Job ID = 14521265 SRX = SRX8245394 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 7813270 spots for SRR11684605/SRR11684605.sra Written 7813270 spots for SRR11684605/SRR11684605.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: 00:05:18 7813270 reads; of these: 7813270 (100.00%) were paired; of these: 4708769 (60.27%) aligned concordantly 0 times 2847798 (36.45%) aligned concordantly exactly 1 time 256703 (3.29%) aligned concordantly >1 times ---- 4708769 pairs aligned concordantly 0 times; of these: 12774 (0.27%) aligned discordantly 1 time ---- 4695995 pairs aligned 0 times concordantly or discordantly; of these: 9391990 mates make up the pairs; of these: 6379865 (67.93%) aligned 0 times 2688512 (28.63%) aligned exactly 1 time 323613 (3.45%) aligned >1 times 59.17% overall alignment rate Time searching: 00:05:18 Overall time: 00:05:18 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] 193949 / 3116274 = 0.0622 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 20:53:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245394/SRX8245394.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245394/SRX8245394.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245394/SRX8245394.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245394/SRX8245394.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 20:53:44: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:53:44: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:53:49: 1000000 INFO @ Sat, 15 Jan 2022 20:53:54: 2000000 INFO @ Sat, 15 Jan 2022 20:53:58: 3000000 INFO @ Sat, 15 Jan 2022 20:54:03: 4000000 INFO @ Sat, 15 Jan 2022 20:54:07: 5000000 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 20:54:12: 6000000 INFO @ Sat, 15 Jan 2022 20:54:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245394/SRX8245394.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245394/SRX8245394.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245394/SRX8245394.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245394/SRX8245394.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 20:54:13: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:54:13: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:54:17: 7000000 INFO @ Sat, 15 Jan 2022 20:54:18: 1000000 INFO @ Sat, 15 Jan 2022 20:54:22: 8000000 INFO @ Sat, 15 Jan 2022 20:54:22: 2000000 INFO @ Sat, 15 Jan 2022 20:54:26: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:54:26: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:54:26: #1 total tags in treatment: 2912006 INFO @ Sat, 15 Jan 2022 20:54:26: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:54:26: #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 20:54:26: #1 tags after filtering in treatment: 1475883 INFO @ Sat, 15 Jan 2022 20:54:26: #1 Redundant rate of treatment: 0.49 INFO @ Sat, 15 Jan 2022 20:54:26: #1 finished! INFO @ Sat, 15 Jan 2022 20:54:26: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:54:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:54:26: #2 number of paired peaks: 172 WARNING @ Sat, 15 Jan 2022 20:54:26: 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 20:54:26: start model_add_line... INFO @ Sat, 15 Jan 2022 20:54:26: start X-correlation... INFO @ Sat, 15 Jan 2022 20:54:26: end of X-cor INFO @ Sat, 15 Jan 2022 20:54:26: #2 finished! INFO @ Sat, 15 Jan 2022 20:54:26: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 20:54:26: #2 alternative fragment length(s) may be 0,31,50,71,90,120,146,205,246,267,314,316,349,370,395,420,459,473,487,546,568,583 bps INFO @ Sat, 15 Jan 2022 20:54:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245394/SRX8245394.05_model.r WARNING @ Sat, 15 Jan 2022 20:54:26: #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 20:54:26: #2 You may need to consider one of the other alternative d(s): 0,31,50,71,90,120,146,205,246,267,314,316,349,370,395,420,459,473,487,546,568,583 WARNING @ Sat, 15 Jan 2022 20:54:26: #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 20:54:26: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:54:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:54:27: 3000000 INFO @ Sat, 15 Jan 2022 20:54:31: 4000000 INFO @ Sat, 15 Jan 2022 20:54:35: 5000000 INFO @ Sat, 15 Jan 2022 20:54:40: 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 20:54:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245394/SRX8245394.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245394/SRX8245394.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245394/SRX8245394.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245394/SRX8245394.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 20:54:44: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:54:44: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:54:44: 7000000 INFO @ Sat, 15 Jan 2022 20:54:49: 1000000 INFO @ Sat, 15 Jan 2022 20:54:50: 8000000 INFO @ Sat, 15 Jan 2022 20:54:53: 2000000 INFO @ Sat, 15 Jan 2022 20:54:54: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:54:54: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:54:54: #1 total tags in treatment: 2912006 INFO @ Sat, 15 Jan 2022 20:54:54: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:54:54: #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 20:54:54: #1 tags after filtering in treatment: 1475883 INFO @ Sat, 15 Jan 2022 20:54:54: #1 Redundant rate of treatment: 0.49 INFO @ Sat, 15 Jan 2022 20:54:54: #1 finished! INFO @ Sat, 15 Jan 2022 20:54:54: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:54:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:54:54: #2 number of paired peaks: 172 WARNING @ Sat, 15 Jan 2022 20:54:54: 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 20:54:54: start model_add_line... INFO @ Sat, 15 Jan 2022 20:54:54: start X-correlation... INFO @ Sat, 15 Jan 2022 20:54:54: end of X-cor INFO @ Sat, 15 Jan 2022 20:54:54: #2 finished! INFO @ Sat, 15 Jan 2022 20:54:54: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 20:54:54: #2 alternative fragment length(s) may be 0,31,50,71,90,120,146,205,246,267,314,316,349,370,395,420,459,473,487,546,568,583 bps INFO @ Sat, 15 Jan 2022 20:54:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245394/SRX8245394.10_model.r WARNING @ Sat, 15 Jan 2022 20:54:54: #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 20:54:54: #2 You may need to consider one of the other alternative d(s): 0,31,50,71,90,120,146,205,246,267,314,316,349,370,395,420,459,473,487,546,568,583 WARNING @ Sat, 15 Jan 2022 20:54:54: #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 20:54:54: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:54:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:54:58: 3000000 INFO @ Sat, 15 Jan 2022 20:55:02: 4000000 INFO @ Sat, 15 Jan 2022 20:55:06: 5000000 INFO @ Sat, 15 Jan 2022 20:55:11: 6000000 INFO @ Sat, 15 Jan 2022 20:55:15: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:55:20: 8000000 INFO @ Sat, 15 Jan 2022 20:55:24: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:55:24: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:55:24: #1 total tags in treatment: 2912006 INFO @ Sat, 15 Jan 2022 20:55:24: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:55:24: #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 20:55:24: #1 tags after filtering in treatment: 1475883 INFO @ Sat, 15 Jan 2022 20:55:24: #1 Redundant rate of treatment: 0.49 INFO @ Sat, 15 Jan 2022 20:55:24: #1 finished! INFO @ Sat, 15 Jan 2022 20:55:24: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:55:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:55:24: #2 number of paired peaks: 172 WARNING @ Sat, 15 Jan 2022 20:55:24: 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 20:55:24: start model_add_line... INFO @ Sat, 15 Jan 2022 20:55:24: start X-correlation... INFO @ Sat, 15 Jan 2022 20:55:24: end of X-cor INFO @ Sat, 15 Jan 2022 20:55:24: #2 finished! INFO @ Sat, 15 Jan 2022 20:55:24: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 20:55:24: #2 alternative fragment length(s) may be 0,31,50,71,90,120,146,205,246,267,314,316,349,370,395,420,459,473,487,546,568,583 bps INFO @ Sat, 15 Jan 2022 20:55:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245394/SRX8245394.20_model.r WARNING @ Sat, 15 Jan 2022 20:55:24: #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 20:55:24: #2 You may need to consider one of the other alternative d(s): 0,31,50,71,90,120,146,205,246,267,314,316,349,370,395,420,459,473,487,546,568,583 WARNING @ Sat, 15 Jan 2022 20:55:24: #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 20:55:24: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:55:24: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 /var/spool/uge/it007/job_scripts/14521265: line 297: 31044 Terminated MACS $i /var/spool/uge/it007/job_scripts/14521265: line 297: 876 Terminated MACS $i /var/spool/uge/it007/job_scripts/14521265: line 297: 2244 Terminated MACS $i ls: cannot access SRX8245394.05.bed: No such file or directory mv: cannot stat ‘SRX8245394.05.bed’: No such file or directory mv: cannot stat ‘SRX8245394.05.bb’: No such file or directory ls: cannot access SRX8245394.10.bed: No such file or directory mv: cannot stat ‘SRX8245394.10.bed’: No such file or directory mv: cannot stat ‘SRX8245394.10.bb’: No such file or directory ls: cannot access SRX8245394.20.bed: No such file or directory mv: cannot stat ‘SRX8245394.20.bed’: No such file or directory mv: cannot stat ‘SRX8245394.20.bb’: No such file or directory