Job ID = 14520797 SRX = SRX8245524 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 6895996 spots for SRR11684735/SRR11684735.sra Written 6895996 spots for SRR11684735/SRR11684735.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: 00:03:37 6895996 reads; of these: 6895996 (100.00%) were paired; of these: 4098864 (59.44%) aligned concordantly 0 times 2487372 (36.07%) aligned concordantly exactly 1 time 309760 (4.49%) aligned concordantly >1 times ---- 4098864 pairs aligned concordantly 0 times; of these: 56121 (1.37%) aligned discordantly 1 time ---- 4042743 pairs aligned 0 times concordantly or discordantly; of these: 8085486 mates make up the pairs; of these: 4794650 (59.30%) aligned 0 times 2870640 (35.50%) aligned exactly 1 time 420196 (5.20%) aligned >1 times 65.24% overall alignment rate Time searching: 00:03:37 Overall time: 00:03:37 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_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] 135872 / 2852740 = 0.0476 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 19:59:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245524/SRX8245524.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245524/SRX8245524.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245524/SRX8245524.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245524/SRX8245524.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 19:59:22: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:59:22: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:59:28: 1000000 INFO @ Sat, 15 Jan 2022 19:59:34: 2000000 INFO @ Sat, 15 Jan 2022 19:59:39: 3000000 INFO @ Sat, 15 Jan 2022 19:59:45: 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 19:59:51: 5000000 INFO @ Sat, 15 Jan 2022 19:59:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245524/SRX8245524.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245524/SRX8245524.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245524/SRX8245524.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245524/SRX8245524.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 19:59:52: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:59:52: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:59:57: 6000000 INFO @ Sat, 15 Jan 2022 19:59:59: 1000000 INFO @ Sat, 15 Jan 2022 20:00:03: 7000000 INFO @ Sat, 15 Jan 2022 20:00:05: 2000000 INFO @ Sat, 15 Jan 2022 20:00:09: 8000000 INFO @ Sat, 15 Jan 2022 20:00:12: 3000000 INFO @ Sat, 15 Jan 2022 20:00:14: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:00:14: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:00:14: #1 total tags in treatment: 2662305 INFO @ Sat, 15 Jan 2022 20:00:14: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:00:14: #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 20:00:14: #1 tags after filtering in treatment: 1871078 INFO @ Sat, 15 Jan 2022 20:00:14: #1 Redundant rate of treatment: 0.30 INFO @ Sat, 15 Jan 2022 20:00:14: #1 finished! INFO @ Sat, 15 Jan 2022 20:00:14: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:00:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:00:14: #2 number of paired peaks: 175 WARNING @ Sat, 15 Jan 2022 20:00:14: Fewer paired peaks (175) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 175 pairs to build model! INFO @ Sat, 15 Jan 2022 20:00:14: start model_add_line... INFO @ Sat, 15 Jan 2022 20:00:14: start X-correlation... INFO @ Sat, 15 Jan 2022 20:00:14: end of X-cor INFO @ Sat, 15 Jan 2022 20:00:14: #2 finished! INFO @ Sat, 15 Jan 2022 20:00:14: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 20:00:14: #2 alternative fragment length(s) may be 0,62,69,94,115,145,182,202,248,296,343,445,464,492,519,543,565,590,595 bps INFO @ Sat, 15 Jan 2022 20:00:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245524/SRX8245524.05_model.r WARNING @ Sat, 15 Jan 2022 20:00:14: #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 20:00:14: #2 You may need to consider one of the other alternative d(s): 0,62,69,94,115,145,182,202,248,296,343,445,464,492,519,543,565,590,595 WARNING @ Sat, 15 Jan 2022 20:00:14: #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 20:00:14: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:00:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:00:18: 4000000 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 20:00:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245524/SRX8245524.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245524/SRX8245524.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245524/SRX8245524.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245524/SRX8245524.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 20:00:22: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:00:22: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:00:24: 5000000 INFO @ Sat, 15 Jan 2022 20:00:28: 1000000 INFO @ Sat, 15 Jan 2022 20:00:30: 6000000 INFO @ Sat, 15 Jan 2022 20:00:34: 2000000 INFO @ Sat, 15 Jan 2022 20:00:37: 7000000 INFO @ Sat, 15 Jan 2022 20:00:40: 3000000 INFO @ Sat, 15 Jan 2022 20:00:43: 8000000 INFO @ Sat, 15 Jan 2022 20:00:46: 4000000 INFO @ Sat, 15 Jan 2022 20:00:48: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:00:48: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:00:48: #1 total tags in treatment: 2662305 INFO @ Sat, 15 Jan 2022 20:00:48: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:00:48: #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 20:00:48: #1 tags after filtering in treatment: 1871078 INFO @ Sat, 15 Jan 2022 20:00:48: #1 Redundant rate of treatment: 0.30 INFO @ Sat, 15 Jan 2022 20:00:48: #1 finished! INFO @ Sat, 15 Jan 2022 20:00:48: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:00:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:00:48: #2 number of paired peaks: 175 WARNING @ Sat, 15 Jan 2022 20:00:48: Fewer paired peaks (175) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 175 pairs to build model! INFO @ Sat, 15 Jan 2022 20:00:48: start model_add_line... INFO @ Sat, 15 Jan 2022 20:00:48: start X-correlation... INFO @ Sat, 15 Jan 2022 20:00:48: end of X-cor INFO @ Sat, 15 Jan 2022 20:00:48: #2 finished! INFO @ Sat, 15 Jan 2022 20:00:48: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 20:00:48: #2 alternative fragment length(s) may be 0,62,69,94,115,145,182,202,248,296,343,445,464,492,519,543,565,590,595 bps INFO @ Sat, 15 Jan 2022 20:00:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245524/SRX8245524.10_model.r WARNING @ Sat, 15 Jan 2022 20:00:48: #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 20:00:48: #2 You may need to consider one of the other alternative d(s): 0,62,69,94,115,145,182,202,248,296,343,445,464,492,519,543,565,590,595 WARNING @ Sat, 15 Jan 2022 20:00:48: #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 20:00:48: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:00:48: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:00:52: 5000000 INFO @ Sat, 15 Jan 2022 20:00:58: 6000000 BigWig に変換しました。 /var/spool/uge/at147/job_scripts/14520797: line 297: 55189 Terminated MACS $i /var/spool/uge/at147/job_scripts/14520797: line 297: 62507 Terminated MACS $i /var/spool/uge/at147/job_scripts/14520797: line 297: 71272 Terminated MACS $i ls: cannot access SRX8245524.05.bed: No such file or directory mv: cannot stat ‘SRX8245524.05.bed’: No such file or directory mv: cannot stat ‘SRX8245524.05.bb’: No such file or directory ls: cannot access SRX8245524.10.bed: No such file or directory mv: cannot stat ‘SRX8245524.10.bed’: No such file or directory mv: cannot stat ‘SRX8245524.10.bb’: No such file or directory ls: cannot access SRX8245524.20.bed: No such file or directory mv: cannot stat ‘SRX8245524.20.bed’: No such file or directory mv: cannot stat ‘SRX8245524.20.bb’: No such file or directory