Job ID = 14522127 SRX = SRX9786302 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 14845052 spots for SRR13362134/SRR13362134.sra Written 14845052 spots for SRR13362134/SRR13362134.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: 00:10:36 14845052 reads; of these: 14845052 (100.00%) were paired; of these: 8434419 (56.82%) aligned concordantly 0 times 5839763 (39.34%) aligned concordantly exactly 1 time 570870 (3.85%) aligned concordantly >1 times ---- 8434419 pairs aligned concordantly 0 times; of these: 179903 (2.13%) aligned discordantly 1 time ---- 8254516 pairs aligned 0 times concordantly or discordantly; of these: 16509032 mates make up the pairs; of these: 11539055 (69.90%) aligned 0 times 4398584 (26.64%) aligned exactly 1 time 571393 (3.46%) aligned >1 times 61.14% overall alignment rate Time searching: 00:10:36 Overall time: 00:10:36 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] 612628 / 6589373 = 0.0930 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 22:31:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9786302/SRX9786302.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9786302/SRX9786302.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9786302/SRX9786302.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9786302/SRX9786302.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 22:31:56: #1 read tag files... INFO @ Sat, 15 Jan 2022 22:31:56: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 22:32:05: 1000000 INFO @ Sat, 15 Jan 2022 22:32:12: 2000000 INFO @ Sat, 15 Jan 2022 22:32:19: 3000000 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 22:32:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9786302/SRX9786302.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9786302/SRX9786302.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9786302/SRX9786302.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9786302/SRX9786302.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 22:32:26: #1 read tag files... INFO @ Sat, 15 Jan 2022 22:32:26: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 22:32:26: 4000000 INFO @ Sat, 15 Jan 2022 22:32:34: 5000000 INFO @ Sat, 15 Jan 2022 22:32:34: 1000000 INFO @ Sat, 15 Jan 2022 22:32:41: 6000000 INFO @ Sat, 15 Jan 2022 22:32:43: 2000000 INFO @ Sat, 15 Jan 2022 22:32:48: 7000000 INFO @ Sat, 15 Jan 2022 22:32:51: 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 22:32:56: 8000000 INFO @ Sat, 15 Jan 2022 22:32:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9786302/SRX9786302.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9786302/SRX9786302.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9786302/SRX9786302.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9786302/SRX9786302.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 22:32:56: #1 read tag files... INFO @ Sat, 15 Jan 2022 22:32:56: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 22:33:00: 4000000 INFO @ Sat, 15 Jan 2022 22:33:04: 9000000 INFO @ Sat, 15 Jan 2022 22:33:04: 1000000 INFO @ Sat, 15 Jan 2022 22:33:08: 5000000 INFO @ Sat, 15 Jan 2022 22:33:11: 10000000 INFO @ Sat, 15 Jan 2022 22:33:13: 2000000 INFO @ Sat, 15 Jan 2022 22:33:16: 6000000 INFO @ Sat, 15 Jan 2022 22:33:19: 11000000 INFO @ Sat, 15 Jan 2022 22:33:21: 3000000 INFO @ Sat, 15 Jan 2022 22:33:24: 7000000 INFO @ Sat, 15 Jan 2022 22:33:27: 12000000 INFO @ Sat, 15 Jan 2022 22:33:30: 4000000 INFO @ Sat, 15 Jan 2022 22:33:33: 8000000 INFO @ Sat, 15 Jan 2022 22:33:34: 13000000 INFO @ Sat, 15 Jan 2022 22:33:39: 5000000 INFO @ Sat, 15 Jan 2022 22:33:41: 9000000 INFO @ Sat, 15 Jan 2022 22:33:42: 14000000 INFO @ Sat, 15 Jan 2022 22:33:47: 6000000 INFO @ Sat, 15 Jan 2022 22:33:49: 15000000 INFO @ Sat, 15 Jan 2022 22:33:50: 10000000 INFO @ Sat, 15 Jan 2022 22:33:56: 7000000 INFO @ Sat, 15 Jan 2022 22:33:57: 16000000 INFO @ Sat, 15 Jan 2022 22:33:58: 11000000 INFO @ Sat, 15 Jan 2022 22:34:04: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 22:34:04: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 22:34:04: #1 total tags in treatment: 5804813 INFO @ Sat, 15 Jan 2022 22:34:04: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 22:34:04: #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 22:34:04: #1 tags after filtering in treatment: 3949869 INFO @ Sat, 15 Jan 2022 22:34:04: #1 Redundant rate of treatment: 0.32 INFO @ Sat, 15 Jan 2022 22:34:04: #1 finished! INFO @ Sat, 15 Jan 2022 22:34:04: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 22:34:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 22:34:04: #2 number of paired peaks: 162 WARNING @ Sat, 15 Jan 2022 22:34:04: 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 22:34:04: start model_add_line... INFO @ Sat, 15 Jan 2022 22:34:04: start X-correlation... INFO @ Sat, 15 Jan 2022 22:34:04: end of X-cor INFO @ Sat, 15 Jan 2022 22:34:04: #2 finished! INFO @ Sat, 15 Jan 2022 22:34:04: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 22:34:04: #2 alternative fragment length(s) may be 0,12,58,105,111,117,126,183,209,230,266,269,301,315,319,336,369,384,412,428,463,507,530,551,589 bps INFO @ Sat, 15 Jan 2022 22:34:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX9786302/SRX9786302.05_model.r WARNING @ Sat, 15 Jan 2022 22:34:04: #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 22:34:04: #2 You may need to consider one of the other alternative d(s): 0,12,58,105,111,117,126,183,209,230,266,269,301,315,319,336,369,384,412,428,463,507,530,551,589 WARNING @ Sat, 15 Jan 2022 22:34:04: #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 22:34:04: #3 Call peaks... INFO @ Sat, 15 Jan 2022 22:34:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 22:34:05: 8000000 INFO @ Sat, 15 Jan 2022 22:34:06: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 22:34:13: 9000000 INFO @ Sat, 15 Jan 2022 22:34:15: 13000000 INFO @ Sat, 15 Jan 2022 22:34:22: 10000000 INFO @ Sat, 15 Jan 2022 22:34:23: 14000000 BigWig に変換しました。 /var/spool/uge/at073/job_scripts/14522127: line 297: 535 Terminated MACS $i /var/spool/uge/at073/job_scripts/14522127: line 297: 1744 Terminated MACS $i /var/spool/uge/at073/job_scripts/14522127: line 297: 1974 Terminated MACS $i ls: cannot access SRX9786302.05.bed: No such file or directory mv: cannot stat ‘SRX9786302.05.bed’: No such file or directory mv: cannot stat ‘SRX9786302.05.bb’: No such file or directory ls: cannot access SRX9786302.10.bed: No such file or directory mv: cannot stat ‘SRX9786302.10.bed’: No such file or directory mv: cannot stat ‘SRX9786302.10.bb’: No such file or directory ls: cannot access SRX9786302.20.bed: No such file or directory mv: cannot stat ‘SRX9786302.20.bed’: No such file or directory mv: cannot stat ‘SRX9786302.20.bb’: No such file or directory