Job ID = 14521156 SRX = SRX8245488 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 14103051 spots for SRR11684699/SRR11684699.sra Written 14103051 spots for SRR11684699/SRR11684699.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: 00:06:33 14103051 reads; of these: 14103051 (100.00%) were paired; of these: 8837552 (62.66%) aligned concordantly 0 times 4633481 (32.85%) aligned concordantly exactly 1 time 632018 (4.48%) aligned concordantly >1 times ---- 8837552 pairs aligned concordantly 0 times; of these: 118927 (1.35%) aligned discordantly 1 time ---- 8718625 pairs aligned 0 times concordantly or discordantly; of these: 17437250 mates make up the pairs; of these: 12128574 (69.56%) aligned 0 times 4560650 (26.15%) aligned exactly 1 time 748026 (4.29%) aligned >1 times 57.00% overall alignment rate Time searching: 00:06:33 Overall time: 00:06:33 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] 719200 / 5383490 = 0.1336 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 20:48:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245488/SRX8245488.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245488/SRX8245488.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245488/SRX8245488.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245488/SRX8245488.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 20:48:11: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:48:11: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:48:17: 1000000 INFO @ Sat, 15 Jan 2022 20:48:22: 2000000 INFO @ Sat, 15 Jan 2022 20:48:27: 3000000 INFO @ Sat, 15 Jan 2022 20:48:32: 4000000 INFO @ Sat, 15 Jan 2022 20:48:36: 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 20:48:41: 6000000 INFO @ Sat, 15 Jan 2022 20:48:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245488/SRX8245488.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245488/SRX8245488.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245488/SRX8245488.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245488/SRX8245488.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 20:48:41: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:48:41: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:48:47: 7000000 INFO @ Sat, 15 Jan 2022 20:48:47: 1000000 INFO @ Sat, 15 Jan 2022 20:48:53: 8000000 INFO @ Sat, 15 Jan 2022 20:48:54: 2000000 INFO @ Sat, 15 Jan 2022 20:48:59: 9000000 INFO @ Sat, 15 Jan 2022 20:48:59: 3000000 INFO @ Sat, 15 Jan 2022 20:49:05: 10000000 INFO @ Sat, 15 Jan 2022 20:49:05: 4000000 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 20:49:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245488/SRX8245488.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245488/SRX8245488.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245488/SRX8245488.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245488/SRX8245488.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 20:49:11: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:49:11: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:49:11: 11000000 INFO @ Sat, 15 Jan 2022 20:49:11: 5000000 INFO @ Sat, 15 Jan 2022 20:49:17: 6000000 INFO @ Sat, 15 Jan 2022 20:49:17: 1000000 INFO @ Sat, 15 Jan 2022 20:49:17: 12000000 INFO @ Sat, 15 Jan 2022 20:49:23: 7000000 INFO @ Sat, 15 Jan 2022 20:49:23: 13000000 INFO @ Sat, 15 Jan 2022 20:49:24: 2000000 INFO @ Sat, 15 Jan 2022 20:49:30: 8000000 INFO @ Sat, 15 Jan 2022 20:49:30: 3000000 INFO @ Sat, 15 Jan 2022 20:49:30: 14000000 INFO @ Sat, 15 Jan 2022 20:49:34: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:49:34: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:49:34: #1 total tags in treatment: 4554660 INFO @ Sat, 15 Jan 2022 20:49:34: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:49:34: #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 20:49:34: #1 tags after filtering in treatment: 3033636 INFO @ Sat, 15 Jan 2022 20:49:34: #1 Redundant rate of treatment: 0.33 INFO @ Sat, 15 Jan 2022 20:49:34: #1 finished! INFO @ Sat, 15 Jan 2022 20:49:34: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:49:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:49:34: #2 number of paired peaks: 169 WARNING @ Sat, 15 Jan 2022 20:49:34: Fewer paired peaks (169) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 169 pairs to build model! INFO @ Sat, 15 Jan 2022 20:49:34: start model_add_line... INFO @ Sat, 15 Jan 2022 20:49:34: start X-correlation... INFO @ Sat, 15 Jan 2022 20:49:34: end of X-cor INFO @ Sat, 15 Jan 2022 20:49:34: #2 finished! INFO @ Sat, 15 Jan 2022 20:49:34: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 20:49:34: #2 alternative fragment length(s) may be 0,10,51,96,113,125,207,220,244,269,284,305,334,348,369,394,410,413,433,458,483,501,515,546,573 bps INFO @ Sat, 15 Jan 2022 20:49:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245488/SRX8245488.05_model.r WARNING @ Sat, 15 Jan 2022 20:49:34: #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 20:49:34: #2 You may need to consider one of the other alternative d(s): 0,10,51,96,113,125,207,220,244,269,284,305,334,348,369,394,410,413,433,458,483,501,515,546,573 WARNING @ Sat, 15 Jan 2022 20:49:34: #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 20:49:34: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:49:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:49:35: 4000000 INFO @ Sat, 15 Jan 2022 20:49:36: 9000000 INFO @ Sat, 15 Jan 2022 20:49:41: 5000000 INFO @ Sat, 15 Jan 2022 20:49:41: 10000000 INFO @ Sat, 15 Jan 2022 20:49:47: 6000000 INFO @ Sat, 15 Jan 2022 20:49:47: 11000000 INFO @ Sat, 15 Jan 2022 20:49:53: 7000000 INFO @ Sat, 15 Jan 2022 20:49:53: 12000000 INFO @ Sat, 15 Jan 2022 20:49:59: 8000000 INFO @ Sat, 15 Jan 2022 20:49:59: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:50:04: 9000000 INFO @ Sat, 15 Jan 2022 20:50:06: 14000000 INFO @ Sat, 15 Jan 2022 20:50:10: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:50:10: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:50:10: #1 total tags in treatment: 4554660 INFO @ Sat, 15 Jan 2022 20:50:10: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:50:10: #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 20:50:10: #1 tags after filtering in treatment: 3033636 INFO @ Sat, 15 Jan 2022 20:50:10: #1 Redundant rate of treatment: 0.33 INFO @ Sat, 15 Jan 2022 20:50:10: #1 finished! INFO @ Sat, 15 Jan 2022 20:50:10: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:50:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:50:10: #2 number of paired peaks: 169 WARNING @ Sat, 15 Jan 2022 20:50:10: Fewer paired peaks (169) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 169 pairs to build model! INFO @ Sat, 15 Jan 2022 20:50:10: start model_add_line... INFO @ Sat, 15 Jan 2022 20:50:10: start X-correlation... INFO @ Sat, 15 Jan 2022 20:50:10: end of X-cor INFO @ Sat, 15 Jan 2022 20:50:10: #2 finished! INFO @ Sat, 15 Jan 2022 20:50:10: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 20:50:10: #2 alternative fragment length(s) may be 0,10,51,96,113,125,207,220,244,269,284,305,334,348,369,394,410,413,433,458,483,501,515,546,573 bps INFO @ Sat, 15 Jan 2022 20:50:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245488/SRX8245488.10_model.r WARNING @ Sat, 15 Jan 2022 20:50:10: #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 20:50:10: #2 You may need to consider one of the other alternative d(s): 0,10,51,96,113,125,207,220,244,269,284,305,334,348,369,394,410,413,433,458,483,501,515,546,573 WARNING @ Sat, 15 Jan 2022 20:50:10: #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 20:50:10: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:50:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:50:10: 10000000 BigWig に変換しました。 /var/spool/uge/at143/job_scripts/14521156: line 297: 11351 Terminated MACS $i /var/spool/uge/at143/job_scripts/14521156: line 297: 12545 Terminated MACS $i /var/spool/uge/at143/job_scripts/14521156: line 297: 12724 Terminated MACS $i ls: cannot access SRX8245488.05.bed: No such file or directory mv: cannot stat ‘SRX8245488.05.bed’: No such file or directory mv: cannot stat ‘SRX8245488.05.bb’: No such file or directory ls: cannot access SRX8245488.10.bed: No such file or directory mv: cannot stat ‘SRX8245488.10.bed’: No such file or directory mv: cannot stat ‘SRX8245488.10.bb’: No such file or directory ls: cannot access SRX8245488.20.bed: No such file or directory mv: cannot stat ‘SRX8245488.20.bed’: No such file or directory mv: cannot stat ‘SRX8245488.20.bb’: No such file or directory