Job ID = 14521988 SRX = SRX6950514 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 3563545 spots for SRR10231162/SRR10231162.sra Written 3563545 spots for SRR10231162/SRR10231162.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: 00:05:45 3563545 reads; of these: 3563545 (100.00%) were paired; of these: 764301 (21.45%) aligned concordantly 0 times 2574085 (72.23%) aligned concordantly exactly 1 time 225159 (6.32%) aligned concordantly >1 times ---- 764301 pairs aligned concordantly 0 times; of these: 328656 (43.00%) aligned discordantly 1 time ---- 435645 pairs aligned 0 times concordantly or discordantly; of these: 871290 mates make up the pairs; of these: 774477 (88.89%) aligned 0 times 34633 (3.97%) aligned exactly 1 time 62180 (7.14%) aligned >1 times 89.13% overall alignment rate Time searching: 00:05:45 Overall time: 00:05:45 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_sort_core] merging from 8 files... [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] 373739 / 2389540 = 0.1564 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 @ Sat, 15 Jan 2022 22:06:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6950514/SRX6950514.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6950514/SRX6950514.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6950514/SRX6950514.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6950514/SRX6950514.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, 15 Jan 2022 22:06:22: #1 read tag files... INFO @ Sat, 15 Jan 2022 22:06:22: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 22:06:29: 1000000 INFO @ Sat, 15 Jan 2022 22:06:36: 2000000 INFO @ Sat, 15 Jan 2022 22:06:43: 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 @ Sat, 15 Jan 2022 22:06:50: 4000000 INFO @ Sat, 15 Jan 2022 22:06:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6950514/SRX6950514.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6950514/SRX6950514.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6950514/SRX6950514.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6950514/SRX6950514.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, 15 Jan 2022 22:06:52: #1 read tag files... INFO @ Sat, 15 Jan 2022 22:06:52: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 22:06:58: 5000000 INFO @ Sat, 15 Jan 2022 22:07:00: 1000000 INFO @ Sat, 15 Jan 2022 22:07:02: #1 tag size is determined as 59 bps INFO @ Sat, 15 Jan 2022 22:07:02: #1 tag size = 59 INFO @ Sat, 15 Jan 2022 22:07:02: #1 total tags in treatment: 2481686 INFO @ Sat, 15 Jan 2022 22:07:02: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 22:07:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 22:07:02: #1 tags after filtering in treatment: 2049008 INFO @ Sat, 15 Jan 2022 22:07:02: #1 Redundant rate of treatment: 0.17 INFO @ Sat, 15 Jan 2022 22:07:02: #1 finished! INFO @ Sat, 15 Jan 2022 22:07:02: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 22:07:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 22:07:03: #2 number of paired peaks: 170 WARNING @ Sat, 15 Jan 2022 22:07:03: Fewer paired peaks (170) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 170 pairs to build model! INFO @ Sat, 15 Jan 2022 22:07:03: start model_add_line... INFO @ Sat, 15 Jan 2022 22:07:03: start X-correlation... INFO @ Sat, 15 Jan 2022 22:07:03: end of X-cor INFO @ Sat, 15 Jan 2022 22:07:03: #2 finished! INFO @ Sat, 15 Jan 2022 22:07:03: #2 predicted fragment length is 91 bps INFO @ Sat, 15 Jan 2022 22:07:03: #2 alternative fragment length(s) may be 3,75,91,105 bps INFO @ Sat, 15 Jan 2022 22:07:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6950514/SRX6950514.05_model.r WARNING @ Sat, 15 Jan 2022 22:07:03: #2 Since the d (91) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 22:07:03: #2 You may need to consider one of the other alternative d(s): 3,75,91,105 WARNING @ Sat, 15 Jan 2022 22:07:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Jan 2022 22:07:03: #3 Call peaks... INFO @ Sat, 15 Jan 2022 22:07:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 22:07:07: 2000000 INFO @ Sat, 15 Jan 2022 22:07:07: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 22:07:09: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6950514/SRX6950514.05_peaks.xls INFO @ Sat, 15 Jan 2022 22:07:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6950514/SRX6950514.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 22:07:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6950514/SRX6950514.05_summits.bed INFO @ Sat, 15 Jan 2022 22:07:09: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (620 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 22:07:14: 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 @ Sat, 15 Jan 2022 22:07:21: 4000000 INFO @ Sat, 15 Jan 2022 22:07:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6950514/SRX6950514.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6950514/SRX6950514.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6950514/SRX6950514.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6950514/SRX6950514.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, 15 Jan 2022 22:07:22: #1 read tag files... INFO @ Sat, 15 Jan 2022 22:07:22: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 22:07:28: 5000000 INFO @ Sat, 15 Jan 2022 22:07:30: 1000000 INFO @ Sat, 15 Jan 2022 22:07:33: #1 tag size is determined as 59 bps INFO @ Sat, 15 Jan 2022 22:07:33: #1 tag size = 59 INFO @ Sat, 15 Jan 2022 22:07:33: #1 total tags in treatment: 2481686 INFO @ Sat, 15 Jan 2022 22:07:33: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 22:07:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 22:07:33: #1 tags after filtering in treatment: 2049008 INFO @ Sat, 15 Jan 2022 22:07:33: #1 Redundant rate of treatment: 0.17 INFO @ Sat, 15 Jan 2022 22:07:33: #1 finished! INFO @ Sat, 15 Jan 2022 22:07:33: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 22:07:33: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 22:07:33: #2 number of paired peaks: 170 WARNING @ Sat, 15 Jan 2022 22:07:33: Fewer paired peaks (170) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 170 pairs to build model! INFO @ Sat, 15 Jan 2022 22:07:33: start model_add_line... INFO @ Sat, 15 Jan 2022 22:07:33: start X-correlation... INFO @ Sat, 15 Jan 2022 22:07:33: end of X-cor INFO @ Sat, 15 Jan 2022 22:07:33: #2 finished! INFO @ Sat, 15 Jan 2022 22:07:33: #2 predicted fragment length is 91 bps INFO @ Sat, 15 Jan 2022 22:07:33: #2 alternative fragment length(s) may be 3,75,91,105 bps INFO @ Sat, 15 Jan 2022 22:07:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6950514/SRX6950514.10_model.r WARNING @ Sat, 15 Jan 2022 22:07:33: #2 Since the d (91) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 22:07:33: #2 You may need to consider one of the other alternative d(s): 3,75,91,105 WARNING @ Sat, 15 Jan 2022 22:07:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Jan 2022 22:07:33: #3 Call peaks... INFO @ Sat, 15 Jan 2022 22:07:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 22:07:37: 2000000 INFO @ Sat, 15 Jan 2022 22:07:38: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 22:07:40: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6950514/SRX6950514.10_peaks.xls INFO @ Sat, 15 Jan 2022 22:07:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6950514/SRX6950514.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 22:07:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6950514/SRX6950514.10_summits.bed INFO @ Sat, 15 Jan 2022 22:07:40: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (296 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 22:07:44: 3000000 INFO @ Sat, 15 Jan 2022 22:07:51: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 22:07:58: 5000000 INFO @ Sat, 15 Jan 2022 22:08:02: #1 tag size is determined as 59 bps INFO @ Sat, 15 Jan 2022 22:08:02: #1 tag size = 59 INFO @ Sat, 15 Jan 2022 22:08:02: #1 total tags in treatment: 2481686 INFO @ Sat, 15 Jan 2022 22:08:02: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 22:08:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 22:08:02: #1 tags after filtering in treatment: 2049008 INFO @ Sat, 15 Jan 2022 22:08:02: #1 Redundant rate of treatment: 0.17 INFO @ Sat, 15 Jan 2022 22:08:02: #1 finished! INFO @ Sat, 15 Jan 2022 22:08:02: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 22:08:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 22:08:02: #2 number of paired peaks: 170 WARNING @ Sat, 15 Jan 2022 22:08:02: Fewer paired peaks (170) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 170 pairs to build model! INFO @ Sat, 15 Jan 2022 22:08:02: start model_add_line... INFO @ Sat, 15 Jan 2022 22:08:02: start X-correlation... INFO @ Sat, 15 Jan 2022 22:08:02: end of X-cor INFO @ Sat, 15 Jan 2022 22:08:02: #2 finished! INFO @ Sat, 15 Jan 2022 22:08:02: #2 predicted fragment length is 91 bps INFO @ Sat, 15 Jan 2022 22:08:02: #2 alternative fragment length(s) may be 3,75,91,105 bps INFO @ Sat, 15 Jan 2022 22:08:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6950514/SRX6950514.20_model.r WARNING @ Sat, 15 Jan 2022 22:08:02: #2 Since the d (91) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 22:08:02: #2 You may need to consider one of the other alternative d(s): 3,75,91,105 WARNING @ Sat, 15 Jan 2022 22:08:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Jan 2022 22:08:02: #3 Call peaks... INFO @ Sat, 15 Jan 2022 22:08:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 22:08:07: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 22:08:09: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6950514/SRX6950514.20_peaks.xls INFO @ Sat, 15 Jan 2022 22:08:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6950514/SRX6950514.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 22:08:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6950514/SRX6950514.20_summits.bed INFO @ Sat, 15 Jan 2022 22:08:09: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (139 records, 4 fields): 3 millis CompletedMACS2peakCalling