Job ID = 14521202 SRX = SRX8245490 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 10688250 spots for SRR11684701/SRR11684701.sra Written 10688250 spots for SRR11684701/SRR11684701.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: 00:05:03 10688250 reads; of these: 10688250 (100.00%) were paired; of these: 6651904 (62.24%) aligned concordantly 0 times 3682809 (34.46%) aligned concordantly exactly 1 time 353537 (3.31%) aligned concordantly >1 times ---- 6651904 pairs aligned concordantly 0 times; of these: 153923 (2.31%) aligned discordantly 1 time ---- 6497981 pairs aligned 0 times concordantly or discordantly; of these: 12995962 mates make up the pairs; of these: 7630032 (58.71%) aligned 0 times 4753012 (36.57%) aligned exactly 1 time 612918 (4.72%) aligned >1 times 64.31% overall alignment rate Time searching: 00:05:03 Overall time: 00:05:03 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] 587586 / 4189502 = 0.1403 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 20:45:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245490/SRX8245490.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245490/SRX8245490.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245490/SRX8245490.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245490/SRX8245490.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 20:45:37: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:45:37: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:45:43: 1000000 INFO @ Sat, 15 Jan 2022 20:45:48: 2000000 INFO @ Sat, 15 Jan 2022 20:45:53: 3000000 INFO @ Sat, 15 Jan 2022 20:45:59: 4000000 INFO @ Sat, 15 Jan 2022 20:46:04: 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 20:46:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245490/SRX8245490.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245490/SRX8245490.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245490/SRX8245490.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245490/SRX8245490.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 20:46:07: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:46:07: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:46:09: 6000000 INFO @ Sat, 15 Jan 2022 20:46:13: 1000000 INFO @ Sat, 15 Jan 2022 20:46:14: 7000000 INFO @ Sat, 15 Jan 2022 20:46:19: 2000000 INFO @ Sat, 15 Jan 2022 20:46:20: 8000000 INFO @ Sat, 15 Jan 2022 20:46:25: 3000000 INFO @ Sat, 15 Jan 2022 20:46:26: 9000000 INFO @ Sat, 15 Jan 2022 20:46:31: 4000000 INFO @ Sat, 15 Jan 2022 20:46:31: 10000000 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 20:46:37: 11000000 INFO @ Sat, 15 Jan 2022 20:46:37: 5000000 INFO @ Sat, 15 Jan 2022 20:46:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245490/SRX8245490.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245490/SRX8245490.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245490/SRX8245490.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245490/SRX8245490.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 20:46:37: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:46:37: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:46:42: 12000000 INFO @ Sat, 15 Jan 2022 20:46:43: 6000000 INFO @ Sat, 15 Jan 2022 20:46:43: 1000000 INFO @ Sat, 15 Jan 2022 20:46:45: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:46:45: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:46:45: #1 total tags in treatment: 3459501 INFO @ Sat, 15 Jan 2022 20:46:45: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:46:45: #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 20:46:46: #1 tags after filtering in treatment: 2061848 INFO @ Sat, 15 Jan 2022 20:46:46: #1 Redundant rate of treatment: 0.40 INFO @ Sat, 15 Jan 2022 20:46:46: #1 finished! INFO @ Sat, 15 Jan 2022 20:46:46: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:46:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:46:46: #2 number of paired peaks: 176 WARNING @ Sat, 15 Jan 2022 20:46:46: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Sat, 15 Jan 2022 20:46:46: start model_add_line... INFO @ Sat, 15 Jan 2022 20:46:46: start X-correlation... INFO @ Sat, 15 Jan 2022 20:46:46: end of X-cor INFO @ Sat, 15 Jan 2022 20:46:46: #2 finished! INFO @ Sat, 15 Jan 2022 20:46:46: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 20:46:46: #2 alternative fragment length(s) may be 0,33,74,82,148,174,191,208,248,287,303,354,508,528,560,584 bps INFO @ Sat, 15 Jan 2022 20:46:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245490/SRX8245490.05_model.r WARNING @ Sat, 15 Jan 2022 20:46:46: #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 20:46:46: #2 You may need to consider one of the other alternative d(s): 0,33,74,82,148,174,191,208,248,287,303,354,508,528,560,584 WARNING @ Sat, 15 Jan 2022 20:46:46: #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 20:46:46: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:46:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:46:48: 2000000 INFO @ Sat, 15 Jan 2022 20:46:49: 7000000 INFO @ Sat, 15 Jan 2022 20:46:54: 3000000 INFO @ Sat, 15 Jan 2022 20:46:55: 8000000 INFO @ Sat, 15 Jan 2022 20:46:59: 4000000 INFO @ Sat, 15 Jan 2022 20:47:01: 9000000 INFO @ Sat, 15 Jan 2022 20:47:05: 5000000 INFO @ Sat, 15 Jan 2022 20:47:07: 10000000 INFO @ Sat, 15 Jan 2022 20:47:10: 6000000 INFO @ Sat, 15 Jan 2022 20:47:13: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:47:16: 7000000 INFO @ Sat, 15 Jan 2022 20:47:19: 12000000 INFO @ Sat, 15 Jan 2022 20:47:21: 8000000 INFO @ Sat, 15 Jan 2022 20:47:22: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:47:22: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:47:22: #1 total tags in treatment: 3459501 INFO @ Sat, 15 Jan 2022 20:47:22: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:47:22: #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 20:47:23: #1 tags after filtering in treatment: 2061848 INFO @ Sat, 15 Jan 2022 20:47:23: #1 Redundant rate of treatment: 0.40 INFO @ Sat, 15 Jan 2022 20:47:23: #1 finished! INFO @ Sat, 15 Jan 2022 20:47:23: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:47:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:47:23: #2 number of paired peaks: 176 WARNING @ Sat, 15 Jan 2022 20:47:23: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Sat, 15 Jan 2022 20:47:23: start model_add_line... INFO @ Sat, 15 Jan 2022 20:47:23: start X-correlation... INFO @ Sat, 15 Jan 2022 20:47:23: end of X-cor INFO @ Sat, 15 Jan 2022 20:47:23: #2 finished! INFO @ Sat, 15 Jan 2022 20:47:23: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 20:47:23: #2 alternative fragment length(s) may be 0,33,74,82,148,174,191,208,248,287,303,354,508,528,560,584 bps INFO @ Sat, 15 Jan 2022 20:47:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245490/SRX8245490.10_model.r WARNING @ Sat, 15 Jan 2022 20:47:23: #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 20:47:23: #2 You may need to consider one of the other alternative d(s): 0,33,74,82,148,174,191,208,248,287,303,354,508,528,560,584 WARNING @ Sat, 15 Jan 2022 20:47:23: #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 20:47:23: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:47:23: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 /var/spool/uge/at161/job_scripts/14521202: line 297: 109597 Terminated MACS $i /var/spool/uge/at161/job_scripts/14521202: line 297: 110698 Terminated MACS $i /var/spool/uge/at161/job_scripts/14521202: line 297: 110800 Terminated MACS $i ls: cannot access SRX8245490.05.bed: No such file or directory mv: cannot stat ‘SRX8245490.05.bed’: No such file or directory mv: cannot stat ‘SRX8245490.05.bb’: No such file or directory ls: cannot access SRX8245490.10.bed: No such file or directory mv: cannot stat ‘SRX8245490.10.bed’: No such file or directory mv: cannot stat ‘SRX8245490.10.bb’: No such file or directory ls: cannot access SRX8245490.20.bed: No such file or directory mv: cannot stat ‘SRX8245490.20.bed’: No such file or directory mv: cannot stat ‘SRX8245490.20.bb’: No such file or directory