Job ID = 12531699 SRX = SRX5521485 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 1921524 spots for SRR8728296/SRR8728296.sra Written 1921524 spots for SRR8728296/SRR8728296.sra 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: 00:01:46 1921524 reads; of these: 1921524 (100.00%) were paired; of these: 530585 (27.61%) aligned concordantly 0 times 770731 (40.11%) aligned concordantly exactly 1 time 620208 (32.28%) aligned concordantly >1 times ---- 530585 pairs aligned concordantly 0 times; of these: 96728 (18.23%) aligned discordantly 1 time ---- 433857 pairs aligned 0 times concordantly or discordantly; of these: 867714 mates make up the pairs; of these: 690014 (79.52%) aligned 0 times 23265 (2.68%) aligned exactly 1 time 154435 (17.80%) aligned >1 times 82.05% overall alignment rate Time searching: 00:01:46 Overall time: 00:01:46 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 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 chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 264903 / 1477997 = 0.1792 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, 17 Apr 2021 09:15:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5521485/SRX5521485.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5521485/SRX5521485.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5521485/SRX5521485.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5521485/SRX5521485.bam'] # control file = None # effective genome size = 1.21e+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, 17 Apr 2021 09:15:24: #1 read tag files... INFO @ Sat, 17 Apr 2021 09:15:24: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 09:15:30: 1000000 INFO @ Sat, 17 Apr 2021 09:15:36: 2000000 INFO @ Sat, 17 Apr 2021 09:15:39: #1 tag size is determined as 76 bps INFO @ Sat, 17 Apr 2021 09:15:39: #1 tag size = 76 INFO @ Sat, 17 Apr 2021 09:15:39: #1 total tags in treatment: 1132017 INFO @ Sat, 17 Apr 2021 09:15:39: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 09:15:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 17 Apr 2021 09:15:39: #1 tags after filtering in treatment: 711437 INFO @ Sat, 17 Apr 2021 09:15:39: #1 Redundant rate of treatment: 0.37 INFO @ Sat, 17 Apr 2021 09:15:39: #1 finished! INFO @ Sat, 17 Apr 2021 09:15:39: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 09:15:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 09:15:40: #2 number of paired peaks: 298 WARNING @ Sat, 17 Apr 2021 09:15:40: Fewer paired peaks (298) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 298 pairs to build model! INFO @ Sat, 17 Apr 2021 09:15:40: start model_add_line... INFO @ Sat, 17 Apr 2021 09:15:40: start X-correlation... INFO @ Sat, 17 Apr 2021 09:15:40: end of X-cor INFO @ Sat, 17 Apr 2021 09:15:40: #2 finished! INFO @ Sat, 17 Apr 2021 09:15:40: #2 predicted fragment length is 137 bps INFO @ Sat, 17 Apr 2021 09:15:40: #2 alternative fragment length(s) may be 20,103,137 bps INFO @ Sat, 17 Apr 2021 09:15:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5521485/SRX5521485.05_model.r WARNING @ Sat, 17 Apr 2021 09:15:40: #2 Since the d (137) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 09:15:40: #2 You may need to consider one of the other alternative d(s): 20,103,137 WARNING @ Sat, 17 Apr 2021 09:15:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 17 Apr 2021 09:15:40: #3 Call peaks... INFO @ Sat, 17 Apr 2021 09:15:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 09:15:42: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 09:15:43: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5521485/SRX5521485.05_peaks.xls INFO @ Sat, 17 Apr 2021 09:15:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5521485/SRX5521485.05_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 09:15:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5521485/SRX5521485.05_summits.bed INFO @ Sat, 17 Apr 2021 09:15:43: Done! pass1 - making usageList (17 chroms): 2 millis pass2 - checking and writing primary data (855 records, 4 fields): 5 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, 17 Apr 2021 09:15:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5521485/SRX5521485.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5521485/SRX5521485.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5521485/SRX5521485.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5521485/SRX5521485.bam'] # control file = None # effective genome size = 1.21e+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, 17 Apr 2021 09:15:54: #1 read tag files... INFO @ Sat, 17 Apr 2021 09:15:54: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 09:16:04: 1000000 INFO @ Sat, 17 Apr 2021 09:16:16: 2000000 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, 17 Apr 2021 09:16:23: #1 tag size is determined as 76 bps INFO @ Sat, 17 Apr 2021 09:16:23: #1 tag size = 76 INFO @ Sat, 17 Apr 2021 09:16:23: #1 total tags in treatment: 1132017 INFO @ Sat, 17 Apr 2021 09:16:23: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 09:16:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 17 Apr 2021 09:16:23: #1 tags after filtering in treatment: 711437 INFO @ Sat, 17 Apr 2021 09:16:23: #1 Redundant rate of treatment: 0.37 INFO @ Sat, 17 Apr 2021 09:16:23: #1 finished! INFO @ Sat, 17 Apr 2021 09:16:23: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 09:16:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 09:16:23: #2 number of paired peaks: 298 WARNING @ Sat, 17 Apr 2021 09:16:23: Fewer paired peaks (298) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 298 pairs to build model! INFO @ Sat, 17 Apr 2021 09:16:23: start model_add_line... INFO @ Sat, 17 Apr 2021 09:16:23: start X-correlation... INFO @ Sat, 17 Apr 2021 09:16:23: end of X-cor INFO @ Sat, 17 Apr 2021 09:16:23: #2 finished! INFO @ Sat, 17 Apr 2021 09:16:23: #2 predicted fragment length is 137 bps INFO @ Sat, 17 Apr 2021 09:16:23: #2 alternative fragment length(s) may be 20,103,137 bps INFO @ Sat, 17 Apr 2021 09:16:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5521485/SRX5521485.10_model.r WARNING @ Sat, 17 Apr 2021 09:16:23: #2 Since the d (137) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 09:16:23: #2 You may need to consider one of the other alternative d(s): 20,103,137 WARNING @ Sat, 17 Apr 2021 09:16:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 17 Apr 2021 09:16:23: #3 Call peaks... INFO @ Sat, 17 Apr 2021 09:16:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 09:16:26: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 09:16:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5521485/SRX5521485.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5521485/SRX5521485.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5521485/SRX5521485.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5521485/SRX5521485.bam'] # control file = None # effective genome size = 1.21e+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, 17 Apr 2021 09:16:26: #1 read tag files... INFO @ Sat, 17 Apr 2021 09:16:26: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 09:16:27: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5521485/SRX5521485.10_peaks.xls INFO @ Sat, 17 Apr 2021 09:16:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5521485/SRX5521485.10_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 09:16:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5521485/SRX5521485.10_summits.bed INFO @ Sat, 17 Apr 2021 09:16:27: Done! pass1 - making usageList (17 chroms): 2 millis pass2 - checking and writing primary data (484 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sat, 17 Apr 2021 09:16:32: 1000000 INFO @ Sat, 17 Apr 2021 09:16:37: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 17 Apr 2021 09:16:41: #1 tag size is determined as 76 bps INFO @ Sat, 17 Apr 2021 09:16:41: #1 tag size = 76 INFO @ Sat, 17 Apr 2021 09:16:41: #1 total tags in treatment: 1132017 INFO @ Sat, 17 Apr 2021 09:16:41: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 09:16:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 17 Apr 2021 09:16:41: #1 tags after filtering in treatment: 711437 INFO @ Sat, 17 Apr 2021 09:16:41: #1 Redundant rate of treatment: 0.37 INFO @ Sat, 17 Apr 2021 09:16:41: #1 finished! INFO @ Sat, 17 Apr 2021 09:16:41: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 09:16:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 09:16:41: #2 number of paired peaks: 298 WARNING @ Sat, 17 Apr 2021 09:16:41: Fewer paired peaks (298) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 298 pairs to build model! INFO @ Sat, 17 Apr 2021 09:16:41: start model_add_line... INFO @ Sat, 17 Apr 2021 09:16:41: start X-correlation... INFO @ Sat, 17 Apr 2021 09:16:41: end of X-cor INFO @ Sat, 17 Apr 2021 09:16:41: #2 finished! INFO @ Sat, 17 Apr 2021 09:16:41: #2 predicted fragment length is 137 bps INFO @ Sat, 17 Apr 2021 09:16:41: #2 alternative fragment length(s) may be 20,103,137 bps INFO @ Sat, 17 Apr 2021 09:16:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5521485/SRX5521485.20_model.r WARNING @ Sat, 17 Apr 2021 09:16:41: #2 Since the d (137) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 09:16:41: #2 You may need to consider one of the other alternative d(s): 20,103,137 WARNING @ Sat, 17 Apr 2021 09:16:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 17 Apr 2021 09:16:41: #3 Call peaks... INFO @ Sat, 17 Apr 2021 09:16:41: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 17 Apr 2021 09:16:43: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 09:16:44: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5521485/SRX5521485.20_peaks.xls INFO @ Sat, 17 Apr 2021 09:16:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5521485/SRX5521485.20_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 09:16:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5521485/SRX5521485.20_summits.bed INFO @ Sat, 17 Apr 2021 09:16:44: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (163 records, 4 fields): 3 millis CompletedMACS2peakCalling