Job ID = 14521212 SRX = SRX10468510 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 4125895 spots for SRR14094821/SRR14094821.sra Written 4125895 spots for SRR14094821/SRR14094821.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: 00:02:08 4125895 reads; of these: 4125895 (100.00%) were paired; of these: 507581 (12.30%) aligned concordantly 0 times 3262876 (79.08%) aligned concordantly exactly 1 time 355438 (8.61%) aligned concordantly >1 times ---- 507581 pairs aligned concordantly 0 times; of these: 65729 (12.95%) aligned discordantly 1 time ---- 441852 pairs aligned 0 times concordantly or discordantly; of these: 883704 mates make up the pairs; of these: 801975 (90.75%) aligned 0 times 58733 (6.65%) aligned exactly 1 time 22996 (2.60%) aligned >1 times 90.28% overall alignment rate Time searching: 00:02:08 Overall time: 00:02:08 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] 141771 / 3634410 = 0.0390 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 20:41:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10468510/SRX10468510.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10468510/SRX10468510.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10468510/SRX10468510.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10468510/SRX10468510.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 20:41:27: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:41:27: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:41:31: 1000000 INFO @ Sat, 15 Jan 2022 20:41:36: 2000000 INFO @ Sat, 15 Jan 2022 20:41:40: 3000000 INFO @ Sat, 15 Jan 2022 20:41:45: 4000000 INFO @ Sat, 15 Jan 2022 20:41:49: 5000000 INFO @ Sat, 15 Jan 2022 20:41:54: 6000000 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 20:41:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10468510/SRX10468510.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10468510/SRX10468510.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10468510/SRX10468510.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10468510/SRX10468510.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 20:41:57: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:41:57: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:41:58: 7000000 INFO @ Sat, 15 Jan 2022 20:41:59: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:41:59: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:41:59: #1 total tags in treatment: 3476858 INFO @ Sat, 15 Jan 2022 20:41:59: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:41:59: #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 20:41:59: #1 tags after filtering in treatment: 2891252 INFO @ Sat, 15 Jan 2022 20:41:59: #1 Redundant rate of treatment: 0.17 INFO @ Sat, 15 Jan 2022 20:41:59: #1 finished! INFO @ Sat, 15 Jan 2022 20:41:59: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:41:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:41:59: #2 number of paired peaks: 163 WARNING @ Sat, 15 Jan 2022 20:41:59: Fewer paired peaks (163) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 163 pairs to build model! INFO @ Sat, 15 Jan 2022 20:41:59: start model_add_line... INFO @ Sat, 15 Jan 2022 20:41:59: start X-correlation... INFO @ Sat, 15 Jan 2022 20:41:59: end of X-cor INFO @ Sat, 15 Jan 2022 20:41:59: #2 finished! INFO @ Sat, 15 Jan 2022 20:41:59: #2 predicted fragment length is 3 bps INFO @ Sat, 15 Jan 2022 20:41:59: #2 alternative fragment length(s) may be 3,27 bps INFO @ Sat, 15 Jan 2022 20:41:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10468510/SRX10468510.05_model.r WARNING @ Sat, 15 Jan 2022 20:41:59: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:41:59: #2 You may need to consider one of the other alternative d(s): 3,27 WARNING @ Sat, 15 Jan 2022 20:41:59: #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 20:41:59: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:41:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:42:02: 1000000 INFO @ Sat, 15 Jan 2022 20:42:03: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:42:05: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10468510/SRX10468510.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:42:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10468510/SRX10468510.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:42:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10468510/SRX10468510.05_summits.bed INFO @ Sat, 15 Jan 2022 20:42:05: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:42:06: 2000000 INFO @ Sat, 15 Jan 2022 20:42:11: 3000000 INFO @ Sat, 15 Jan 2022 20:42:16: 4000000 INFO @ Sat, 15 Jan 2022 20:42:20: 5000000 INFO @ Sat, 15 Jan 2022 20:42:25: 6000000 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 20:42:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10468510/SRX10468510.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10468510/SRX10468510.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10468510/SRX10468510.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10468510/SRX10468510.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 20:42:27: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:42:27: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:42:29: 7000000 INFO @ Sat, 15 Jan 2022 20:42:30: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:42:30: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:42:30: #1 total tags in treatment: 3476858 INFO @ Sat, 15 Jan 2022 20:42:30: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:42:30: #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 20:42:30: #1 tags after filtering in treatment: 2891252 INFO @ Sat, 15 Jan 2022 20:42:30: #1 Redundant rate of treatment: 0.17 INFO @ Sat, 15 Jan 2022 20:42:30: #1 finished! INFO @ Sat, 15 Jan 2022 20:42:30: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:42:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:42:30: #2 number of paired peaks: 163 WARNING @ Sat, 15 Jan 2022 20:42:30: Fewer paired peaks (163) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 163 pairs to build model! INFO @ Sat, 15 Jan 2022 20:42:30: start model_add_line... INFO @ Sat, 15 Jan 2022 20:42:30: start X-correlation... INFO @ Sat, 15 Jan 2022 20:42:30: end of X-cor INFO @ Sat, 15 Jan 2022 20:42:30: #2 finished! INFO @ Sat, 15 Jan 2022 20:42:30: #2 predicted fragment length is 3 bps INFO @ Sat, 15 Jan 2022 20:42:30: #2 alternative fragment length(s) may be 3,27 bps INFO @ Sat, 15 Jan 2022 20:42:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10468510/SRX10468510.10_model.r WARNING @ Sat, 15 Jan 2022 20:42:30: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:42:30: #2 You may need to consider one of the other alternative d(s): 3,27 WARNING @ Sat, 15 Jan 2022 20:42:30: #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 20:42:30: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:42:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:42:32: 1000000 INFO @ Sat, 15 Jan 2022 20:42:34: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:42:36: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10468510/SRX10468510.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:42:36: 2000000 INFO @ Sat, 15 Jan 2022 20:42:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10468510/SRX10468510.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:42:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10468510/SRX10468510.10_summits.bed INFO @ Sat, 15 Jan 2022 20:42:36: Done! pass1 - making usageList (0 chroms): 320 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:42:41: 3000000 INFO @ Sat, 15 Jan 2022 20:42:46: 4000000 INFO @ Sat, 15 Jan 2022 20:42:50: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:42:55: 6000000 INFO @ Sat, 15 Jan 2022 20:42:59: 7000000 INFO @ Sat, 15 Jan 2022 20:43:00: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:43:00: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:43:00: #1 total tags in treatment: 3476858 INFO @ Sat, 15 Jan 2022 20:43:00: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:43:00: #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 20:43:00: #1 tags after filtering in treatment: 2891252 INFO @ Sat, 15 Jan 2022 20:43:00: #1 Redundant rate of treatment: 0.17 INFO @ Sat, 15 Jan 2022 20:43:00: #1 finished! INFO @ Sat, 15 Jan 2022 20:43:00: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:43:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:43:00: #2 number of paired peaks: 163 WARNING @ Sat, 15 Jan 2022 20:43:00: Fewer paired peaks (163) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 163 pairs to build model! INFO @ Sat, 15 Jan 2022 20:43:00: start model_add_line... INFO @ Sat, 15 Jan 2022 20:43:00: start X-correlation... INFO @ Sat, 15 Jan 2022 20:43:00: end of X-cor INFO @ Sat, 15 Jan 2022 20:43:00: #2 finished! INFO @ Sat, 15 Jan 2022 20:43:00: #2 predicted fragment length is 3 bps INFO @ Sat, 15 Jan 2022 20:43:00: #2 alternative fragment length(s) may be 3,27 bps INFO @ Sat, 15 Jan 2022 20:43:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10468510/SRX10468510.20_model.r WARNING @ Sat, 15 Jan 2022 20:43:00: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:43:00: #2 You may need to consider one of the other alternative d(s): 3,27 WARNING @ Sat, 15 Jan 2022 20:43:00: #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 20:43:00: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:43:00: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:43:04: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:43:06: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10468510/SRX10468510.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:43:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10468510/SRX10468510.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:43:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10468510/SRX10468510.20_summits.bed INFO @ Sat, 15 Jan 2022 20:43:06: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling