Job ID = 14519660 SRX = SRX9786320 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 9879291 spots for SRR13362152/SRR13362152.sra Written 9879291 spots for SRR13362152/SRR13362152.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: 00:07:39 9879291 reads; of these: 9879291 (100.00%) were paired; of these: 1800127 (18.22%) aligned concordantly 0 times 7445905 (75.37%) aligned concordantly exactly 1 time 633259 (6.41%) aligned concordantly >1 times ---- 1800127 pairs aligned concordantly 0 times; of these: 198680 (11.04%) aligned discordantly 1 time ---- 1601447 pairs aligned 0 times concordantly or discordantly; of these: 3202894 mates make up the pairs; of these: 1992295 (62.20%) aligned 0 times 1062878 (33.18%) aligned exactly 1 time 147721 (4.61%) aligned >1 times 89.92% overall alignment rate Time searching: 00:07:39 Overall time: 00:07:39 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] 544604 / 8277027 = 0.0658 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 17:30:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9786320/SRX9786320.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9786320/SRX9786320.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9786320/SRX9786320.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9786320/SRX9786320.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 17:30:07: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:30:07: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:30:14: 1000000 INFO @ Sat, 15 Jan 2022 17:30:20: 2000000 INFO @ Sat, 15 Jan 2022 17:30:26: 3000000 INFO @ Sat, 15 Jan 2022 17:30:32: 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 17:30:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9786320/SRX9786320.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9786320/SRX9786320.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9786320/SRX9786320.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9786320/SRX9786320.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 17:30:37: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:30:37: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:30:38: 5000000 INFO @ Sat, 15 Jan 2022 17:30:45: 1000000 INFO @ Sat, 15 Jan 2022 17:30:46: 6000000 INFO @ Sat, 15 Jan 2022 17:30:54: 2000000 INFO @ Sat, 15 Jan 2022 17:30:54: 7000000 INFO @ Sat, 15 Jan 2022 17:31:02: 8000000 INFO @ Sat, 15 Jan 2022 17:31:02: 3000000 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 17:31:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9786320/SRX9786320.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9786320/SRX9786320.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9786320/SRX9786320.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9786320/SRX9786320.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 17:31:07: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:31:07: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:31:10: 9000000 INFO @ Sat, 15 Jan 2022 17:31:11: 4000000 INFO @ Sat, 15 Jan 2022 17:31:15: 1000000 INFO @ Sat, 15 Jan 2022 17:31:18: 10000000 INFO @ Sat, 15 Jan 2022 17:31:19: 5000000 INFO @ Sat, 15 Jan 2022 17:31:23: 2000000 INFO @ Sat, 15 Jan 2022 17:31:27: 11000000 INFO @ Sat, 15 Jan 2022 17:31:28: 6000000 INFO @ Sat, 15 Jan 2022 17:31:31: 3000000 INFO @ Sat, 15 Jan 2022 17:31:35: 12000000 INFO @ Sat, 15 Jan 2022 17:31:36: 7000000 INFO @ Sat, 15 Jan 2022 17:31:39: 4000000 INFO @ Sat, 15 Jan 2022 17:31:43: 13000000 INFO @ Sat, 15 Jan 2022 17:31:44: 8000000 INFO @ Sat, 15 Jan 2022 17:31:47: 5000000 INFO @ Sat, 15 Jan 2022 17:31:51: 14000000 INFO @ Sat, 15 Jan 2022 17:31:53: 9000000 INFO @ Sat, 15 Jan 2022 17:31:55: 6000000 INFO @ Sat, 15 Jan 2022 17:31:59: 15000000 INFO @ Sat, 15 Jan 2022 17:32:02: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 17:32:03: 7000000 INFO @ Sat, 15 Jan 2022 17:32:07: 16000000 INFO @ Sat, 15 Jan 2022 17:32:10: 11000000 INFO @ Sat, 15 Jan 2022 17:32:11: 8000000 INFO @ Sat, 15 Jan 2022 17:32:12: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 17:32:12: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 17:32:12: #1 total tags in treatment: 7539895 INFO @ Sat, 15 Jan 2022 17:32:12: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:32:12: #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 17:32:12: #1 tags after filtering in treatment: 4537871 INFO @ Sat, 15 Jan 2022 17:32:12: #1 Redundant rate of treatment: 0.40 INFO @ Sat, 15 Jan 2022 17:32:12: #1 finished! INFO @ Sat, 15 Jan 2022 17:32:12: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:32:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:32:13: #2 number of paired peaks: 143 WARNING @ Sat, 15 Jan 2022 17:32:13: Fewer paired peaks (143) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 143 pairs to build model! INFO @ Sat, 15 Jan 2022 17:32:13: start model_add_line... INFO @ Sat, 15 Jan 2022 17:32:13: start X-correlation... INFO @ Sat, 15 Jan 2022 17:32:13: end of X-cor INFO @ Sat, 15 Jan 2022 17:32:13: #2 finished! INFO @ Sat, 15 Jan 2022 17:32:13: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 17:32:13: #2 alternative fragment length(s) may be 0,35,81,121,164,194,202,233,260,292,311,329,353,370,391,420,464,476,542,577,596 bps INFO @ Sat, 15 Jan 2022 17:32:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX9786320/SRX9786320.05_model.r WARNING @ Sat, 15 Jan 2022 17:32:13: #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 17:32:13: #2 You may need to consider one of the other alternative d(s): 0,35,81,121,164,194,202,233,260,292,311,329,353,370,391,420,464,476,542,577,596 WARNING @ Sat, 15 Jan 2022 17:32:13: #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 17:32:13: #3 Call peaks... INFO @ Sat, 15 Jan 2022 17:32:13: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 /var/spool/uge/at149/job_scripts/14519660: line 297: 31734 Terminated MACS $i /var/spool/uge/at149/job_scripts/14519660: line 297: 31895 Terminated MACS $i /var/spool/uge/at149/job_scripts/14519660: line 297: 32049 Terminated MACS $i ls: cannot access SRX9786320.05.bed: No such file or directory mv: cannot stat ‘SRX9786320.05.bed’: No such file or directory mv: cannot stat ‘SRX9786320.05.bb’: No such file or directory ls: cannot access SRX9786320.10.bed: No such file or directory mv: cannot stat ‘SRX9786320.10.bed’: No such file or directory mv: cannot stat ‘SRX9786320.10.bb’: No such file or directory ls: cannot access SRX9786320.20.bed: No such file or directory mv: cannot stat ‘SRX9786320.20.bed’: No such file or directory mv: cannot stat ‘SRX9786320.20.bb’: No such file or directory