Job ID = 14520761 SRX = SRX8245512 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 5636504 spots for SRR11684723/SRR11684723.sra Written 5636504 spots for SRR11684723/SRR11684723.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: 00:03:07 5636504 reads; of these: 5636504 (100.00%) were paired; of these: 2865153 (50.83%) aligned concordantly 0 times 2413174 (42.81%) aligned concordantly exactly 1 time 358177 (6.35%) aligned concordantly >1 times ---- 2865153 pairs aligned concordantly 0 times; of these: 34224 (1.19%) aligned discordantly 1 time ---- 2830929 pairs aligned 0 times concordantly or discordantly; of these: 5661858 mates make up the pairs; of these: 3549980 (62.70%) aligned 0 times 1811416 (31.99%) aligned exactly 1 time 300462 (5.31%) aligned >1 times 68.51% overall alignment rate Time searching: 00:03:07 Overall time: 00:03:07 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] 126197 / 2805157 = 0.0450 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 19:55:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245512/SRX8245512.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245512/SRX8245512.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245512/SRX8245512.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245512/SRX8245512.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 19:55:20: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:55:20: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:55:25: 1000000 INFO @ Sat, 15 Jan 2022 19:55:30: 2000000 INFO @ Sat, 15 Jan 2022 19:55:35: 3000000 INFO @ Sat, 15 Jan 2022 19:55:40: 4000000 INFO @ Sat, 15 Jan 2022 19:55:45: 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 19:55:50: 6000000 INFO @ Sat, 15 Jan 2022 19:55:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245512/SRX8245512.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245512/SRX8245512.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245512/SRX8245512.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245512/SRX8245512.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 19:55:50: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:55:50: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:55:56: 7000000 INFO @ Sat, 15 Jan 2022 19:55:56: 1000000 INFO @ Sat, 15 Jan 2022 19:55:58: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 19:55:58: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 19:55:58: #1 total tags in treatment: 2645810 INFO @ Sat, 15 Jan 2022 19:55:58: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:55:58: #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 19:55:58: #1 tags after filtering in treatment: 1866536 INFO @ Sat, 15 Jan 2022 19:55:58: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 15 Jan 2022 19:55:58: #1 finished! INFO @ Sat, 15 Jan 2022 19:55:58: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:55:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:55:58: #2 number of paired peaks: 170 WARNING @ Sat, 15 Jan 2022 19:55:58: 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 19:55:58: start model_add_line... INFO @ Sat, 15 Jan 2022 19:55:58: start X-correlation... INFO @ Sat, 15 Jan 2022 19:55:58: end of X-cor INFO @ Sat, 15 Jan 2022 19:55:58: #2 finished! INFO @ Sat, 15 Jan 2022 19:55:58: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 19:55:58: #2 alternative fragment length(s) may be 0,23,46,60,68,88,109,128,149,190,206,224,256,279,313,369,437,492,516,536,558,565,584 bps INFO @ Sat, 15 Jan 2022 19:55:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245512/SRX8245512.05_model.r WARNING @ Sat, 15 Jan 2022 19:55:58: #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 19:55:58: #2 You may need to consider one of the other alternative d(s): 0,23,46,60,68,88,109,128,149,190,206,224,256,279,313,369,437,492,516,536,558,565,584 WARNING @ Sat, 15 Jan 2022 19:55:58: #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 19:55:58: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:55:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:56:01: 2000000 INFO @ Sat, 15 Jan 2022 19:56:07: 3000000 INFO @ Sat, 15 Jan 2022 19:56:12: 4000000 INFO @ Sat, 15 Jan 2022 19:56:17: 5000000 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 19:56:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245512/SRX8245512.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245512/SRX8245512.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245512/SRX8245512.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245512/SRX8245512.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 19:56:20: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:56:20: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:56:22: 6000000 INFO @ Sat, 15 Jan 2022 19:56:26: 1000000 INFO @ Sat, 15 Jan 2022 19:56:28: 7000000 INFO @ Sat, 15 Jan 2022 19:56:31: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 19:56:31: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 19:56:31: #1 total tags in treatment: 2645810 INFO @ Sat, 15 Jan 2022 19:56:31: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:56:31: #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 19:56:31: #1 tags after filtering in treatment: 1866536 INFO @ Sat, 15 Jan 2022 19:56:31: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 15 Jan 2022 19:56:31: #1 finished! INFO @ Sat, 15 Jan 2022 19:56:31: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:56:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:56:31: #2 number of paired peaks: 170 WARNING @ Sat, 15 Jan 2022 19:56:31: 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 19:56:31: start model_add_line... INFO @ Sat, 15 Jan 2022 19:56:31: start X-correlation... INFO @ Sat, 15 Jan 2022 19:56:31: end of X-cor INFO @ Sat, 15 Jan 2022 19:56:31: #2 finished! INFO @ Sat, 15 Jan 2022 19:56:31: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 19:56:31: #2 alternative fragment length(s) may be 0,23,46,60,68,88,109,128,149,190,206,224,256,279,313,369,437,492,516,536,558,565,584 bps INFO @ Sat, 15 Jan 2022 19:56:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245512/SRX8245512.10_model.r WARNING @ Sat, 15 Jan 2022 19:56:31: #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 19:56:31: #2 You may need to consider one of the other alternative d(s): 0,23,46,60,68,88,109,128,149,190,206,224,256,279,313,369,437,492,516,536,558,565,584 WARNING @ Sat, 15 Jan 2022 19:56:31: #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 19:56:31: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:56:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:56:32: 2000000 INFO @ Sat, 15 Jan 2022 19:56:37: 3000000 INFO @ Sat, 15 Jan 2022 19:56:42: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 19:56:48: 5000000 INFO @ Sat, 15 Jan 2022 19:56:53: 6000000 BigWig に変換しました。 /var/spool/uge/at157/job_scripts/14520761: line 297: 67437 Terminated MACS $i /var/spool/uge/at157/job_scripts/14520761: line 297: 67539 Terminated MACS $i /var/spool/uge/at157/job_scripts/14520761: line 297: 68672 Terminated MACS $i ls: cannot access SRX8245512.05.bed: No such file or directory mv: cannot stat ‘SRX8245512.05.bed’: No such file or directory mv: cannot stat ‘SRX8245512.05.bb’: No such file or directory ls: cannot access SRX8245512.10.bed: No such file or directory mv: cannot stat ‘SRX8245512.10.bed’: No such file or directory mv: cannot stat ‘SRX8245512.10.bb’: No such file or directory ls: cannot access SRX8245512.20.bed: No such file or directory mv: cannot stat ‘SRX8245512.20.bed’: No such file or directory mv: cannot stat ‘SRX8245512.20.bb’: No such file or directory