Job ID = 14522131 SRX = SRX9786306 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 8589978 spots for SRR13362170/SRR13362170.sra Written 8589978 spots for SRR13362170/SRR13362170.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: 00:06:50 8589978 reads; of these: 8589978 (100.00%) were paired; of these: 1364400 (15.88%) aligned concordantly 0 times 6552979 (76.29%) aligned concordantly exactly 1 time 672599 (7.83%) aligned concordantly >1 times ---- 1364400 pairs aligned concordantly 0 times; of these: 123386 (9.04%) aligned discordantly 1 time ---- 1241014 pairs aligned 0 times concordantly or discordantly; of these: 2482028 mates make up the pairs; of these: 1572112 (63.34%) aligned 0 times 788331 (31.76%) aligned exactly 1 time 121585 (4.90%) aligned >1 times 90.85% overall alignment rate Time searching: 00:06:50 Overall time: 00:06:50 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] 482936 / 7348388 = 0.0657 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 22:28:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9786306/SRX9786306.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9786306/SRX9786306.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9786306/SRX9786306.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9786306/SRX9786306.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 22:28:03: #1 read tag files... INFO @ Sat, 15 Jan 2022 22:28:03: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 22:28:09: 1000000 INFO @ Sat, 15 Jan 2022 22:28:14: 2000000 INFO @ Sat, 15 Jan 2022 22:28:19: 3000000 INFO @ Sat, 15 Jan 2022 22:28:25: 4000000 INFO @ Sat, 15 Jan 2022 22:28:29: 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 22:28:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9786306/SRX9786306.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9786306/SRX9786306.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9786306/SRX9786306.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9786306/SRX9786306.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 22:28:33: #1 read tag files... INFO @ Sat, 15 Jan 2022 22:28:33: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 22:28:35: 6000000 INFO @ Sat, 15 Jan 2022 22:28:40: 1000000 INFO @ Sat, 15 Jan 2022 22:28:40: 7000000 INFO @ Sat, 15 Jan 2022 22:28:46: 2000000 INFO @ Sat, 15 Jan 2022 22:28:46: 8000000 INFO @ Sat, 15 Jan 2022 22:28:52: 9000000 INFO @ Sat, 15 Jan 2022 22:28:53: 3000000 INFO @ Sat, 15 Jan 2022 22:28:58: 10000000 INFO @ Sat, 15 Jan 2022 22:28:58: 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 22:29:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9786306/SRX9786306.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9786306/SRX9786306.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9786306/SRX9786306.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9786306/SRX9786306.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 22:29:03: #1 read tag files... INFO @ Sat, 15 Jan 2022 22:29:03: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 22:29:04: 11000000 INFO @ Sat, 15 Jan 2022 22:29:04: 5000000 INFO @ Sat, 15 Jan 2022 22:29:09: 1000000 INFO @ Sat, 15 Jan 2022 22:29:10: 12000000 INFO @ Sat, 15 Jan 2022 22:29:10: 6000000 INFO @ Sat, 15 Jan 2022 22:29:16: 7000000 INFO @ Sat, 15 Jan 2022 22:29:16: 13000000 INFO @ Sat, 15 Jan 2022 22:29:16: 2000000 INFO @ Sat, 15 Jan 2022 22:29:22: 14000000 INFO @ Sat, 15 Jan 2022 22:29:22: 8000000 INFO @ Sat, 15 Jan 2022 22:29:22: 3000000 INFO @ Sat, 15 Jan 2022 22:29:25: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 22:29:25: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 22:29:25: #1 total tags in treatment: 6746080 INFO @ Sat, 15 Jan 2022 22:29:25: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 22:29:25: #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 22:29:26: #1 tags after filtering in treatment: 4130026 INFO @ Sat, 15 Jan 2022 22:29:26: #1 Redundant rate of treatment: 0.39 INFO @ Sat, 15 Jan 2022 22:29:26: #1 finished! INFO @ Sat, 15 Jan 2022 22:29:26: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 22:29:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 22:29:26: #2 number of paired peaks: 162 WARNING @ Sat, 15 Jan 2022 22:29:26: Fewer paired peaks (162) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 162 pairs to build model! INFO @ Sat, 15 Jan 2022 22:29:26: start model_add_line... INFO @ Sat, 15 Jan 2022 22:29:26: start X-correlation... INFO @ Sat, 15 Jan 2022 22:29:26: end of X-cor INFO @ Sat, 15 Jan 2022 22:29:26: #2 finished! INFO @ Sat, 15 Jan 2022 22:29:26: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 22:29:26: #2 alternative fragment length(s) may be 0,43,75,79,104,167,202,221,255,286,310,312,319,343,369,412,433,461,479,537,567,587 bps INFO @ Sat, 15 Jan 2022 22:29:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX9786306/SRX9786306.05_model.r WARNING @ Sat, 15 Jan 2022 22:29:26: #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 22:29:26: #2 You may need to consider one of the other alternative d(s): 0,43,75,79,104,167,202,221,255,286,310,312,319,343,369,412,433,461,479,537,567,587 WARNING @ Sat, 15 Jan 2022 22:29:26: #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 22:29:26: #3 Call peaks... INFO @ Sat, 15 Jan 2022 22:29:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 22:29:28: 9000000 INFO @ Sat, 15 Jan 2022 22:29:29: 4000000 INFO @ Sat, 15 Jan 2022 22:29:34: 10000000 INFO @ Sat, 15 Jan 2022 22:29:35: 5000000 INFO @ Sat, 15 Jan 2022 22:29:40: 11000000 INFO @ Sat, 15 Jan 2022 22:29:42: 6000000 INFO @ Sat, 15 Jan 2022 22:29:46: 12000000 INFO @ Sat, 15 Jan 2022 22:29:49: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 22:29:52: 13000000 INFO @ Sat, 15 Jan 2022 22:29:56: 8000000 INFO @ Sat, 15 Jan 2022 22:29:58: 14000000 INFO @ Sat, 15 Jan 2022 22:30:01: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 22:30:01: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 22:30:01: #1 total tags in treatment: 6746080 INFO @ Sat, 15 Jan 2022 22:30:01: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 22:30:01: #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 22:30:02: #1 tags after filtering in treatment: 4130026 INFO @ Sat, 15 Jan 2022 22:30:02: #1 Redundant rate of treatment: 0.39 INFO @ Sat, 15 Jan 2022 22:30:02: #1 finished! INFO @ Sat, 15 Jan 2022 22:30:02: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 22:30:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 22:30:02: #2 number of paired peaks: 162 WARNING @ Sat, 15 Jan 2022 22:30:02: Fewer paired peaks (162) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 162 pairs to build model! INFO @ Sat, 15 Jan 2022 22:30:02: start model_add_line... INFO @ Sat, 15 Jan 2022 22:30:02: start X-correlation... INFO @ Sat, 15 Jan 2022 22:30:02: end of X-cor INFO @ Sat, 15 Jan 2022 22:30:02: #2 finished! INFO @ Sat, 15 Jan 2022 22:30:02: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 22:30:02: #2 alternative fragment length(s) may be 0,43,75,79,104,167,202,221,255,286,310,312,319,343,369,412,433,461,479,537,567,587 bps INFO @ Sat, 15 Jan 2022 22:30:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX9786306/SRX9786306.10_model.r WARNING @ Sat, 15 Jan 2022 22:30:02: #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 22:30:02: #2 You may need to consider one of the other alternative d(s): 0,43,75,79,104,167,202,221,255,286,310,312,319,343,369,412,433,461,479,537,567,587 WARNING @ Sat, 15 Jan 2022 22:30:02: #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 22:30:02: #3 Call peaks... INFO @ Sat, 15 Jan 2022 22:30:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 22:30:02: 9000000 BigWig に変換しました。 /var/spool/uge/at149/job_scripts/14522131: line 297: 103302 Terminated MACS $i /var/spool/uge/at149/job_scripts/14522131: line 297: 104191 Terminated MACS $i /var/spool/uge/at149/job_scripts/14522131: line 297: 104803 Terminated MACS $i ls: cannot access SRX9786306.05.bed: No such file or directory mv: cannot stat ‘SRX9786306.05.bed’: No such file or directory mv: cannot stat ‘SRX9786306.05.bb’: No such file or directory ls: cannot access SRX9786306.10.bed: No such file or directory mv: cannot stat ‘SRX9786306.10.bed’: No such file or directory mv: cannot stat ‘SRX9786306.10.bb’: No such file or directory ls: cannot access SRX9786306.20.bed: No such file or directory mv: cannot stat ‘SRX9786306.20.bed’: No such file or directory mv: cannot stat ‘SRX9786306.20.bb’: No such file or directory