Job ID = 14521046 SRX = SRX8245467 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 15773038 spots for SRR11684678/SRR11684678.sra Written 15773038 spots for SRR11684678/SRR11684678.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: 00:11:30 15773038 reads; of these: 15773038 (100.00%) were paired; of these: 7601581 (48.19%) aligned concordantly 0 times 7184257 (45.55%) aligned concordantly exactly 1 time 987200 (6.26%) aligned concordantly >1 times ---- 7601581 pairs aligned concordantly 0 times; of these: 34086 (0.45%) aligned discordantly 1 time ---- 7567495 pairs aligned 0 times concordantly or discordantly; of these: 15134990 mates make up the pairs; of these: 8743251 (57.77%) aligned 0 times 5486410 (36.25%) aligned exactly 1 time 905329 (5.98%) aligned >1 times 72.28% overall alignment rate Time searching: 00:11:30 Overall time: 00:11:30 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] 666335 / 8204222 = 0.0812 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 20:43:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245467/SRX8245467.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245467/SRX8245467.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245467/SRX8245467.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245467/SRX8245467.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 20:43:37: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:43:37: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:43:43: 1000000 INFO @ Sat, 15 Jan 2022 20:43:50: 2000000 INFO @ Sat, 15 Jan 2022 20:43:56: 3000000 INFO @ Sat, 15 Jan 2022 20:44:03: 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 20:44:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245467/SRX8245467.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245467/SRX8245467.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245467/SRX8245467.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245467/SRX8245467.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 20:44:07: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:44:07: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:44:10: 5000000 INFO @ Sat, 15 Jan 2022 20:44:14: 1000000 INFO @ Sat, 15 Jan 2022 20:44:18: 6000000 INFO @ Sat, 15 Jan 2022 20:44:20: 2000000 INFO @ Sat, 15 Jan 2022 20:44:26: 7000000 INFO @ Sat, 15 Jan 2022 20:44:27: 3000000 INFO @ Sat, 15 Jan 2022 20:44:33: 8000000 BedGraph に変換中... INFO @ Sat, 15 Jan 2022 20:44:34: 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 20:44:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245467/SRX8245467.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245467/SRX8245467.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245467/SRX8245467.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245467/SRX8245467.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 20:44:37: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:44:37: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:44:41: 9000000 INFO @ Sat, 15 Jan 2022 20:44:41: 5000000 INFO @ Sat, 15 Jan 2022 20:44:44: 1000000 INFO @ Sat, 15 Jan 2022 20:44:49: 6000000 INFO @ Sat, 15 Jan 2022 20:44:49: 10000000 INFO @ Sat, 15 Jan 2022 20:44:51: 2000000 INFO @ Sat, 15 Jan 2022 20:44:55: 7000000 INFO @ Sat, 15 Jan 2022 20:45:00: 3000000 INFO @ Sat, 15 Jan 2022 20:45:01: 11000000 INFO @ Sat, 15 Jan 2022 20:45:02: 8000000 INFO @ Sat, 15 Jan 2022 20:45:06: 4000000 INFO @ Sat, 15 Jan 2022 20:45:09: 9000000 INFO @ Sat, 15 Jan 2022 20:45:10: 12000000 INFO @ Sat, 15 Jan 2022 20:45:13: 5000000 INFO @ Sat, 15 Jan 2022 20:45:16: 10000000 INFO @ Sat, 15 Jan 2022 20:45:19: 13000000 INFO @ Sat, 15 Jan 2022 20:45:20: 6000000 INFO @ Sat, 15 Jan 2022 20:45:22: 11000000 INFO @ Sat, 15 Jan 2022 20:45:27: 7000000 INFO @ Sat, 15 Jan 2022 20:45:28: 14000000 INFO @ Sat, 15 Jan 2022 20:45:29: 12000000 INFO @ Sat, 15 Jan 2022 20:45:34: 8000000 INFO @ Sat, 15 Jan 2022 20:45:36: 13000000 INFO @ Sat, 15 Jan 2022 20:45:37: 15000000 INFO @ Sat, 15 Jan 2022 20:45:41: 9000000 INFO @ Sat, 15 Jan 2022 20:45:43: 14000000 INFO @ Sat, 15 Jan 2022 20:45:46: 16000000 INFO @ Sat, 15 Jan 2022 20:45:48: 10000000 INFO @ Sat, 15 Jan 2022 20:45:50: 15000000 INFO @ Sat, 15 Jan 2022 20:45:54: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:45:55: 11000000 INFO @ Sat, 15 Jan 2022 20:45:57: 16000000 INFO @ Sat, 15 Jan 2022 20:46:02: 18000000 INFO @ Sat, 15 Jan 2022 20:46:02: 12000000 INFO @ Sat, 15 Jan 2022 20:46:04: 17000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:46:10: 13000000 INFO @ Sat, 15 Jan 2022 20:46:11: 19000000 INFO @ Sat, 15 Jan 2022 20:46:11: 18000000 INFO @ Sat, 15 Jan 2022 20:46:17: 14000000 INFO @ Sat, 15 Jan 2022 20:46:18: 19000000 INFO @ Sat, 15 Jan 2022 20:46:19: 20000000 INFO @ Sat, 15 Jan 2022 20:46:24: 15000000 INFO @ Sat, 15 Jan 2022 20:46:25: 20000000 INFO @ Sat, 15 Jan 2022 20:46:27: 21000000 INFO @ Sat, 15 Jan 2022 20:46:30: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:46:30: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:46:30: #1 total tags in treatment: 7506438 INFO @ Sat, 15 Jan 2022 20:46:30: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:46:30: #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 20:46:31: #1 tags after filtering in treatment: 4051838 INFO @ Sat, 15 Jan 2022 20:46:31: #1 Redundant rate of treatment: 0.46 INFO @ Sat, 15 Jan 2022 20:46:31: #1 finished! INFO @ Sat, 15 Jan 2022 20:46:31: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:46:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:46:31: #2 number of paired peaks: 162 WARNING @ Sat, 15 Jan 2022 20:46:31: 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 20:46:31: start model_add_line... INFO @ Sat, 15 Jan 2022 20:46:31: start X-correlation... INFO @ Sat, 15 Jan 2022 20:46:31: end of X-cor INFO @ Sat, 15 Jan 2022 20:46:31: #2 finished! INFO @ Sat, 15 Jan 2022 20:46:31: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 20:46:31: #2 alternative fragment length(s) may be 0,10,52,128,187,250,271,299,328,364,418,429,432,497,525,532,577 bps INFO @ Sat, 15 Jan 2022 20:46:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245467/SRX8245467.05_model.r WARNING @ Sat, 15 Jan 2022 20:46:31: #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 20:46:31: #2 You may need to consider one of the other alternative d(s): 0,10,52,128,187,250,271,299,328,364,418,429,432,497,525,532,577 WARNING @ Sat, 15 Jan 2022 20:46:31: #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 20:46:31: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:46:31: #3 Pre-compute pvalue-qvalue table... /var/spool/uge/it010/job_scripts/14521046: line 297: 16558 Terminated MACS $i /var/spool/uge/it010/job_scripts/14521046: line 297: 18904 Terminated MACS $i /var/spool/uge/it010/job_scripts/14521046: line 297: 19027 Terminated MACS $i ls: cannot access SRX8245467.05.bed: No such file or directory mv: cannot stat ‘SRX8245467.05.bed’: No such file or directory mv: cannot stat ‘SRX8245467.05.bb’: No such file or directory ls: cannot access SRX8245467.10.bed: No such file or directory mv: cannot stat ‘SRX8245467.10.bed’: No such file or directory mv: cannot stat ‘SRX8245467.10.bb’: No such file or directory ls: cannot access SRX8245467.20.bed: No such file or directory mv: cannot stat ‘SRX8245467.20.bed’: No such file or directory mv: cannot stat ‘SRX8245467.20.bb’: No such file or directory