Job ID = 14521139 SRX = SRX8245365 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 11434421 spots for SRR11684576/SRR11684576.sra Written 11434421 spots for SRR11684576/SRR11684576.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: 00:06:26 11434421 reads; of these: 11434421 (100.00%) were paired; of these: 5895712 (51.56%) aligned concordantly 0 times 4541833 (39.72%) aligned concordantly exactly 1 time 996876 (8.72%) aligned concordantly >1 times ---- 5895712 pairs aligned concordantly 0 times; of these: 75974 (1.29%) aligned discordantly 1 time ---- 5819738 pairs aligned 0 times concordantly or discordantly; of these: 11639476 mates make up the pairs; of these: 6448082 (55.40%) aligned 0 times 4208935 (36.16%) aligned exactly 1 time 982459 (8.44%) aligned >1 times 71.80% overall alignment rate Time searching: 00:06:26 Overall time: 00:06:26 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] 193267 / 5613964 = 0.0344 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 20:43:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245365/SRX8245365.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245365/SRX8245365.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245365/SRX8245365.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245365/SRX8245365.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 20:43:42: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:43:42: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:43:47: 1000000 INFO @ Sat, 15 Jan 2022 20:43:53: 2000000 INFO @ Sat, 15 Jan 2022 20:43:58: 3000000 INFO @ Sat, 15 Jan 2022 20:44:03: 4000000 INFO @ Sat, 15 Jan 2022 20:44:08: 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 20:44:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245365/SRX8245365.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245365/SRX8245365.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245365/SRX8245365.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245365/SRX8245365.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 20:44:12: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:44:12: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:44:14: 6000000 INFO @ Sat, 15 Jan 2022 20:44:20: 1000000 INFO @ Sat, 15 Jan 2022 20:44:21: 7000000 INFO @ Sat, 15 Jan 2022 20:44:27: 8000000 INFO @ Sat, 15 Jan 2022 20:44:28: 2000000 INFO @ Sat, 15 Jan 2022 20:44:34: 9000000 INFO @ Sat, 15 Jan 2022 20:44:36: 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 20:44:41: 10000000 INFO @ Sat, 15 Jan 2022 20:44:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245365/SRX8245365.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245365/SRX8245365.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245365/SRX8245365.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245365/SRX8245365.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 20:44:42: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:44:42: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:44:43: 4000000 INFO @ Sat, 15 Jan 2022 20:44:47: 11000000 INFO @ Sat, 15 Jan 2022 20:44:50: 1000000 INFO @ Sat, 15 Jan 2022 20:44:51: 5000000 INFO @ Sat, 15 Jan 2022 20:44:54: 12000000 INFO @ Sat, 15 Jan 2022 20:44:57: 2000000 INFO @ Sat, 15 Jan 2022 20:44:58: 6000000 INFO @ Sat, 15 Jan 2022 20:45:01: 13000000 INFO @ Sat, 15 Jan 2022 20:45:05: 3000000 INFO @ Sat, 15 Jan 2022 20:45:06: 7000000 INFO @ Sat, 15 Jan 2022 20:45:08: 14000000 INFO @ Sat, 15 Jan 2022 20:45:12: 4000000 INFO @ Sat, 15 Jan 2022 20:45:14: 8000000 INFO @ Sat, 15 Jan 2022 20:45:14: 15000000 INFO @ Sat, 15 Jan 2022 20:45:20: 5000000 INFO @ Sat, 15 Jan 2022 20:45:21: 16000000 INFO @ Sat, 15 Jan 2022 20:45:21: 9000000 INFO @ Sat, 15 Jan 2022 20:45:21: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:45:21: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:45:21: #1 total tags in treatment: 5345991 INFO @ Sat, 15 Jan 2022 20:45:21: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:45:21: #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 20:45:21: #1 tags after filtering in treatment: 3649073 INFO @ Sat, 15 Jan 2022 20:45:21: #1 Redundant rate of treatment: 0.32 INFO @ Sat, 15 Jan 2022 20:45:21: #1 finished! INFO @ Sat, 15 Jan 2022 20:45:21: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:45:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:45:22: #2 number of paired peaks: 163 WARNING @ Sat, 15 Jan 2022 20:45:22: Fewer paired peaks (163) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 163 pairs to build model! INFO @ Sat, 15 Jan 2022 20:45:22: start model_add_line... INFO @ Sat, 15 Jan 2022 20:45:22: start X-correlation... INFO @ Sat, 15 Jan 2022 20:45:22: end of X-cor INFO @ Sat, 15 Jan 2022 20:45:22: #2 finished! INFO @ Sat, 15 Jan 2022 20:45:22: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 20:45:22: #2 alternative fragment length(s) may be 0,36,60,66,72,112,136,154,158,196,207,210,213,222,226,257,280,299,324,339,358,379,405,433,453,472,491,532,589 bps INFO @ Sat, 15 Jan 2022 20:45:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245365/SRX8245365.05_model.r WARNING @ Sat, 15 Jan 2022 20:45:22: #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 20:45:22: #2 You may need to consider one of the other alternative d(s): 0,36,60,66,72,112,136,154,158,196,207,210,213,222,226,257,280,299,324,339,358,379,405,433,453,472,491,532,589 WARNING @ Sat, 15 Jan 2022 20:45:22: #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 20:45:22: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:45:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:45:27: 6000000 INFO @ Sat, 15 Jan 2022 20:45:29: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:45:35: 7000000 INFO @ Sat, 15 Jan 2022 20:45:37: 11000000 BigWig に変換しました。 /var/spool/uge/at160/job_scripts/14521139: line 297: 86705 Terminated MACS $i /var/spool/uge/at160/job_scripts/14521139: line 297: 90022 Terminated MACS $i /var/spool/uge/at160/job_scripts/14521139: line 297: 90224 Terminated MACS $i ls: cannot access SRX8245365.05.bed: No such file or directory mv: cannot stat ‘SRX8245365.05.bed’: No such file or directory mv: cannot stat ‘SRX8245365.05.bb’: No such file or directory ls: cannot access SRX8245365.10.bed: No such file or directory mv: cannot stat ‘SRX8245365.10.bed’: No such file or directory mv: cannot stat ‘SRX8245365.10.bb’: No such file or directory ls: cannot access SRX8245365.20.bed: No such file or directory mv: cannot stat ‘SRX8245365.20.bed’: No such file or directory mv: cannot stat ‘SRX8245365.20.bb’: No such file or directory INFO @ Sat, 15 Jan 2022 20:45:43: 8000000