Job ID = 12265145 SRX = SRX2333000 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED 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: 00:06:41 21258521 reads; of these: 21258521 (100.00%) were paired; of these: 19296521 (90.77%) aligned concordantly 0 times 1640571 (7.72%) aligned concordantly exactly 1 time 321429 (1.51%) aligned concordantly >1 times ---- 19296521 pairs aligned concordantly 0 times; of these: 423699 (2.20%) aligned discordantly 1 time ---- 18872822 pairs aligned 0 times concordantly or discordantly; of these: 37745644 mates make up the pairs; of these: 37547784 (99.48%) aligned 0 times 71502 (0.19%) aligned exactly 1 time 126358 (0.33%) aligned >1 times 11.69% overall alignment rate Time searching: 00:06:41 Overall time: 00:06:41 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_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 975702 / 2365693 = 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 06:18:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2333000/SRX2333000.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2333000/SRX2333000.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2333000/SRX2333000.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2333000/SRX2333000.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 06:18:52: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:18:52: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:19:00: 1000000 INFO @ Sat, 03 Apr 2021 06:19:08: 2000000 INFO @ Sat, 03 Apr 2021 06:19:15: 3000000 INFO @ Sat, 03 Apr 2021 06:19:16: #1 tag size is determined as 101 bps INFO @ Sat, 03 Apr 2021 06:19:16: #1 tag size = 101 INFO @ Sat, 03 Apr 2021 06:19:16: #1 total tags in treatment: 1183345 INFO @ Sat, 03 Apr 2021 06:19:16: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:19:16: #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 06:19:16: #1 tags after filtering in treatment: 902815 INFO @ Sat, 03 Apr 2021 06:19:16: #1 Redundant rate of treatment: 0.24 INFO @ Sat, 03 Apr 2021 06:19:16: #1 finished! INFO @ Sat, 03 Apr 2021 06:19:16: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:19:16: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:19:16: #2 number of paired peaks: 668 WARNING @ Sat, 03 Apr 2021 06:19:16: Fewer paired peaks (668) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 668 pairs to build model! INFO @ Sat, 03 Apr 2021 06:19:16: start model_add_line... INFO @ Sat, 03 Apr 2021 06:19:16: start X-correlation... INFO @ Sat, 03 Apr 2021 06:19:16: end of X-cor INFO @ Sat, 03 Apr 2021 06:19:16: #2 finished! INFO @ Sat, 03 Apr 2021 06:19:16: #2 predicted fragment length is 172 bps INFO @ Sat, 03 Apr 2021 06:19:16: #2 alternative fragment length(s) may be 172 bps INFO @ Sat, 03 Apr 2021 06:19:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2333000/SRX2333000.05_model.r WARNING @ Sat, 03 Apr 2021 06:19:16: #2 Since the d (172) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:19:16: #2 You may need to consider one of the other alternative d(s): 172 WARNING @ Sat, 03 Apr 2021 06:19:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:19:16: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:19:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:19:18: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:19:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2333000/SRX2333000.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:19:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2333000/SRX2333000.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:19:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2333000/SRX2333000.05_summits.bed INFO @ Sat, 03 Apr 2021 06:19:19: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (343 records, 4 fields): 2 millis CompletedMACS2peakCalling 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 06:19:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2333000/SRX2333000.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2333000/SRX2333000.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2333000/SRX2333000.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2333000/SRX2333000.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 06:19:22: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:19:22: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:19:30: 1000000 INFO @ Sat, 03 Apr 2021 06:19:38: 2000000 INFO @ Sat, 03 Apr 2021 06:19:45: 3000000 INFO @ Sat, 03 Apr 2021 06:19:45: #1 tag size is determined as 101 bps INFO @ Sat, 03 Apr 2021 06:19:45: #1 tag size = 101 INFO @ Sat, 03 Apr 2021 06:19:45: #1 total tags in treatment: 1183345 INFO @ Sat, 03 Apr 2021 06:19:45: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:19:45: #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 06:19:45: #1 tags after filtering in treatment: 902815 INFO @ Sat, 03 Apr 2021 06:19:45: #1 Redundant rate of treatment: 0.24 INFO @ Sat, 03 Apr 2021 06:19:45: #1 finished! INFO @ Sat, 03 Apr 2021 06:19:45: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:19:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:19:46: #2 number of paired peaks: 668 WARNING @ Sat, 03 Apr 2021 06:19:46: Fewer paired peaks (668) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 668 pairs to build model! INFO @ Sat, 03 Apr 2021 06:19:46: start model_add_line... INFO @ Sat, 03 Apr 2021 06:19:46: start X-correlation... INFO @ Sat, 03 Apr 2021 06:19:46: end of X-cor INFO @ Sat, 03 Apr 2021 06:19:46: #2 finished! INFO @ Sat, 03 Apr 2021 06:19:46: #2 predicted fragment length is 172 bps INFO @ Sat, 03 Apr 2021 06:19:46: #2 alternative fragment length(s) may be 172 bps INFO @ Sat, 03 Apr 2021 06:19:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2333000/SRX2333000.10_model.r WARNING @ Sat, 03 Apr 2021 06:19:46: #2 Since the d (172) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:19:46: #2 You may need to consider one of the other alternative d(s): 172 WARNING @ Sat, 03 Apr 2021 06:19:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:19:46: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:19:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:19:48: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:19:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2333000/SRX2333000.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:19:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2333000/SRX2333000.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:19:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2333000/SRX2333000.10_summits.bed INFO @ Sat, 03 Apr 2021 06:19:49: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (145 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 06:19:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2333000/SRX2333000.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2333000/SRX2333000.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2333000/SRX2333000.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2333000/SRX2333000.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 06:19:52: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:19:52: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:20:00: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:20:08: 2000000 BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 06:20:15: 3000000 INFO @ Sat, 03 Apr 2021 06:20:15: #1 tag size is determined as 101 bps INFO @ Sat, 03 Apr 2021 06:20:15: #1 tag size = 101 INFO @ Sat, 03 Apr 2021 06:20:15: #1 total tags in treatment: 1183345 INFO @ Sat, 03 Apr 2021 06:20:15: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:20:15: #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 06:20:15: #1 tags after filtering in treatment: 902815 INFO @ Sat, 03 Apr 2021 06:20:15: #1 Redundant rate of treatment: 0.24 INFO @ Sat, 03 Apr 2021 06:20:15: #1 finished! INFO @ Sat, 03 Apr 2021 06:20:15: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:20:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:20:15: #2 number of paired peaks: 668 WARNING @ Sat, 03 Apr 2021 06:20:15: Fewer paired peaks (668) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 668 pairs to build model! INFO @ Sat, 03 Apr 2021 06:20:15: start model_add_line... INFO @ Sat, 03 Apr 2021 06:20:15: start X-correlation... INFO @ Sat, 03 Apr 2021 06:20:15: end of X-cor INFO @ Sat, 03 Apr 2021 06:20:15: #2 finished! INFO @ Sat, 03 Apr 2021 06:20:15: #2 predicted fragment length is 172 bps INFO @ Sat, 03 Apr 2021 06:20:15: #2 alternative fragment length(s) may be 172 bps INFO @ Sat, 03 Apr 2021 06:20:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2333000/SRX2333000.20_model.r WARNING @ Sat, 03 Apr 2021 06:20:15: #2 Since the d (172) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:20:15: #2 You may need to consider one of the other alternative d(s): 172 WARNING @ Sat, 03 Apr 2021 06:20:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:20:15: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:20:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:20:17: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:20:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2333000/SRX2333000.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:20:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2333000/SRX2333000.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:20:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2333000/SRX2333000.20_summits.bed INFO @ Sat, 03 Apr 2021 06:20:19: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (46 records, 4 fields): 2 millis CompletedMACS2peakCalling