Job ID = 14521269 SRX = SRX8245398 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 8486327 spots for SRR11684609/SRR11684609.sra Written 8486327 spots for SRR11684609/SRR11684609.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: 00:04:23 8486327 reads; of these: 8486327 (100.00%) were paired; of these: 4469300 (52.66%) aligned concordantly 0 times 3559947 (41.95%) aligned concordantly exactly 1 time 457080 (5.39%) aligned concordantly >1 times ---- 4469300 pairs aligned concordantly 0 times; of these: 8426 (0.19%) aligned discordantly 1 time ---- 4460874 pairs aligned 0 times concordantly or discordantly; of these: 8921748 mates make up the pairs; of these: 5662974 (63.47%) aligned 0 times 2859229 (32.05%) aligned exactly 1 time 399545 (4.48%) aligned >1 times 66.63% overall alignment rate Time searching: 00:04:23 Overall time: 00:04:23 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] 342559 / 4024801 = 0.0851 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 20:54:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245398/SRX8245398.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245398/SRX8245398.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245398/SRX8245398.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245398/SRX8245398.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 20:54:09: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:54:09: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:54:13: 1000000 INFO @ Sat, 15 Jan 2022 20:54:18: 2000000 INFO @ Sat, 15 Jan 2022 20:54:23: 3000000 INFO @ Sat, 15 Jan 2022 20:54:28: 4000000 INFO @ Sat, 15 Jan 2022 20:54:32: 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 20:54:37: 6000000 INFO @ Sat, 15 Jan 2022 20:54:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245398/SRX8245398.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245398/SRX8245398.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245398/SRX8245398.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245398/SRX8245398.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 20:54:39: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:54:39: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:54:42: 7000000 INFO @ Sat, 15 Jan 2022 20:54:43: 1000000 INFO @ Sat, 15 Jan 2022 20:54:47: 8000000 INFO @ Sat, 15 Jan 2022 20:54:48: 2000000 INFO @ Sat, 15 Jan 2022 20:54:53: 9000000 INFO @ Sat, 15 Jan 2022 20:54:53: 3000000 INFO @ Sat, 15 Jan 2022 20:54:58: 10000000 INFO @ Sat, 15 Jan 2022 20:54:58: 4000000 INFO @ Sat, 15 Jan 2022 20:55:01: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:55:01: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:55:01: #1 total tags in treatment: 3676035 INFO @ Sat, 15 Jan 2022 20:55:01: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:55:01: #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 20:55:01: #1 tags after filtering in treatment: 2372639 INFO @ Sat, 15 Jan 2022 20:55:01: #1 Redundant rate of treatment: 0.35 INFO @ Sat, 15 Jan 2022 20:55:01: #1 finished! INFO @ Sat, 15 Jan 2022 20:55:01: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:55:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:55:02: #2 number of paired peaks: 173 WARNING @ Sat, 15 Jan 2022 20:55:02: Fewer paired peaks (173) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 173 pairs to build model! INFO @ Sat, 15 Jan 2022 20:55:02: start model_add_line... INFO @ Sat, 15 Jan 2022 20:55:02: start X-correlation... INFO @ Sat, 15 Jan 2022 20:55:02: end of X-cor INFO @ Sat, 15 Jan 2022 20:55:02: #2 finished! INFO @ Sat, 15 Jan 2022 20:55:02: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 20:55:02: #2 alternative fragment length(s) may be 0,36,43,49,78,106,138,153,191,210,213,244,271,293,320,353,381,424,441,447,480,499,540,568,572,597 bps INFO @ Sat, 15 Jan 2022 20:55:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245398/SRX8245398.05_model.r WARNING @ Sat, 15 Jan 2022 20:55:02: #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 20:55:02: #2 You may need to consider one of the other alternative d(s): 0,36,43,49,78,106,138,153,191,210,213,244,271,293,320,353,381,424,441,447,480,499,540,568,572,597 WARNING @ Sat, 15 Jan 2022 20:55:02: #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 20:55:02: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:55:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:55:03: 5000000 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 20:55:08: 6000000 INFO @ Sat, 15 Jan 2022 20:55:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245398/SRX8245398.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245398/SRX8245398.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245398/SRX8245398.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245398/SRX8245398.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 20:55:09: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:55:09: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:55:13: 7000000 INFO @ Sat, 15 Jan 2022 20:55:14: 1000000 INFO @ Sat, 15 Jan 2022 20:55:18: 8000000 INFO @ Sat, 15 Jan 2022 20:55:19: 2000000 INFO @ Sat, 15 Jan 2022 20:55:24: 9000000 INFO @ Sat, 15 Jan 2022 20:55:24: 3000000 INFO @ Sat, 15 Jan 2022 20:55:29: 4000000 INFO @ Sat, 15 Jan 2022 20:55:29: 10000000 INFO @ Sat, 15 Jan 2022 20:55:32: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:55:32: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:55:32: #1 total tags in treatment: 3676035 INFO @ Sat, 15 Jan 2022 20:55:32: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:55:32: #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 20:55:32: #1 tags after filtering in treatment: 2372639 INFO @ Sat, 15 Jan 2022 20:55:32: #1 Redundant rate of treatment: 0.35 INFO @ Sat, 15 Jan 2022 20:55:32: #1 finished! INFO @ Sat, 15 Jan 2022 20:55:32: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:55:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:55:32: #2 number of paired peaks: 173 WARNING @ Sat, 15 Jan 2022 20:55:32: Fewer paired peaks (173) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 173 pairs to build model! INFO @ Sat, 15 Jan 2022 20:55:32: start model_add_line... INFO @ Sat, 15 Jan 2022 20:55:32: start X-correlation... INFO @ Sat, 15 Jan 2022 20:55:32: end of X-cor INFO @ Sat, 15 Jan 2022 20:55:32: #2 finished! INFO @ Sat, 15 Jan 2022 20:55:32: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 20:55:32: #2 alternative fragment length(s) may be 0,36,43,49,78,106,138,153,191,210,213,244,271,293,320,353,381,424,441,447,480,499,540,568,572,597 bps INFO @ Sat, 15 Jan 2022 20:55:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245398/SRX8245398.10_model.r WARNING @ Sat, 15 Jan 2022 20:55:32: #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 20:55:32: #2 You may need to consider one of the other alternative d(s): 0,36,43,49,78,106,138,153,191,210,213,244,271,293,320,353,381,424,441,447,480,499,540,568,572,597 WARNING @ Sat, 15 Jan 2022 20:55:32: #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 20:55:32: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:55:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:55:34: 5000000 INFO @ Sat, 15 Jan 2022 20:55:39: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:55:44: 7000000 INFO @ Sat, 15 Jan 2022 20:55:49: 8000000 BigWig に変換しました。 /var/spool/uge/at145/job_scripts/14521269: line 297: 3393 Terminated MACS $i /var/spool/uge/at145/job_scripts/14521269: line 297: 4228 Terminated MACS $i /var/spool/uge/at145/job_scripts/14521269: line 297: 7718 Terminated MACS $i ls: cannot access SRX8245398.05.bed: No such file or directory mv: cannot stat ‘SRX8245398.05.bed’: No such file or directory mv: cannot stat ‘SRX8245398.05.bb’: No such file or directory ls: cannot access SRX8245398.10.bed: No such file or directory mv: cannot stat ‘SRX8245398.10.bed’: No such file or directory mv: cannot stat ‘SRX8245398.10.bb’: No such file or directory ls: cannot access SRX8245398.20.bed: No such file or directory mv: cannot stat ‘SRX8245398.20.bed’: No such file or directory mv: cannot stat ‘SRX8245398.20.bb’: No such file or directory