Job ID = 14521983 SRX = SRX6950510 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 3553984 spots for SRR10231170/SRR10231170.sra Written 3553984 spots for SRR10231170/SRR10231170.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: 00:04:15 3553984 reads; of these: 3553984 (100.00%) were paired; of these: 515980 (14.52%) aligned concordantly 0 times 2774605 (78.07%) aligned concordantly exactly 1 time 263399 (7.41%) aligned concordantly >1 times ---- 515980 pairs aligned concordantly 0 times; of these: 232271 (45.02%) aligned discordantly 1 time ---- 283709 pairs aligned 0 times concordantly or discordantly; of these: 567418 mates make up the pairs; of these: 479295 (84.47%) aligned 0 times 32979 (5.81%) aligned exactly 1 time 55144 (9.72%) aligned >1 times 93.26% overall alignment rate Time searching: 00:04:15 Overall time: 00:04:15 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] 292437 / 2820121 = 0.1037 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 22:04:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6950510/SRX6950510.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6950510/SRX6950510.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6950510/SRX6950510.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6950510/SRX6950510.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 22:04:14: #1 read tag files... INFO @ Sat, 15 Jan 2022 22:04:14: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 22:04:22: 1000000 INFO @ Sat, 15 Jan 2022 22:04:29: 2000000 INFO @ Sat, 15 Jan 2022 22:04:36: 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 22:04:43: 4000000 INFO @ Sat, 15 Jan 2022 22:04:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6950510/SRX6950510.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6950510/SRX6950510.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6950510/SRX6950510.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6950510/SRX6950510.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 22:04:44: #1 read tag files... INFO @ Sat, 15 Jan 2022 22:04:44: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 22:04:51: 5000000 INFO @ Sat, 15 Jan 2022 22:04:54: 1000000 INFO @ Sat, 15 Jan 2022 22:05:00: 6000000 INFO @ Sat, 15 Jan 2022 22:05:00: #1 tag size is determined as 99 bps INFO @ Sat, 15 Jan 2022 22:05:00: #1 tag size = 99 INFO @ Sat, 15 Jan 2022 22:05:00: #1 total tags in treatment: 2769567 INFO @ Sat, 15 Jan 2022 22:05:00: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 22:05:00: #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 22:05:00: #1 tags after filtering in treatment: 2383633 INFO @ Sat, 15 Jan 2022 22:05:00: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 15 Jan 2022 22:05:00: #1 finished! INFO @ Sat, 15 Jan 2022 22:05:00: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 22:05:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 22:05:00: #2 number of paired peaks: 100 WARNING @ Sat, 15 Jan 2022 22:05:00: Fewer paired peaks (100) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 100 pairs to build model! INFO @ Sat, 15 Jan 2022 22:05:00: start model_add_line... INFO @ Sat, 15 Jan 2022 22:05:00: start X-correlation... INFO @ Sat, 15 Jan 2022 22:05:00: end of X-cor INFO @ Sat, 15 Jan 2022 22:05:00: #2 finished! INFO @ Sat, 15 Jan 2022 22:05:00: #2 predicted fragment length is 139 bps INFO @ Sat, 15 Jan 2022 22:05:00: #2 alternative fragment length(s) may be 3,139,184 bps INFO @ Sat, 15 Jan 2022 22:05:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6950510/SRX6950510.05_model.r WARNING @ Sat, 15 Jan 2022 22:05:00: #2 Since the d (139) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 22:05:00: #2 You may need to consider one of the other alternative d(s): 3,139,184 WARNING @ Sat, 15 Jan 2022 22:05:00: #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 22:05:00: #3 Call peaks... INFO @ Sat, 15 Jan 2022 22:05:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 22:05:04: 2000000 INFO @ Sat, 15 Jan 2022 22:05:05: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 22:05:07: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6950510/SRX6950510.05_peaks.xls INFO @ Sat, 15 Jan 2022 22:05:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6950510/SRX6950510.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 22:05:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6950510/SRX6950510.05_summits.bed INFO @ Sat, 15 Jan 2022 22:05:08: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (703 records, 4 fields): 3 millis CompletedMACS2peakCalling 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 22:05:14: 3000000 INFO @ Sat, 15 Jan 2022 22:05:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6950510/SRX6950510.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6950510/SRX6950510.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6950510/SRX6950510.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6950510/SRX6950510.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 22:05:14: #1 read tag files... INFO @ Sat, 15 Jan 2022 22:05:14: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 22:05:23: 1000000 INFO @ Sat, 15 Jan 2022 22:05:24: 4000000 INFO @ Sat, 15 Jan 2022 22:05:32: 2000000 INFO @ Sat, 15 Jan 2022 22:05:35: 5000000 INFO @ Sat, 15 Jan 2022 22:05:40: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 22:05:44: 6000000 INFO @ Sat, 15 Jan 2022 22:05:44: #1 tag size is determined as 99 bps INFO @ Sat, 15 Jan 2022 22:05:44: #1 tag size = 99 INFO @ Sat, 15 Jan 2022 22:05:44: #1 total tags in treatment: 2769567 INFO @ Sat, 15 Jan 2022 22:05:44: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 22:05:44: #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 22:05:44: #1 tags after filtering in treatment: 2383633 INFO @ Sat, 15 Jan 2022 22:05:44: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 15 Jan 2022 22:05:44: #1 finished! INFO @ Sat, 15 Jan 2022 22:05:44: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 22:05:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 22:05:44: #2 number of paired peaks: 100 WARNING @ Sat, 15 Jan 2022 22:05:44: Fewer paired peaks (100) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 100 pairs to build model! INFO @ Sat, 15 Jan 2022 22:05:44: start model_add_line... INFO @ Sat, 15 Jan 2022 22:05:44: start X-correlation... INFO @ Sat, 15 Jan 2022 22:05:44: end of X-cor INFO @ Sat, 15 Jan 2022 22:05:44: #2 finished! INFO @ Sat, 15 Jan 2022 22:05:44: #2 predicted fragment length is 139 bps INFO @ Sat, 15 Jan 2022 22:05:44: #2 alternative fragment length(s) may be 3,139,184 bps INFO @ Sat, 15 Jan 2022 22:05:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6950510/SRX6950510.10_model.r WARNING @ Sat, 15 Jan 2022 22:05:44: #2 Since the d (139) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 22:05:44: #2 You may need to consider one of the other alternative d(s): 3,139,184 WARNING @ Sat, 15 Jan 2022 22:05:44: #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 22:05:44: #3 Call peaks... INFO @ Sat, 15 Jan 2022 22:05:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 22:05:49: 4000000 INFO @ Sat, 15 Jan 2022 22:05:49: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 22:05:51: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6950510/SRX6950510.10_peaks.xls INFO @ Sat, 15 Jan 2022 22:05:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6950510/SRX6950510.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 22:05:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6950510/SRX6950510.10_summits.bed INFO @ Sat, 15 Jan 2022 22:05:51: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (344 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 22:05:57: 5000000 INFO @ Sat, 15 Jan 2022 22:06:04: 6000000 INFO @ Sat, 15 Jan 2022 22:06:04: #1 tag size is determined as 99 bps INFO @ Sat, 15 Jan 2022 22:06:04: #1 tag size = 99 INFO @ Sat, 15 Jan 2022 22:06:04: #1 total tags in treatment: 2769567 INFO @ Sat, 15 Jan 2022 22:06:04: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 22:06:04: #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 22:06:04: #1 tags after filtering in treatment: 2383633 INFO @ Sat, 15 Jan 2022 22:06:04: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 15 Jan 2022 22:06:04: #1 finished! INFO @ Sat, 15 Jan 2022 22:06:04: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 22:06:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 22:06:04: #2 number of paired peaks: 100 WARNING @ Sat, 15 Jan 2022 22:06:04: Fewer paired peaks (100) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 100 pairs to build model! INFO @ Sat, 15 Jan 2022 22:06:04: start model_add_line... INFO @ Sat, 15 Jan 2022 22:06:04: start X-correlation... INFO @ Sat, 15 Jan 2022 22:06:04: end of X-cor INFO @ Sat, 15 Jan 2022 22:06:04: #2 finished! INFO @ Sat, 15 Jan 2022 22:06:04: #2 predicted fragment length is 139 bps INFO @ Sat, 15 Jan 2022 22:06:04: #2 alternative fragment length(s) may be 3,139,184 bps INFO @ Sat, 15 Jan 2022 22:06:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6950510/SRX6950510.20_model.r WARNING @ Sat, 15 Jan 2022 22:06:04: #2 Since the d (139) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 22:06:04: #2 You may need to consider one of the other alternative d(s): 3,139,184 WARNING @ Sat, 15 Jan 2022 22:06:04: #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 22:06:04: #3 Call peaks... INFO @ Sat, 15 Jan 2022 22:06:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 22:06:09: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 22:06:11: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6950510/SRX6950510.20_peaks.xls INFO @ Sat, 15 Jan 2022 22:06:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6950510/SRX6950510.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 22:06:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6950510/SRX6950510.20_summits.bed INFO @ Sat, 15 Jan 2022 22:06:11: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (143 records, 4 fields): 1 millis CompletedMACS2peakCalling