Job ID = 14520425 SRX = SRX11781022 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-01-15T10:04:51 prefetch.2.10.7: 1) Downloading 'SRR15480965'... 2022-01-15T10:04:51 prefetch.2.10.7: Downloading via HTTPS... 2022-01-15T10:05:22 prefetch.2.10.7: HTTPS download succeed 2022-01-15T10:05:23 prefetch.2.10.7: 'SRR15480965' is valid 2022-01-15T10:05:23 prefetch.2.10.7: 1) 'SRR15480965' was downloaded successfully 2022-01-15T10:05:23 prefetch.2.10.7: 'SRR15480965' has 0 unresolved dependencies Read 8848532 spots for SRR15480965/SRR15480965.sra Written 8848532 spots for SRR15480965/SRR15480965.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: 00:05:44 8848532 reads; of these: 8848532 (100.00%) were paired; of these: 2051964 (23.19%) aligned concordantly 0 times 5763514 (65.14%) aligned concordantly exactly 1 time 1033054 (11.67%) aligned concordantly >1 times ---- 2051964 pairs aligned concordantly 0 times; of these: 97800 (4.77%) aligned discordantly 1 time ---- 1954164 pairs aligned 0 times concordantly or discordantly; of these: 3908328 mates make up the pairs; of these: 3434446 (87.88%) aligned 0 times 428907 (10.97%) aligned exactly 1 time 44975 (1.15%) aligned >1 times 80.59% overall alignment rate Time searching: 00:05:44 Overall time: 00:05:44 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] 4020416 / 6880829 = 0.5843 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 19:15:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781022/SRX11781022.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781022/SRX11781022.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781022/SRX11781022.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781022/SRX11781022.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 19:15:11: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:15:11: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:15:16: 1000000 INFO @ Sat, 15 Jan 2022 19:15:20: 2000000 INFO @ Sat, 15 Jan 2022 19:15:25: 3000000 INFO @ Sat, 15 Jan 2022 19:15:30: 4000000 INFO @ Sat, 15 Jan 2022 19:15:35: 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 19:15:40: 6000000 INFO @ Sat, 15 Jan 2022 19:15:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781022/SRX11781022.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781022/SRX11781022.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781022/SRX11781022.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781022/SRX11781022.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 19:15:41: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:15:41: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:15:41: #1 tag size is determined as 80 bps INFO @ Sat, 15 Jan 2022 19:15:41: #1 tag size = 80 INFO @ Sat, 15 Jan 2022 19:15:41: #1 total tags in treatment: 2812158 INFO @ Sat, 15 Jan 2022 19:15:41: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:15:41: #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 19:15:41: #1 tags after filtering in treatment: 1400143 INFO @ Sat, 15 Jan 2022 19:15:41: #1 Redundant rate of treatment: 0.50 INFO @ Sat, 15 Jan 2022 19:15:41: #1 finished! INFO @ Sat, 15 Jan 2022 19:15:41: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:15:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:15:41: #2 number of paired peaks: 186 WARNING @ Sat, 15 Jan 2022 19:15:41: Fewer paired peaks (186) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 186 pairs to build model! INFO @ Sat, 15 Jan 2022 19:15:41: start model_add_line... INFO @ Sat, 15 Jan 2022 19:15:41: start X-correlation... INFO @ Sat, 15 Jan 2022 19:15:41: end of X-cor INFO @ Sat, 15 Jan 2022 19:15:41: #2 finished! INFO @ Sat, 15 Jan 2022 19:15:41: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 19:15:41: #2 alternative fragment length(s) may be 0,77,93,118,138,178,197,217,223,249,290,310,327,414,416,429,451,476,493,534,557 bps INFO @ Sat, 15 Jan 2022 19:15:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781022/SRX11781022.05_model.r WARNING @ Sat, 15 Jan 2022 19:15:41: #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 19:15:41: #2 You may need to consider one of the other alternative d(s): 0,77,93,118,138,178,197,217,223,249,290,310,327,414,416,429,451,476,493,534,557 WARNING @ Sat, 15 Jan 2022 19:15:41: #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 19:15:41: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:15:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:15:46: 1000000 INFO @ Sat, 15 Jan 2022 19:15:50: 2000000 INFO @ Sat, 15 Jan 2022 19:15:55: 3000000 INFO @ Sat, 15 Jan 2022 19:16:00: 4000000 INFO @ Sat, 15 Jan 2022 19:16:05: 5000000 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 19:16:10: 6000000 INFO @ Sat, 15 Jan 2022 19:16:11: #1 tag size is determined as 80 bps INFO @ Sat, 15 Jan 2022 19:16:11: #1 tag size = 80 INFO @ Sat, 15 Jan 2022 19:16:11: #1 total tags in treatment: 2812158 INFO @ Sat, 15 Jan 2022 19:16:11: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:16:11: #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 19:16:11: #1 tags after filtering in treatment: 1400143 INFO @ Sat, 15 Jan 2022 19:16:11: #1 Redundant rate of treatment: 0.50 INFO @ Sat, 15 Jan 2022 19:16:11: #1 finished! INFO @ Sat, 15 Jan 2022 19:16:11: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:16:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:16:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781022/SRX11781022.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781022/SRX11781022.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781022/SRX11781022.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781022/SRX11781022.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 19:16:11: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:16:11: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:16:11: #2 number of paired peaks: 186 WARNING @ Sat, 15 Jan 2022 19:16:11: Fewer paired peaks (186) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 186 pairs to build model! INFO @ Sat, 15 Jan 2022 19:16:11: start model_add_line... INFO @ Sat, 15 Jan 2022 19:16:11: start X-correlation... INFO @ Sat, 15 Jan 2022 19:16:11: end of X-cor INFO @ Sat, 15 Jan 2022 19:16:11: #2 finished! INFO @ Sat, 15 Jan 2022 19:16:11: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 19:16:11: #2 alternative fragment length(s) may be 0,77,93,118,138,178,197,217,223,249,290,310,327,414,416,429,451,476,493,534,557 bps INFO @ Sat, 15 Jan 2022 19:16:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781022/SRX11781022.10_model.r WARNING @ Sat, 15 Jan 2022 19:16:11: #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 19:16:11: #2 You may need to consider one of the other alternative d(s): 0,77,93,118,138,178,197,217,223,249,290,310,327,414,416,429,451,476,493,534,557 WARNING @ Sat, 15 Jan 2022 19:16:11: #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 19:16:11: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:16:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:16:17: 1000000 INFO @ Sat, 15 Jan 2022 19:16:23: 2000000 INFO @ Sat, 15 Jan 2022 19:16:29: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 19:16:35: 4000000 BigWig に変換しました。 /var/spool/uge/at141/job_scripts/14520425: line 297: 131017 Terminated MACS $i /var/spool/uge/at141/job_scripts/14520425: line 297: 729 Terminated MACS $i /var/spool/uge/at141/job_scripts/14520425: line 297: 1960 Terminated MACS $i ls: cannot access SRX11781022.05.bed: No such file or directory mv: cannot stat ‘SRX11781022.05.bed’: No such file or directory mv: cannot stat ‘SRX11781022.05.bb’: No such file or directory ls: cannot access SRX11781022.10.bed: No such file or directory mv: cannot stat ‘SRX11781022.10.bed’: No such file or directory mv: cannot stat ‘SRX11781022.10.bb’: No such file or directory ls: cannot access SRX11781022.20.bed: No such file or directory mv: cannot stat ‘SRX11781022.20.bed’: No such file or directory mv: cannot stat ‘SRX11781022.20.bb’: No such file or directory