Job ID = 14519819 SRX = SRX9786279 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 13119424 spots for SRR13362143/SRR13362143.sra Written 13119424 spots for SRR13362143/SRR13362143.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: 00:08:35 13119424 reads; of these: 13119424 (100.00%) were paired; of these: 7780039 (59.30%) aligned concordantly 0 times 4871956 (37.14%) aligned concordantly exactly 1 time 467429 (3.56%) aligned concordantly >1 times ---- 7780039 pairs aligned concordantly 0 times; of these: 171010 (2.20%) aligned discordantly 1 time ---- 7609029 pairs aligned 0 times concordantly or discordantly; of these: 15218058 mates make up the pairs; of these: 10279580 (67.55%) aligned 0 times 4375886 (28.75%) aligned exactly 1 time 562592 (3.70%) aligned >1 times 60.82% overall alignment rate Time searching: 00:08:35 Overall time: 00:08:35 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] 610342 / 5509338 = 0.1108 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 18:03:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9786279/SRX9786279.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9786279/SRX9786279.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9786279/SRX9786279.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9786279/SRX9786279.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 18:03:58: #1 read tag files... INFO @ Sat, 15 Jan 2022 18:03:58: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 18:04:05: 1000000 INFO @ Sat, 15 Jan 2022 18:04:11: 2000000 INFO @ Sat, 15 Jan 2022 18:04:18: 3000000 INFO @ Sat, 15 Jan 2022 18:04:24: 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 18:04:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9786279/SRX9786279.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9786279/SRX9786279.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9786279/SRX9786279.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9786279/SRX9786279.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 18:04:28: #1 read tag files... INFO @ Sat, 15 Jan 2022 18:04:28: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 18:04:30: 5000000 INFO @ Sat, 15 Jan 2022 18:04:34: 1000000 INFO @ Sat, 15 Jan 2022 18:04:36: 6000000 INFO @ Sat, 15 Jan 2022 18:04:40: 2000000 INFO @ Sat, 15 Jan 2022 18:04:43: 7000000 INFO @ Sat, 15 Jan 2022 18:04:47: 3000000 INFO @ Sat, 15 Jan 2022 18:04:49: 8000000 INFO @ Sat, 15 Jan 2022 18:04:53: 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 18:04:56: 9000000 INFO @ Sat, 15 Jan 2022 18:04:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9786279/SRX9786279.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9786279/SRX9786279.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9786279/SRX9786279.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9786279/SRX9786279.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 18:04:58: #1 read tag files... INFO @ Sat, 15 Jan 2022 18:04:58: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 18:04:59: 5000000 INFO @ Sat, 15 Jan 2022 18:05:02: 10000000 INFO @ Sat, 15 Jan 2022 18:05:05: 6000000 INFO @ Sat, 15 Jan 2022 18:05:05: 1000000 INFO @ Sat, 15 Jan 2022 18:05:09: 11000000 INFO @ Sat, 15 Jan 2022 18:05:11: 7000000 INFO @ Sat, 15 Jan 2022 18:05:12: 2000000 INFO @ Sat, 15 Jan 2022 18:05:16: 12000000 INFO @ Sat, 15 Jan 2022 18:05:17: 8000000 INFO @ Sat, 15 Jan 2022 18:05:19: 3000000 INFO @ Sat, 15 Jan 2022 18:05:23: 13000000 INFO @ Sat, 15 Jan 2022 18:05:23: 9000000 INFO @ Sat, 15 Jan 2022 18:05:26: 4000000 INFO @ Sat, 15 Jan 2022 18:05:29: 10000000 INFO @ Sat, 15 Jan 2022 18:05:30: 14000000 INFO @ Sat, 15 Jan 2022 18:05:33: 5000000 INFO @ Sat, 15 Jan 2022 18:05:34: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 18:05:34: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 18:05:34: #1 total tags in treatment: 4737170 INFO @ Sat, 15 Jan 2022 18:05:34: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 18:05:34: #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 18:05:35: #1 tags after filtering in treatment: 3234578 INFO @ Sat, 15 Jan 2022 18:05:35: #1 Redundant rate of treatment: 0.32 INFO @ Sat, 15 Jan 2022 18:05:35: #1 finished! INFO @ Sat, 15 Jan 2022 18:05:35: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 18:05:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 18:05:35: #2 number of paired peaks: 166 WARNING @ Sat, 15 Jan 2022 18:05:35: Fewer paired peaks (166) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 166 pairs to build model! INFO @ Sat, 15 Jan 2022 18:05:35: start model_add_line... INFO @ Sat, 15 Jan 2022 18:05:35: start X-correlation... INFO @ Sat, 15 Jan 2022 18:05:35: end of X-cor INFO @ Sat, 15 Jan 2022 18:05:35: #2 finished! INFO @ Sat, 15 Jan 2022 18:05:35: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 18:05:35: #2 alternative fragment length(s) may be 0,10,48,73,137,149,209,234,253,270,294,315,348,363,393,405,422,446,473,492,525,550,577 bps INFO @ Sat, 15 Jan 2022 18:05:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX9786279/SRX9786279.05_model.r WARNING @ Sat, 15 Jan 2022 18:05:35: #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 18:05:35: #2 You may need to consider one of the other alternative d(s): 0,10,48,73,137,149,209,234,253,270,294,315,348,363,393,405,422,446,473,492,525,550,577 WARNING @ Sat, 15 Jan 2022 18:05:35: #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 18:05:35: #3 Call peaks... INFO @ Sat, 15 Jan 2022 18:05:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 18:05:35: 11000000 INFO @ Sat, 15 Jan 2022 18:05:39: 6000000 INFO @ Sat, 15 Jan 2022 18:05:41: 12000000 INFO @ Sat, 15 Jan 2022 18:05:46: 7000000 INFO @ Sat, 15 Jan 2022 18:05:48: 13000000 INFO @ Sat, 15 Jan 2022 18:05:54: 8000000 INFO @ Sat, 15 Jan 2022 18:05:54: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 18:05:59: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 18:05:59: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 18:05:59: #1 total tags in treatment: 4737170 INFO @ Sat, 15 Jan 2022 18:05:59: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 18:05:59: #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 18:05:59: #1 tags after filtering in treatment: 3234578 INFO @ Sat, 15 Jan 2022 18:05:59: #1 Redundant rate of treatment: 0.32 INFO @ Sat, 15 Jan 2022 18:05:59: #1 finished! INFO @ Sat, 15 Jan 2022 18:05:59: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 18:05:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 18:06:00: #2 number of paired peaks: 166 WARNING @ Sat, 15 Jan 2022 18:06:00: Fewer paired peaks (166) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 166 pairs to build model! INFO @ Sat, 15 Jan 2022 18:06:00: start model_add_line... INFO @ Sat, 15 Jan 2022 18:06:00: start X-correlation... INFO @ Sat, 15 Jan 2022 18:06:00: end of X-cor INFO @ Sat, 15 Jan 2022 18:06:00: #2 finished! INFO @ Sat, 15 Jan 2022 18:06:00: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 18:06:00: #2 alternative fragment length(s) may be 0,10,48,73,137,149,209,234,253,270,294,315,348,363,393,405,422,446,473,492,525,550,577 bps INFO @ Sat, 15 Jan 2022 18:06:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX9786279/SRX9786279.10_model.r WARNING @ Sat, 15 Jan 2022 18:06:00: #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 18:06:00: #2 You may need to consider one of the other alternative d(s): 0,10,48,73,137,149,209,234,253,270,294,315,348,363,393,405,422,446,473,492,525,550,577 WARNING @ Sat, 15 Jan 2022 18:06:00: #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 18:06:00: #3 Call peaks... INFO @ Sat, 15 Jan 2022 18:06:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 18:06:00: 9000000 INFO @ Sat, 15 Jan 2022 18:06:07: 10000000 BigWig に変換しました。 /var/spool/uge/it015/job_scripts/14519819: line 297: 21757 Terminated MACS $i /var/spool/uge/it015/job_scripts/14519819: line 297: 22961 Terminated MACS $i /var/spool/uge/it015/job_scripts/14519819: line 297: 23123 Terminated MACS $i ls: cannot access SRX9786279.05.bed: No such file or directory mv: cannot stat ‘SRX9786279.05.bed’: No such file or directory mv: cannot stat ‘SRX9786279.05.bb’: No such file or directory ls: cannot access SRX9786279.10.bed: No such file or directory mv: cannot stat ‘SRX9786279.10.bed’: No such file or directory mv: cannot stat ‘SRX9786279.10.bb’: No such file or directory ls: cannot access SRX9786279.20.bed: No such file or directory mv: cannot stat ‘SRX9786279.20.bed’: No such file or directory mv: cannot stat ‘SRX9786279.20.bb’: No such file or directory