Job ID = 14520825 SRX = SRX8245532 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 7709872 spots for SRR11684743/SRR11684743.sra Written 7709872 spots for SRR11684743/SRR11684743.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: 00:05:52 7709872 reads; of these: 7709872 (100.00%) were paired; of these: 4787702 (62.10%) aligned concordantly 0 times 2628918 (34.10%) aligned concordantly exactly 1 time 293252 (3.80%) aligned concordantly >1 times ---- 4787702 pairs aligned concordantly 0 times; of these: 30439 (0.64%) aligned discordantly 1 time ---- 4757263 pairs aligned 0 times concordantly or discordantly; of these: 9514526 mates make up the pairs; of these: 6419709 (67.47%) aligned 0 times 2704647 (28.43%) aligned exactly 1 time 390170 (4.10%) aligned >1 times 58.37% overall alignment rate Time searching: 00:05:52 Overall time: 00:05:52 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] 220473 / 2952046 = 0.0747 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 20:09:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245532/SRX8245532.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245532/SRX8245532.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245532/SRX8245532.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245532/SRX8245532.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 20:09:13: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:09:13: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:09:21: 1000000 INFO @ Sat, 15 Jan 2022 20:09:29: 2000000 INFO @ Sat, 15 Jan 2022 20:09:36: 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 20:09:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245532/SRX8245532.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245532/SRX8245532.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245532/SRX8245532.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245532/SRX8245532.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 20:09:42: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:09:42: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:09:44: 4000000 INFO @ Sat, 15 Jan 2022 20:09:51: 1000000 INFO @ Sat, 15 Jan 2022 20:09:53: 5000000 INFO @ Sat, 15 Jan 2022 20:09:59: 2000000 INFO @ Sat, 15 Jan 2022 20:10:01: 6000000 INFO @ Sat, 15 Jan 2022 20:10:07: 3000000 INFO @ Sat, 15 Jan 2022 20:10:08: 7000000 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 20:10:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245532/SRX8245532.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245532/SRX8245532.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245532/SRX8245532.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245532/SRX8245532.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 20:10:12: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:10:12: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:10:16: 8000000 INFO @ Sat, 15 Jan 2022 20:10:16: 4000000 INFO @ Sat, 15 Jan 2022 20:10:20: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:10:20: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:10:20: #1 total tags in treatment: 2702429 INFO @ Sat, 15 Jan 2022 20:10:20: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:10:20: #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 20:10:20: #1 tags after filtering in treatment: 1531178 INFO @ Sat, 15 Jan 2022 20:10:20: #1 Redundant rate of treatment: 0.43 INFO @ Sat, 15 Jan 2022 20:10:20: #1 finished! INFO @ Sat, 15 Jan 2022 20:10:20: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:10:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:10:20: #2 number of paired peaks: 172 WARNING @ Sat, 15 Jan 2022 20:10:20: Fewer paired peaks (172) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 172 pairs to build model! INFO @ Sat, 15 Jan 2022 20:10:20: start model_add_line... INFO @ Sat, 15 Jan 2022 20:10:20: start X-correlation... INFO @ Sat, 15 Jan 2022 20:10:20: end of X-cor INFO @ Sat, 15 Jan 2022 20:10:20: #2 finished! INFO @ Sat, 15 Jan 2022 20:10:20: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 20:10:20: #2 alternative fragment length(s) may be 0,60,109,126,165,172,188,202,219,258,285,312,337,351,390,408,433,457,495,528,572,589 bps INFO @ Sat, 15 Jan 2022 20:10:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245532/SRX8245532.05_model.r WARNING @ Sat, 15 Jan 2022 20:10:20: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:10:20: #2 You may need to consider one of the other alternative d(s): 0,60,109,126,165,172,188,202,219,258,285,312,337,351,390,408,433,457,495,528,572,589 WARNING @ Sat, 15 Jan 2022 20:10:20: #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 20:10:20: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:10:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:10:22: 1000000 INFO @ Sat, 15 Jan 2022 20:10:25: 5000000 INFO @ Sat, 15 Jan 2022 20:10:31: 2000000 INFO @ Sat, 15 Jan 2022 20:10:35: 6000000 INFO @ Sat, 15 Jan 2022 20:10:41: 3000000 INFO @ Sat, 15 Jan 2022 20:10:45: 7000000 INFO @ Sat, 15 Jan 2022 20:10:50: 4000000 INFO @ Sat, 15 Jan 2022 20:10:55: 8000000 INFO @ Sat, 15 Jan 2022 20:10:59: 5000000 INFO @ Sat, 15 Jan 2022 20:11:00: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:11:00: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:11:00: #1 total tags in treatment: 2702429 INFO @ Sat, 15 Jan 2022 20:11:00: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:11:00: #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 20:11:00: #1 tags after filtering in treatment: 1531178 INFO @ Sat, 15 Jan 2022 20:11:00: #1 Redundant rate of treatment: 0.43 INFO @ Sat, 15 Jan 2022 20:11:00: #1 finished! INFO @ Sat, 15 Jan 2022 20:11:00: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:11:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:11:00: #2 number of paired peaks: 172 WARNING @ Sat, 15 Jan 2022 20:11:00: Fewer paired peaks (172) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 172 pairs to build model! INFO @ Sat, 15 Jan 2022 20:11:00: start model_add_line... INFO @ Sat, 15 Jan 2022 20:11:00: start X-correlation... INFO @ Sat, 15 Jan 2022 20:11:00: end of X-cor INFO @ Sat, 15 Jan 2022 20:11:00: #2 finished! INFO @ Sat, 15 Jan 2022 20:11:00: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 20:11:00: #2 alternative fragment length(s) may be 0,60,109,126,165,172,188,202,219,258,285,312,337,351,390,408,433,457,495,528,572,589 bps INFO @ Sat, 15 Jan 2022 20:11:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245532/SRX8245532.10_model.r WARNING @ Sat, 15 Jan 2022 20:11:00: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:11:00: #2 You may need to consider one of the other alternative d(s): 0,60,109,126,165,172,188,202,219,258,285,312,337,351,390,408,433,457,495,528,572,589 WARNING @ Sat, 15 Jan 2022 20:11:00: #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 20:11:00: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:11:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:11:08: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:11:18: 7000000 INFO @ Sat, 15 Jan 2022 20:11:27: 8000000 INFO @ Sat, 15 Jan 2022 20:11:32: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:11:32: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:11:32: #1 total tags in treatment: 2702429 INFO @ Sat, 15 Jan 2022 20:11:32: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:11:32: #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 20:11:32: #1 tags after filtering in treatment: 1531178 INFO @ Sat, 15 Jan 2022 20:11:32: #1 Redundant rate of treatment: 0.43 INFO @ Sat, 15 Jan 2022 20:11:32: #1 finished! INFO @ Sat, 15 Jan 2022 20:11:32: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:11:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:11:32: #2 number of paired peaks: 172 WARNING @ Sat, 15 Jan 2022 20:11:32: Fewer paired peaks (172) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 172 pairs to build model! INFO @ Sat, 15 Jan 2022 20:11:32: start model_add_line... INFO @ Sat, 15 Jan 2022 20:11:32: start X-correlation... INFO @ Sat, 15 Jan 2022 20:11:32: end of X-cor INFO @ Sat, 15 Jan 2022 20:11:32: #2 finished! INFO @ Sat, 15 Jan 2022 20:11:32: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 20:11:32: #2 alternative fragment length(s) may be 0,60,109,126,165,172,188,202,219,258,285,312,337,351,390,408,433,457,495,528,572,589 bps INFO @ Sat, 15 Jan 2022 20:11:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245532/SRX8245532.20_model.r WARNING @ Sat, 15 Jan 2022 20:11:32: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:11:32: #2 You may need to consider one of the other alternative d(s): 0,60,109,126,165,172,188,202,219,258,285,312,337,351,390,408,433,457,495,528,572,589 WARNING @ Sat, 15 Jan 2022 20:11:32: #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 20:11:32: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:11:32: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 /var/spool/uge/at077/job_scripts/14520825: line 297: 57398 Terminated MACS $i /var/spool/uge/at077/job_scripts/14520825: line 297: 57611 Terminated MACS $i /var/spool/uge/at077/job_scripts/14520825: line 297: 58856 Terminated MACS $i ls: cannot access SRX8245532.05.bed: No such file or directory mv: cannot stat ‘SRX8245532.05.bed’: No such file or directory mv: cannot stat ‘SRX8245532.05.bb’: No such file or directory ls: cannot access SRX8245532.10.bed: No such file or directory mv: cannot stat ‘SRX8245532.10.bed’: No such file or directory mv: cannot stat ‘SRX8245532.10.bb’: No such file or directory ls: cannot access SRX8245532.20.bed: No such file or directory mv: cannot stat ‘SRX8245532.20.bed’: No such file or directory mv: cannot stat ‘SRX8245532.20.bb’: No such file or directory