): 4 millis pass2 - checking and writing primary data (6771 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 18:15:05: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 18:15:22: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:15:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7665448/SRX7665448.10_peaks.xls INFO @ Wed, 08 Dec 2021 18:15:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7665448/SRX7665448.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:15:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7665448/SRX7665448.10_summits.bed INFO @ Wed, 08 Dec 2021 18:15:23: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (4783 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 18:15:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7665448/SRX7665448.20_peaks.xls INFO @ Wed, 08 Dec 2021 18:15:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7665448/SRX7665448.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:15:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7665448/SRX7665448.20_summits.bed INFO @ Wed, 08 Dec 2021 18:15:40: Done! pass1 - making usageList (7 chroms): 5 millis pass2 - checking and writing primary data (3015 records, 4 fields): 9 millis CompletedMACS2peakCalling