Job ID = 14520802 SRX = SRX8245529 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 9582757 spots for SRR11684740/SRR11684740.sra Written 9582757 spots for SRR11684740/SRR11684740.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: 00:05:57 9582757 reads; of these: 9582757 (100.00%) were paired; of these: 5717367 (59.66%) aligned concordantly 0 times 3556268 (37.11%) aligned concordantly exactly 1 time 309122 (3.23%) aligned concordantly >1 times ---- 5717367 pairs aligned concordantly 0 times; of these: 37710 (0.66%) aligned discordantly 1 time ---- 5679657 pairs aligned 0 times concordantly or discordantly; of these: 11359314 mates make up the pairs; of these: 7330911 (64.54%) aligned 0 times 3608222 (31.76%) aligned exactly 1 time 420181 (3.70%) aligned >1 times 61.75% overall alignment rate Time searching: 00:05:57 Overall time: 00:05:57 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] 358811 / 3902459 = 0.0919 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 20:05:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245529/SRX8245529.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245529/SRX8245529.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245529/SRX8245529.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245529/SRX8245529.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 20:05:23: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:05:23: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:05:29: 1000000 INFO @ Sat, 15 Jan 2022 20:05:35: 2000000 INFO @ Sat, 15 Jan 2022 20:05:41: 3000000 INFO @ Sat, 15 Jan 2022 20:05:46: 4000000 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 20:05:52: 5000000 INFO @ Sat, 15 Jan 2022 20:05:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245529/SRX8245529.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245529/SRX8245529.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245529/SRX8245529.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245529/SRX8245529.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 20:05:53: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:05:53: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:05:58: 6000000 INFO @ Sat, 15 Jan 2022 20:06:01: 1000000 INFO @ Sat, 15 Jan 2022 20:06:04: 7000000 INFO @ Sat, 15 Jan 2022 20:06:08: 2000000 INFO @ Sat, 15 Jan 2022 20:06:11: 8000000 INFO @ Sat, 15 Jan 2022 20:06:16: 3000000 INFO @ Sat, 15 Jan 2022 20:06:17: 9000000 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 20:06:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245529/SRX8245529.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245529/SRX8245529.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245529/SRX8245529.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245529/SRX8245529.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 20:06:23: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:06:23: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:06:23: 4000000 INFO @ Sat, 15 Jan 2022 20:06:24: 10000000 INFO @ Sat, 15 Jan 2022 20:06:29: 1000000 INFO @ Sat, 15 Jan 2022 20:06:31: 11000000 INFO @ Sat, 15 Jan 2022 20:06:31: 5000000 INFO @ Sat, 15 Jan 2022 20:06:31: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:06:31: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:06:31: #1 total tags in treatment: 3507895 INFO @ Sat, 15 Jan 2022 20:06:31: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:06:31: #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 20:06:31: #1 tags after filtering in treatment: 2105196 INFO @ Sat, 15 Jan 2022 20:06:31: #1 Redundant rate of treatment: 0.40 INFO @ Sat, 15 Jan 2022 20:06:31: #1 finished! INFO @ Sat, 15 Jan 2022 20:06:31: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:06:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:06:32: #2 number of paired peaks: 171 WARNING @ Sat, 15 Jan 2022 20:06:32: Fewer paired peaks (171) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 171 pairs to build model! INFO @ Sat, 15 Jan 2022 20:06:32: start model_add_line... INFO @ Sat, 15 Jan 2022 20:06:32: start X-correlation... INFO @ Sat, 15 Jan 2022 20:06:32: end of X-cor INFO @ Sat, 15 Jan 2022 20:06:32: #2 finished! INFO @ Sat, 15 Jan 2022 20:06:32: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 20:06:32: #2 alternative fragment length(s) may be 0,16,50,76,108,140,192,200,216,248,312,327,352,387,405,409,462,483,526,555,585 bps INFO @ Sat, 15 Jan 2022 20:06:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245529/SRX8245529.05_model.r WARNING @ Sat, 15 Jan 2022 20:06:32: #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 20:06:32: #2 You may need to consider one of the other alternative d(s): 0,16,50,76,108,140,192,200,216,248,312,327,352,387,405,409,462,483,526,555,585 WARNING @ Sat, 15 Jan 2022 20:06:32: #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 20:06:32: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:06:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:06:36: 2000000 INFO @ Sat, 15 Jan 2022 20:06:36: 6000000 INFO @ Sat, 15 Jan 2022 20:06:42: 3000000 INFO @ Sat, 15 Jan 2022 20:06:42: 7000000 INFO @ Sat, 15 Jan 2022 20:06:48: 4000000 INFO @ Sat, 15 Jan 2022 20:06:49: 8000000 INFO @ Sat, 15 Jan 2022 20:06:55: 9000000 INFO @ Sat, 15 Jan 2022 20:06:55: 5000000 INFO @ Sat, 15 Jan 2022 20:07:01: 10000000 INFO @ Sat, 15 Jan 2022 20:07:01: 6000000 INFO @ Sat, 15 Jan 2022 20:07:07: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:07:07: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:07:07: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:07:07: #1 total tags in treatment: 3507895 INFO @ Sat, 15 Jan 2022 20:07:07: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:07:07: #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 20:07:07: #1 tags after filtering in treatment: 2105196 INFO @ Sat, 15 Jan 2022 20:07:07: #1 Redundant rate of treatment: 0.40 INFO @ Sat, 15 Jan 2022 20:07:07: #1 finished! INFO @ Sat, 15 Jan 2022 20:07:07: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:07:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:07:07: 7000000 INFO @ Sat, 15 Jan 2022 20:07:08: #2 number of paired peaks: 171 WARNING @ Sat, 15 Jan 2022 20:07:08: Fewer paired peaks (171) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 171 pairs to build model! INFO @ Sat, 15 Jan 2022 20:07:08: start model_add_line... INFO @ Sat, 15 Jan 2022 20:07:08: start X-correlation... INFO @ Sat, 15 Jan 2022 20:07:08: end of X-cor INFO @ Sat, 15 Jan 2022 20:07:08: #2 finished! INFO @ Sat, 15 Jan 2022 20:07:08: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 20:07:08: #2 alternative fragment length(s) may be 0,16,50,76,108,140,192,200,216,248,312,327,352,387,405,409,462,483,526,555,585 bps INFO @ Sat, 15 Jan 2022 20:07:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245529/SRX8245529.10_model.r WARNING @ Sat, 15 Jan 2022 20:07:08: #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 20:07:08: #2 You may need to consider one of the other alternative d(s): 0,16,50,76,108,140,192,200,216,248,312,327,352,387,405,409,462,483,526,555,585 WARNING @ Sat, 15 Jan 2022 20:07:08: #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 20:07:08: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:07:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:07:14: 8000000 BigWig に変換しました。 /var/spool/uge/it005/job_scripts/14520802: line 297: 4954 Terminated MACS $i /var/spool/uge/it005/job_scripts/14520802: line 297: 5066 Terminated MACS $i /var/spool/uge/it005/job_scripts/14520802: line 297: 6192 Terminated MACS $i ls: cannot access SRX8245529.05.bed: No such file or directory mv: cannot stat ‘SRX8245529.05.bed’: No such file or directory mv: cannot stat ‘SRX8245529.05.bb’: No such file or directory ls: cannot access SRX8245529.10.bed: No such file or directory mv: cannot stat ‘SRX8245529.10.bed’: No such file or directory mv: cannot stat ‘SRX8245529.10.bb’: No such file or directory ls: cannot access SRX8245529.20.bed: No such file or directory mv: cannot stat ‘SRX8245529.20.bed’: No such file or directory mv: cannot stat ‘SRX8245529.20.bb’: No such file or directory