Job ID = 14520866 SRX = SRX8245545 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 16235947 spots for SRR11684756/SRR11684756.sra Written 16235947 spots for SRR11684756/SRR11684756.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: 00:08:23 16235947 reads; of these: 16235947 (100.00%) were paired; of these: 9010878 (55.50%) aligned concordantly 0 times 6462391 (39.80%) aligned concordantly exactly 1 time 762678 (4.70%) aligned concordantly >1 times ---- 9010878 pairs aligned concordantly 0 times; of these: 128500 (1.43%) aligned discordantly 1 time ---- 8882378 pairs aligned 0 times concordantly or discordantly; of these: 17764756 mates make up the pairs; of these: 11458445 (64.50%) aligned 0 times 5523348 (31.09%) aligned exactly 1 time 782963 (4.41%) aligned >1 times 64.71% overall alignment rate Time searching: 00:08:23 Overall time: 00:08:23 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 12 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] 654135 / 7352231 = 0.0890 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 20:19:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245545/SRX8245545.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245545/SRX8245545.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245545/SRX8245545.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245545/SRX8245545.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 20:19:28: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:19:28: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:19:34: 1000000 INFO @ Sat, 15 Jan 2022 20:19:40: 2000000 INFO @ Sat, 15 Jan 2022 20:19:46: 3000000 INFO @ Sat, 15 Jan 2022 20:19:52: 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 20:19:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245545/SRX8245545.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245545/SRX8245545.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245545/SRX8245545.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245545/SRX8245545.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 20:19:58: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:19:58: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:19:58: 5000000 INFO @ Sat, 15 Jan 2022 20:20:04: 1000000 INFO @ Sat, 15 Jan 2022 20:20:04: 6000000 INFO @ Sat, 15 Jan 2022 20:20:10: 2000000 INFO @ Sat, 15 Jan 2022 20:20:11: 7000000 INFO @ Sat, 15 Jan 2022 20:20:16: 3000000 INFO @ Sat, 15 Jan 2022 20:20:17: 8000000 INFO @ Sat, 15 Jan 2022 20:20:21: 4000000 INFO @ Sat, 15 Jan 2022 20:20:24: 9000000 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 20:20:27: 5000000 INFO @ Sat, 15 Jan 2022 20:20:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245545/SRX8245545.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245545/SRX8245545.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245545/SRX8245545.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245545/SRX8245545.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 20:20:28: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:20:28: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:20:31: 10000000 INFO @ Sat, 15 Jan 2022 20:20:33: 6000000 INFO @ Sat, 15 Jan 2022 20:20:35: 1000000 INFO @ Sat, 15 Jan 2022 20:20:37: 11000000 INFO @ Sat, 15 Jan 2022 20:20:39: 7000000 INFO @ Sat, 15 Jan 2022 20:20:41: 2000000 INFO @ Sat, 15 Jan 2022 20:20:44: 12000000 INFO @ Sat, 15 Jan 2022 20:20:45: 8000000 INFO @ Sat, 15 Jan 2022 20:20:48: 3000000 INFO @ Sat, 15 Jan 2022 20:20:51: 9000000 INFO @ Sat, 15 Jan 2022 20:20:51: 13000000 INFO @ Sat, 15 Jan 2022 20:20:55: 4000000 INFO @ Sat, 15 Jan 2022 20:20:57: 10000000 INFO @ Sat, 15 Jan 2022 20:20:57: 14000000 INFO @ Sat, 15 Jan 2022 20:21:02: 5000000 INFO @ Sat, 15 Jan 2022 20:21:03: 11000000 INFO @ Sat, 15 Jan 2022 20:21:04: 15000000 INFO @ Sat, 15 Jan 2022 20:21:08: 6000000 INFO @ Sat, 15 Jan 2022 20:21:09: 12000000 INFO @ Sat, 15 Jan 2022 20:21:11: 16000000 INFO @ Sat, 15 Jan 2022 20:21:15: 13000000 INFO @ Sat, 15 Jan 2022 20:21:15: 7000000 INFO @ Sat, 15 Jan 2022 20:21:18: 17000000 INFO @ Sat, 15 Jan 2022 20:21:21: 14000000 INFO @ Sat, 15 Jan 2022 20:21:21: 8000000 INFO @ Sat, 15 Jan 2022 20:21:25: 18000000 INFO @ Sat, 15 Jan 2022 20:21:27: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:21:28: 9000000 INFO @ Sat, 15 Jan 2022 20:21:31: 19000000 INFO @ Sat, 15 Jan 2022 20:21:33: 16000000 INFO @ Sat, 15 Jan 2022 20:21:34: 10000000 INFO @ Sat, 15 Jan 2022 20:21:36: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:21:36: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:21:36: #1 total tags in treatment: 6575516 INFO @ Sat, 15 Jan 2022 20:21:36: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:21:36: #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 20:21:36: #1 tags after filtering in treatment: 4182721 INFO @ Sat, 15 Jan 2022 20:21:36: #1 Redundant rate of treatment: 0.36 INFO @ Sat, 15 Jan 2022 20:21:36: #1 finished! INFO @ Sat, 15 Jan 2022 20:21:36: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:21:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:21:36: #2 number of paired peaks: 160 WARNING @ Sat, 15 Jan 2022 20:21:36: Fewer paired peaks (160) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 160 pairs to build model! INFO @ Sat, 15 Jan 2022 20:21:36: start model_add_line... INFO @ Sat, 15 Jan 2022 20:21:36: start X-correlation... INFO @ Sat, 15 Jan 2022 20:21:36: end of X-cor INFO @ Sat, 15 Jan 2022 20:21:36: #2 finished! INFO @ Sat, 15 Jan 2022 20:21:36: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 20:21:36: #2 alternative fragment length(s) may be 0,18,52,81,111,125,141,183,215,236,253,274,298,301,323,335,338,356,371,375,409,437,465,496,542,571 bps INFO @ Sat, 15 Jan 2022 20:21:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245545/SRX8245545.05_model.r WARNING @ Sat, 15 Jan 2022 20:21:37: #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 20:21:37: #2 You may need to consider one of the other alternative d(s): 0,18,52,81,111,125,141,183,215,236,253,274,298,301,323,335,338,356,371,375,409,437,465,496,542,571 WARNING @ Sat, 15 Jan 2022 20:21:37: #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 20:21:37: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:21:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:21:38: 17000000 BigWig に変換しました。 /var/spool/uge/at141/job_scripts/14520866: line 297: 116576 Terminated MACS $i /var/spool/uge/at141/job_scripts/14520866: line 297: 2699 Terminated MACS $i /var/spool/uge/at141/job_scripts/14520866: line 297: 16235 Terminated MACS $i ls: cannot access SRX8245545.05.bed: No such file or directory mv: cannot stat ‘SRX8245545.05.bed’: No such file or directory mv: cannot stat ‘SRX8245545.05.bb’: No such file or directory ls: cannot access SRX8245545.10.bed: No such file or directory mv: cannot stat ‘SRX8245545.10.bed’: No such file or directory mv: cannot stat ‘SRX8245545.10.bb’: No such file or directory ls: cannot access SRX8245545.20.bed: No such file or directory mv: cannot stat ‘SRX8245545.20.bed’: No such file or directory mv: cannot stat ‘SRX8245545.20.bb’: No such file or directory