Job ID = 14521228 SRX = SRX8245383 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 7342047 spots for SRR11684594/SRR11684594.sra Written 7342047 spots for SRR11684594/SRR11684594.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: 00:03:43 7342047 reads; of these: 7342047 (100.00%) were paired; of these: 4228450 (57.59%) aligned concordantly 0 times 2836047 (38.63%) aligned concordantly exactly 1 time 277550 (3.78%) aligned concordantly >1 times ---- 4228450 pairs aligned concordantly 0 times; of these: 23105 (0.55%) aligned discordantly 1 time ---- 4205345 pairs aligned 0 times concordantly or discordantly; of these: 8410690 mates make up the pairs; of these: 6075707 (72.24%) aligned 0 times 2095470 (24.91%) aligned exactly 1 time 239513 (2.85%) aligned >1 times 58.62% overall alignment rate Time searching: 00:03:43 Overall time: 00:03:43 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] 217729 / 3134766 = 0.0695 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 20:47:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245383/SRX8245383.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245383/SRX8245383.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245383/SRX8245383.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245383/SRX8245383.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 20:47:55: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:47:55: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:48:00: 1000000 INFO @ Sat, 15 Jan 2022 20:48:05: 2000000 INFO @ Sat, 15 Jan 2022 20:48:10: 3000000 INFO @ Sat, 15 Jan 2022 20:48:15: 4000000 INFO @ Sat, 15 Jan 2022 20:48:20: 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 20:48:25: 6000000 INFO @ Sat, 15 Jan 2022 20:48:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245383/SRX8245383.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245383/SRX8245383.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245383/SRX8245383.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245383/SRX8245383.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 20:48:25: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:48:25: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:48:31: 7000000 INFO @ Sat, 15 Jan 2022 20:48:32: 1000000 INFO @ Sat, 15 Jan 2022 20:48:37: 8000000 INFO @ Sat, 15 Jan 2022 20:48:38: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:48:38: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:48:38: #1 total tags in treatment: 2911039 INFO @ Sat, 15 Jan 2022 20:48:38: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:48:38: #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 20:48:38: #1 tags after filtering in treatment: 1997105 INFO @ Sat, 15 Jan 2022 20:48:38: #1 Redundant rate of treatment: 0.31 INFO @ Sat, 15 Jan 2022 20:48:38: #1 finished! INFO @ Sat, 15 Jan 2022 20:48:38: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:48:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:48:38: #2 number of paired peaks: 179 WARNING @ Sat, 15 Jan 2022 20:48:38: Fewer paired peaks (179) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 179 pairs to build model! INFO @ Sat, 15 Jan 2022 20:48:38: start model_add_line... INFO @ Sat, 15 Jan 2022 20:48:38: start X-correlation... INFO @ Sat, 15 Jan 2022 20:48:38: end of X-cor INFO @ Sat, 15 Jan 2022 20:48:38: #2 finished! INFO @ Sat, 15 Jan 2022 20:48:38: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 20:48:38: #2 alternative fragment length(s) may be 0,33,49,73,143,164,187,222,284,306,342,497,556,589 bps INFO @ Sat, 15 Jan 2022 20:48:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245383/SRX8245383.05_model.r WARNING @ Sat, 15 Jan 2022 20:48:38: #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 20:48:38: #2 You may need to consider one of the other alternative d(s): 0,33,49,73,143,164,187,222,284,306,342,497,556,589 WARNING @ Sat, 15 Jan 2022 20:48:38: #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 20:48:38: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:48:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:48:39: 2000000 INFO @ Sat, 15 Jan 2022 20:48:45: 3000000 INFO @ Sat, 15 Jan 2022 20:48:51: 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 20:48:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245383/SRX8245383.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245383/SRX8245383.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245383/SRX8245383.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245383/SRX8245383.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 20:48:55: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:48:55: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:48:58: 5000000 INFO @ Sat, 15 Jan 2022 20:49:01: 1000000 INFO @ Sat, 15 Jan 2022 20:49:05: 6000000 INFO @ Sat, 15 Jan 2022 20:49:07: 2000000 INFO @ Sat, 15 Jan 2022 20:49:12: 7000000 INFO @ Sat, 15 Jan 2022 20:49:13: 3000000 INFO @ Sat, 15 Jan 2022 20:49:18: 8000000 INFO @ Sat, 15 Jan 2022 20:49:19: 4000000 INFO @ Sat, 15 Jan 2022 20:49:20: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:49:20: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:49:20: #1 total tags in treatment: 2911039 INFO @ Sat, 15 Jan 2022 20:49:20: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:49:20: #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 20:49:20: #1 tags after filtering in treatment: 1997105 INFO @ Sat, 15 Jan 2022 20:49:20: #1 Redundant rate of treatment: 0.31 INFO @ Sat, 15 Jan 2022 20:49:20: #1 finished! INFO @ Sat, 15 Jan 2022 20:49:20: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:49:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:49:20: #2 number of paired peaks: 179 WARNING @ Sat, 15 Jan 2022 20:49:20: Fewer paired peaks (179) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 179 pairs to build model! INFO @ Sat, 15 Jan 2022 20:49:20: start model_add_line... INFO @ Sat, 15 Jan 2022 20:49:20: start X-correlation... INFO @ Sat, 15 Jan 2022 20:49:20: end of X-cor INFO @ Sat, 15 Jan 2022 20:49:20: #2 finished! INFO @ Sat, 15 Jan 2022 20:49:20: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 20:49:20: #2 alternative fragment length(s) may be 0,33,49,73,143,164,187,222,284,306,342,497,556,589 bps INFO @ Sat, 15 Jan 2022 20:49:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245383/SRX8245383.10_model.r WARNING @ Sat, 15 Jan 2022 20:49:20: #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 20:49:20: #2 You may need to consider one of the other alternative d(s): 0,33,49,73,143,164,187,222,284,306,342,497,556,589 WARNING @ Sat, 15 Jan 2022 20:49:20: #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 20:49:20: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:49:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:49:24: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:49:29: 6000000 BigWig に変換しました。 /var/spool/uge/at154/job_scripts/14521228: line 297: 75357 Terminated MACS $i /var/spool/uge/at154/job_scripts/14521228: line 297: 79771 Terminated MACS $i /var/spool/uge/at154/job_scripts/14521228: line 297: 97743 Terminated MACS $i ls: cannot access SRX8245383.05.bed: No such file or directory mv: cannot stat ‘SRX8245383.05.bed’: No such file or directory mv: cannot stat ‘SRX8245383.05.bb’: No such file or directory ls: cannot access SRX8245383.10.bed: No such file or directory mv: cannot stat ‘SRX8245383.10.bed’: No such file or directory mv: cannot stat ‘SRX8245383.10.bb’: No such file or directory ls: cannot access SRX8245383.20.bed: No such file or directory mv: cannot stat ‘SRX8245383.20.bed’: No such file or directory mv: cannot stat ‘SRX8245383.20.bb’: No such file or directory