Job ID = 14521091 SRX = SRX8245353 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 12252832 spots for SRR11684564/SRR11684564.sra Written 12252832 spots for SRR11684564/SRR11684564.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: 00:08:26 12252832 reads; of these: 12252832 (100.00%) were paired; of these: 6088470 (49.69%) aligned concordantly 0 times 5437979 (44.38%) aligned concordantly exactly 1 time 726383 (5.93%) aligned concordantly >1 times ---- 6088470 pairs aligned concordantly 0 times; of these: 120881 (1.99%) aligned discordantly 1 time ---- 5967589 pairs aligned 0 times concordantly or discordantly; of these: 11935178 mates make up the pairs; of these: 8304196 (69.58%) aligned 0 times 3112644 (26.08%) aligned exactly 1 time 518338 (4.34%) aligned >1 times 66.11% overall alignment rate Time searching: 00:08:26 Overall time: 00:08:26 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] 2056088 / 6284554 = 0.3272 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 20:40:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245353/SRX8245353.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245353/SRX8245353.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245353/SRX8245353.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245353/SRX8245353.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 20:40:40: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:40:40: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:40:45: 1000000 INFO @ Sat, 15 Jan 2022 20:40:50: 2000000 INFO @ Sat, 15 Jan 2022 20:40:55: 3000000 INFO @ Sat, 15 Jan 2022 20:40:59: 4000000 INFO @ Sat, 15 Jan 2022 20:41:04: 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 20:41:09: 6000000 INFO @ Sat, 15 Jan 2022 20:41:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245353/SRX8245353.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245353/SRX8245353.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245353/SRX8245353.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245353/SRX8245353.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 20:41:10: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:41:10: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:41:14: 7000000 INFO @ Sat, 15 Jan 2022 20:41:16: 1000000 INFO @ Sat, 15 Jan 2022 20:41:19: 8000000 INFO @ Sat, 15 Jan 2022 20:41:22: 2000000 INFO @ Sat, 15 Jan 2022 20:41:25: 9000000 INFO @ Sat, 15 Jan 2022 20:41:28: 3000000 INFO @ Sat, 15 Jan 2022 20:41:30: 10000000 INFO @ Sat, 15 Jan 2022 20:41:33: 4000000 INFO @ Sat, 15 Jan 2022 20:41:35: 11000000 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 20:41:39: 5000000 INFO @ Sat, 15 Jan 2022 20:41:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245353/SRX8245353.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245353/SRX8245353.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245353/SRX8245353.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245353/SRX8245353.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 20:41:40: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:41:40: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:41:40: 12000000 INFO @ Sat, 15 Jan 2022 20:41:41: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:41:41: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:41:41: #1 total tags in treatment: 4134849 INFO @ Sat, 15 Jan 2022 20:41:41: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:41:41: #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 20:41:41: #1 tags after filtering in treatment: 2625113 INFO @ Sat, 15 Jan 2022 20:41:41: #1 Redundant rate of treatment: 0.37 INFO @ Sat, 15 Jan 2022 20:41:41: #1 finished! INFO @ Sat, 15 Jan 2022 20:41:41: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:41:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:41:41: #2 number of paired peaks: 176 WARNING @ Sat, 15 Jan 2022 20:41:41: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Sat, 15 Jan 2022 20:41:41: start model_add_line... INFO @ Sat, 15 Jan 2022 20:41:41: start X-correlation... INFO @ Sat, 15 Jan 2022 20:41:41: end of X-cor INFO @ Sat, 15 Jan 2022 20:41:41: #2 finished! INFO @ Sat, 15 Jan 2022 20:41:41: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 20:41:41: #2 alternative fragment length(s) may be 0,46,59,85,105,127,139,183,214,247,265,270,297,322,349,372,385,405,411,439,464,467,485,502,511,519,548,572,574 bps INFO @ Sat, 15 Jan 2022 20:41:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245353/SRX8245353.05_model.r WARNING @ Sat, 15 Jan 2022 20:41:41: #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 20:41:41: #2 You may need to consider one of the other alternative d(s): 0,46,59,85,105,127,139,183,214,247,265,270,297,322,349,372,385,405,411,439,464,467,485,502,511,519,548,572,574 WARNING @ Sat, 15 Jan 2022 20:41:41: #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 20:41:41: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:41:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:41:44: 6000000 INFO @ Sat, 15 Jan 2022 20:41:46: 1000000 INFO @ Sat, 15 Jan 2022 20:41:50: 7000000 INFO @ Sat, 15 Jan 2022 20:41:52: 2000000 INFO @ Sat, 15 Jan 2022 20:41:56: 8000000 INFO @ Sat, 15 Jan 2022 20:41:58: 3000000 INFO @ Sat, 15 Jan 2022 20:42:01: 9000000 INFO @ Sat, 15 Jan 2022 20:42:04: 4000000 INFO @ Sat, 15 Jan 2022 20:42:06: 10000000 INFO @ Sat, 15 Jan 2022 20:42:09: 5000000 INFO @ Sat, 15 Jan 2022 20:42:10: 11000000 INFO @ Sat, 15 Jan 2022 20:42:15: 6000000 INFO @ Sat, 15 Jan 2022 20:42:15: 12000000 INFO @ Sat, 15 Jan 2022 20:42:16: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:42:16: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:42:16: #1 total tags in treatment: 4134849 INFO @ Sat, 15 Jan 2022 20:42:16: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:42:16: #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 20:42:16: #1 tags after filtering in treatment: 2625113 INFO @ Sat, 15 Jan 2022 20:42:16: #1 Redundant rate of treatment: 0.37 INFO @ Sat, 15 Jan 2022 20:42:16: #1 finished! INFO @ Sat, 15 Jan 2022 20:42:16: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:42:16: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:42:16: #2 number of paired peaks: 176 WARNING @ Sat, 15 Jan 2022 20:42:16: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Sat, 15 Jan 2022 20:42:16: start model_add_line... INFO @ Sat, 15 Jan 2022 20:42:16: start X-correlation... INFO @ Sat, 15 Jan 2022 20:42:16: end of X-cor INFO @ Sat, 15 Jan 2022 20:42:16: #2 finished! INFO @ Sat, 15 Jan 2022 20:42:16: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 20:42:16: #2 alternative fragment length(s) may be 0,46,59,85,105,127,139,183,214,247,265,270,297,322,349,372,385,405,411,439,464,467,485,502,511,519,548,572,574 bps INFO @ Sat, 15 Jan 2022 20:42:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245353/SRX8245353.10_model.r WARNING @ Sat, 15 Jan 2022 20:42:16: #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 20:42:16: #2 You may need to consider one of the other alternative d(s): 0,46,59,85,105,127,139,183,214,247,265,270,297,322,349,372,385,405,411,439,464,467,485,502,511,519,548,572,574 WARNING @ Sat, 15 Jan 2022 20:42:16: #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 20:42:16: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:42:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:42:20: 7000000 INFO @ Sat, 15 Jan 2022 20:42:26: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:42:31: 9000000 INFO @ Sat, 15 Jan 2022 20:42:36: 10000000 BigWig に変換しました。 /var/spool/uge/it007/job_scripts/14521091: line 297: 11911 Terminated MACS $i /var/spool/uge/it007/job_scripts/14521091: line 297: 13080 Terminated MACS $i /var/spool/uge/it007/job_scripts/14521091: line 297: 13257 Terminated MACS $i ls: cannot access SRX8245353.05.bed: No such file or directory mv: cannot stat ‘SRX8245353.05.bed’: No such file or directory mv: cannot stat ‘SRX8245353.05.bb’: No such file or directory ls: cannot access SRX8245353.10.bed: No such file or directory mv: cannot stat ‘SRX8245353.10.bed’: No such file or directory mv: cannot stat ‘SRX8245353.10.bb’: No such file or directory ls: cannot access SRX8245353.20.bed: No such file or directory mv: cannot stat ‘SRX8245353.20.bed’: No such file or directory mv: cannot stat ‘SRX8245353.20.bb’: No such file or directory