Job ID = 14520861 SRX = SRX8245540 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 8597896 spots for SRR11684751/SRR11684751.sra Written 8597896 spots for SRR11684751/SRR11684751.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: 00:05:08 8597896 reads; of these: 8597896 (100.00%) were paired; of these: 5200958 (60.49%) aligned concordantly 0 times 2932317 (34.11%) aligned concordantly exactly 1 time 464621 (5.40%) aligned concordantly >1 times ---- 5200958 pairs aligned concordantly 0 times; of these: 38577 (0.74%) aligned discordantly 1 time ---- 5162381 pairs aligned 0 times concordantly or discordantly; of these: 10324762 mates make up the pairs; of these: 5711536 (55.32%) aligned 0 times 3944177 (38.20%) aligned exactly 1 time 669049 (6.48%) aligned >1 times 66.79% overall alignment rate Time searching: 00:05:08 Overall time: 00:05:08 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] 50756 / 3434882 = 0.0148 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 20:14:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245540/SRX8245540.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245540/SRX8245540.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245540/SRX8245540.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245540/SRX8245540.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 20:14:26: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:14:26: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:14:33: 1000000 INFO @ Sat, 15 Jan 2022 20:14:39: 2000000 INFO @ Sat, 15 Jan 2022 20:14:46: 3000000 INFO @ Sat, 15 Jan 2022 20:14:53: 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 20:14:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245540/SRX8245540.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245540/SRX8245540.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245540/SRX8245540.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245540/SRX8245540.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 20:14:56: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:14:56: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:15:00: 5000000 INFO @ Sat, 15 Jan 2022 20:15:03: 1000000 INFO @ Sat, 15 Jan 2022 20:15:07: 6000000 INFO @ Sat, 15 Jan 2022 20:15:11: 2000000 INFO @ Sat, 15 Jan 2022 20:15:15: 7000000 INFO @ Sat, 15 Jan 2022 20:15:18: 3000000 INFO @ Sat, 15 Jan 2022 20:15:23: 8000000 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 20:15:25: 4000000 INFO @ Sat, 15 Jan 2022 20:15:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245540/SRX8245540.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245540/SRX8245540.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245540/SRX8245540.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245540/SRX8245540.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 20:15:26: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:15:26: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:15:30: 9000000 INFO @ Sat, 15 Jan 2022 20:15:33: 5000000 INFO @ Sat, 15 Jan 2022 20:15:34: 1000000 INFO @ Sat, 15 Jan 2022 20:15:38: 10000000 INFO @ Sat, 15 Jan 2022 20:15:41: 6000000 INFO @ Sat, 15 Jan 2022 20:15:41: 2000000 INFO @ Sat, 15 Jan 2022 20:15:46: 11000000 INFO @ Sat, 15 Jan 2022 20:15:48: 7000000 INFO @ Sat, 15 Jan 2022 20:15:49: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:15:49: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:15:49: #1 total tags in treatment: 3346310 INFO @ Sat, 15 Jan 2022 20:15:49: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:15:49: #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 20:15:49: #1 tags after filtering in treatment: 2466808 INFO @ Sat, 15 Jan 2022 20:15:49: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 15 Jan 2022 20:15:49: #1 finished! INFO @ Sat, 15 Jan 2022 20:15:49: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:15:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:15:49: #2 number of paired peaks: 173 WARNING @ Sat, 15 Jan 2022 20:15:49: Fewer paired peaks (173) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 173 pairs to build model! INFO @ Sat, 15 Jan 2022 20:15:49: start model_add_line... INFO @ Sat, 15 Jan 2022 20:15:49: start X-correlation... INFO @ Sat, 15 Jan 2022 20:15:49: end of X-cor INFO @ Sat, 15 Jan 2022 20:15:49: #2 finished! INFO @ Sat, 15 Jan 2022 20:15:49: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 20:15:49: #2 alternative fragment length(s) may be 0,46,66,98,101,118,141,167,190,214,220,227,246,298,327,495,548,561,580 bps INFO @ Sat, 15 Jan 2022 20:15:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245540/SRX8245540.05_model.r WARNING @ Sat, 15 Jan 2022 20:15:49: #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 20:15:49: #2 You may need to consider one of the other alternative d(s): 0,46,66,98,101,118,141,167,190,214,220,227,246,298,327,495,548,561,580 WARNING @ Sat, 15 Jan 2022 20:15:49: #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 20:15:49: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:15:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:15:49: 3000000 INFO @ Sat, 15 Jan 2022 20:15:56: 8000000 INFO @ Sat, 15 Jan 2022 20:15:56: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:16:04: 9000000 INFO @ Sat, 15 Jan 2022 20:16:04: 5000000 INFO @ Sat, 15 Jan 2022 20:16:11: 10000000 INFO @ Sat, 15 Jan 2022 20:16:12: 6000000 BigWig に変換しました。 /var/spool/uge/at164/job_scripts/14520861: line 297: 66526 Terminated MACS $i /var/spool/uge/at164/job_scripts/14520861: line 297: 66705 Terminated MACS $i /var/spool/uge/at164/job_scripts/14520861: line 297: 66852 Terminated MACS $i ls: cannot access SRX8245540.05.bed: No such file or directory mv: cannot stat ‘SRX8245540.05.bed’: No such file or directory mv: cannot stat ‘SRX8245540.05.bb’: No such file or directory ls: cannot access SRX8245540.10.bed: No such file or directory mv: cannot stat ‘SRX8245540.10.bed’: No such file or directory mv: cannot stat ‘SRX8245540.10.bb’: No such file or directory ls: cannot access SRX8245540.20.bed: No such file or directory mv: cannot stat ‘SRX8245540.20.bed’: No such file or directory mv: cannot stat ‘SRX8245540.20.bb’: No such file or directory