Job ID = 14520981 SRX = SRX8245459 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 13027506 spots for SRR11684670/SRR11684670.sra Written 13027506 spots for SRR11684670/SRR11684670.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: 00:06:13 13027506 reads; of these: 13027506 (100.00%) were paired; of these: 6089528 (46.74%) aligned concordantly 0 times 6346470 (48.72%) aligned concordantly exactly 1 time 591508 (4.54%) aligned concordantly >1 times ---- 6089528 pairs aligned concordantly 0 times; of these: 31531 (0.52%) aligned discordantly 1 time ---- 6057997 pairs aligned 0 times concordantly or discordantly; of these: 12115994 mates make up the pairs; of these: 7064316 (58.31%) aligned 0 times 4469966 (36.89%) aligned exactly 1 time 581712 (4.80%) aligned >1 times 72.89% overall alignment rate Time searching: 00:06:13 Overall time: 00:06:13 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] 562161 / 6967510 = 0.0807 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 20:25:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245459/SRX8245459.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245459/SRX8245459.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245459/SRX8245459.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245459/SRX8245459.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 20:25:33: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:25:33: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:25:38: 1000000 INFO @ Sat, 15 Jan 2022 20:25:43: 2000000 INFO @ Sat, 15 Jan 2022 20:25:48: 3000000 INFO @ Sat, 15 Jan 2022 20:25:53: 4000000 INFO @ Sat, 15 Jan 2022 20:25:57: 5000000 INFO @ Sat, 15 Jan 2022 20:26:01: 6000000 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 20:26:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245459/SRX8245459.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245459/SRX8245459.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245459/SRX8245459.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245459/SRX8245459.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 20:26:03: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:26:03: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:26:06: 7000000 INFO @ Sat, 15 Jan 2022 20:26:09: 1000000 INFO @ Sat, 15 Jan 2022 20:26:10: 8000000 INFO @ Sat, 15 Jan 2022 20:26:14: 2000000 INFO @ Sat, 15 Jan 2022 20:26:15: 9000000 INFO @ Sat, 15 Jan 2022 20:26:19: 10000000 INFO @ Sat, 15 Jan 2022 20:26:20: 3000000 INFO @ Sat, 15 Jan 2022 20:26:24: 11000000 INFO @ Sat, 15 Jan 2022 20:26:25: 4000000 INFO @ Sat, 15 Jan 2022 20:26:28: 12000000 INFO @ Sat, 15 Jan 2022 20:26:30: 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 20:26:33: 13000000 INFO @ Sat, 15 Jan 2022 20:26:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245459/SRX8245459.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245459/SRX8245459.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245459/SRX8245459.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245459/SRX8245459.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 20:26:33: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:26:33: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:26:36: 6000000 INFO @ Sat, 15 Jan 2022 20:26:38: 14000000 INFO @ Sat, 15 Jan 2022 20:26:38: 1000000 INFO @ Sat, 15 Jan 2022 20:26:41: 7000000 INFO @ Sat, 15 Jan 2022 20:26:43: 2000000 INFO @ Sat, 15 Jan 2022 20:26:43: 15000000 INFO @ Sat, 15 Jan 2022 20:26:46: 8000000 INFO @ Sat, 15 Jan 2022 20:26:47: 3000000 INFO @ Sat, 15 Jan 2022 20:26:48: 16000000 INFO @ Sat, 15 Jan 2022 20:26:51: 9000000 INFO @ Sat, 15 Jan 2022 20:26:52: 4000000 INFO @ Sat, 15 Jan 2022 20:26:53: 17000000 INFO @ Sat, 15 Jan 2022 20:26:56: 5000000 INFO @ Sat, 15 Jan 2022 20:26:56: 10000000 INFO @ Sat, 15 Jan 2022 20:26:57: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:26:57: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:26:57: #1 total tags in treatment: 6377099 INFO @ Sat, 15 Jan 2022 20:26:57: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:26:57: #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 20:26:57: #1 tags after filtering in treatment: 3292525 INFO @ Sat, 15 Jan 2022 20:26:57: #1 Redundant rate of treatment: 0.48 INFO @ Sat, 15 Jan 2022 20:26:57: #1 finished! INFO @ Sat, 15 Jan 2022 20:26:57: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:26:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:26:57: #2 number of paired peaks: 170 WARNING @ Sat, 15 Jan 2022 20:26:57: Fewer paired peaks (170) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 170 pairs to build model! INFO @ Sat, 15 Jan 2022 20:26:57: start model_add_line... INFO @ Sat, 15 Jan 2022 20:26:57: start X-correlation... INFO @ Sat, 15 Jan 2022 20:26:57: end of X-cor INFO @ Sat, 15 Jan 2022 20:26:57: #2 finished! INFO @ Sat, 15 Jan 2022 20:26:57: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 20:26:57: #2 alternative fragment length(s) may be 0,58,92,100,126,134,136,177,208,254,341,361,372,393,439,497,535,582 bps INFO @ Sat, 15 Jan 2022 20:26:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245459/SRX8245459.05_model.r WARNING @ Sat, 15 Jan 2022 20:26:57: #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 20:26:57: #2 You may need to consider one of the other alternative d(s): 0,58,92,100,126,134,136,177,208,254,341,361,372,393,439,497,535,582 WARNING @ Sat, 15 Jan 2022 20:26:57: #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 20:26:57: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:26:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:27:01: 6000000 INFO @ Sat, 15 Jan 2022 20:27:02: 11000000 INFO @ Sat, 15 Jan 2022 20:27:05: 7000000 INFO @ Sat, 15 Jan 2022 20:27:07: 12000000 INFO @ Sat, 15 Jan 2022 20:27:10: 8000000 INFO @ Sat, 15 Jan 2022 20:27:13: 13000000 INFO @ Sat, 15 Jan 2022 20:27:14: 9000000 INFO @ Sat, 15 Jan 2022 20:27:18: 14000000 INFO @ Sat, 15 Jan 2022 20:27:19: 10000000 INFO @ Sat, 15 Jan 2022 20:27:23: 11000000 INFO @ Sat, 15 Jan 2022 20:27:24: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:27:28: 12000000 INFO @ Sat, 15 Jan 2022 20:27:29: 16000000 INFO @ Sat, 15 Jan 2022 20:27:32: 13000000 INFO @ Sat, 15 Jan 2022 20:27:35: 17000000 BigWig に変換しました。 /var/spool/uge/at149/job_scripts/14520981: line 297: 60993 Terminated MACS $i /var/spool/uge/at149/job_scripts/14520981: line 297: 62074 Terminated MACS $i /var/spool/uge/at149/job_scripts/14520981: line 297: 68803 Terminated MACS $i ls: cannot access SRX8245459.05.bed: No such file or directory mv: cannot stat ‘SRX8245459.05.bed’: No such file or directory mv: cannot stat ‘SRX8245459.05.bb’: No such file or directory ls: cannot access SRX8245459.10.bed: No such file or directory mv: cannot stat ‘SRX8245459.10.bed’: No such file or directory mv: cannot stat ‘SRX8245459.10.bb’: No such file or directory ls: cannot access SRX8245459.20.bed: No such file or directory mv: cannot stat ‘SRX8245459.20.bed’: No such file or directory mv: cannot stat ‘SRX8245459.20.bb’: No such file or directory