Job ID = 12265006 SRX = SRX7246259 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:58 12346232 reads; of these: 12346232 (100.00%) were unpaired; of these: 215316 (1.74%) aligned 0 times 9877199 (80.00%) aligned exactly 1 time 2253717 (18.25%) aligned >1 times 98.26% overall alignment rate Time searching: 00:02:59 Overall time: 00:02:59 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] 5002540 / 12130916 = 0.4124 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:10:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7246259/SRX7246259.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7246259/SRX7246259.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7246259/SRX7246259.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7246259/SRX7246259.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 @ Sat, 03 Apr 2021 06:10:23: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:10:23: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:10:29: 1000000 INFO @ Sat, 03 Apr 2021 06:10:35: 2000000 INFO @ Sat, 03 Apr 2021 06:10:41: 3000000 INFO @ Sat, 03 Apr 2021 06:10:48: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:10:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7246259/SRX7246259.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7246259/SRX7246259.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7246259/SRX7246259.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7246259/SRX7246259.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 @ Sat, 03 Apr 2021 06:10:52: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:10:52: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:10:54: 5000000 INFO @ Sat, 03 Apr 2021 06:11:00: 1000000 INFO @ Sat, 03 Apr 2021 06:11:01: 6000000 INFO @ Sat, 03 Apr 2021 06:11:08: 2000000 INFO @ Sat, 03 Apr 2021 06:11:09: 7000000 INFO @ Sat, 03 Apr 2021 06:11:10: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 06:11:10: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 06:11:10: #1 total tags in treatment: 7128376 INFO @ Sat, 03 Apr 2021 06:11:10: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:11:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:11:10: #1 tags after filtering in treatment: 7128376 INFO @ Sat, 03 Apr 2021 06:11:10: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:11:10: #1 finished! INFO @ Sat, 03 Apr 2021 06:11:10: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:11:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:11:10: #2 number of paired peaks: 889 WARNING @ Sat, 03 Apr 2021 06:11:10: Fewer paired peaks (889) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 889 pairs to build model! INFO @ Sat, 03 Apr 2021 06:11:10: start model_add_line... INFO @ Sat, 03 Apr 2021 06:11:10: start X-correlation... INFO @ Sat, 03 Apr 2021 06:11:10: end of X-cor INFO @ Sat, 03 Apr 2021 06:11:10: #2 finished! INFO @ Sat, 03 Apr 2021 06:11:10: #2 predicted fragment length is 102 bps INFO @ Sat, 03 Apr 2021 06:11:10: #2 alternative fragment length(s) may be 102 bps INFO @ Sat, 03 Apr 2021 06:11:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7246259/SRX7246259.05_model.r INFO @ Sat, 03 Apr 2021 06:11:10: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:11:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:11:15: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:11:23: 4000000 INFO @ Sat, 03 Apr 2021 06:11:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7246259/SRX7246259.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7246259/SRX7246259.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7246259/SRX7246259.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7246259/SRX7246259.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 @ Sat, 03 Apr 2021 06:11:23: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:11:23: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:11:30: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:11:30: 1000000 INFO @ Sat, 03 Apr 2021 06:11:30: 5000000 INFO @ Sat, 03 Apr 2021 06:11:37: 2000000 INFO @ Sat, 03 Apr 2021 06:11:38: 6000000 INFO @ Sat, 03 Apr 2021 06:11:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7246259/SRX7246259.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:11:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7246259/SRX7246259.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:11:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7246259/SRX7246259.05_summits.bed INFO @ Sat, 03 Apr 2021 06:11:40: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5717 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:11:45: 3000000 INFO @ Sat, 03 Apr 2021 06:11:46: 7000000 INFO @ Sat, 03 Apr 2021 06:11:47: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 06:11:47: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 06:11:47: #1 total tags in treatment: 7128376 INFO @ Sat, 03 Apr 2021 06:11:47: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:11:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:11:47: #1 tags after filtering in treatment: 7128376 INFO @ Sat, 03 Apr 2021 06:11:47: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:11:47: #1 finished! INFO @ Sat, 03 Apr 2021 06:11:47: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:11:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:11:47: #2 number of paired peaks: 889 WARNING @ Sat, 03 Apr 2021 06:11:47: Fewer paired peaks (889) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 889 pairs to build model! INFO @ Sat, 03 Apr 2021 06:11:47: start model_add_line... INFO @ Sat, 03 Apr 2021 06:11:48: start X-correlation... INFO @ Sat, 03 Apr 2021 06:11:48: end of X-cor INFO @ Sat, 03 Apr 2021 06:11:48: #2 finished! INFO @ Sat, 03 Apr 2021 06:11:48: #2 predicted fragment length is 102 bps INFO @ Sat, 03 Apr 2021 06:11:48: #2 alternative fragment length(s) may be 102 bps INFO @ Sat, 03 Apr 2021 06:11:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7246259/SRX7246259.10_model.r INFO @ Sat, 03 Apr 2021 06:11:48: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:11:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:11:51: 4000000 INFO @ Sat, 03 Apr 2021 06:11:58: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:12:04: 6000000 INFO @ Sat, 03 Apr 2021 06:12:06: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:12:10: 7000000 INFO @ Sat, 03 Apr 2021 06:12:11: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 06:12:11: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 06:12:11: #1 total tags in treatment: 7128376 INFO @ Sat, 03 Apr 2021 06:12:11: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:12:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:12:11: #1 tags after filtering in treatment: 7128376 INFO @ Sat, 03 Apr 2021 06:12:11: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:12:11: #1 finished! INFO @ Sat, 03 Apr 2021 06:12:11: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:12:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:12:11: #2 number of paired peaks: 889 WARNING @ Sat, 03 Apr 2021 06:12:11: Fewer paired peaks (889) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 889 pairs to build model! INFO @ Sat, 03 Apr 2021 06:12:11: start model_add_line... INFO @ Sat, 03 Apr 2021 06:12:11: start X-correlation... INFO @ Sat, 03 Apr 2021 06:12:11: end of X-cor INFO @ Sat, 03 Apr 2021 06:12:11: #2 finished! INFO @ Sat, 03 Apr 2021 06:12:11: #2 predicted fragment length is 102 bps INFO @ Sat, 03 Apr 2021 06:12:11: #2 alternative fragment length(s) may be 102 bps INFO @ Sat, 03 Apr 2021 06:12:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7246259/SRX7246259.20_model.r INFO @ Sat, 03 Apr 2021 06:12:11: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:12:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:12:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7246259/SRX7246259.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:12:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7246259/SRX7246259.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:12:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7246259/SRX7246259.10_summits.bed INFO @ Sat, 03 Apr 2021 06:12:15: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3322 records, 4 fields): 5 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 06:12:30: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:12:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7246259/SRX7246259.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:12:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7246259/SRX7246259.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:12:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7246259/SRX7246259.20_summits.bed INFO @ Sat, 03 Apr 2021 06:12:40: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1420 records, 4 fields): 4 millis CompletedMACS2peakCalling