Job ID = 14520829 SRX = SRX8245536 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 9710342 spots for SRR11684747/SRR11684747.sra Written 9710342 spots for SRR11684747/SRR11684747.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: 00:07:26 9710342 reads; of these: 9710342 (100.00%) were paired; of these: 4812572 (49.56%) aligned concordantly 0 times 4337909 (44.67%) aligned concordantly exactly 1 time 559861 (5.77%) aligned concordantly >1 times ---- 4812572 pairs aligned concordantly 0 times; of these: 91282 (1.90%) aligned discordantly 1 time ---- 4721290 pairs aligned 0 times concordantly or discordantly; of these: 9442580 mates make up the pairs; of these: 5744144 (60.83%) aligned 0 times 3194827 (33.83%) aligned exactly 1 time 503609 (5.33%) aligned >1 times 70.42% overall alignment rate Time searching: 00:07:26 Overall time: 00:07:26 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] 333688 / 4988356 = 0.0669 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 20:09:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245536/SRX8245536.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245536/SRX8245536.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245536/SRX8245536.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245536/SRX8245536.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 20:09:49: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:09:49: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:09:54: 1000000 INFO @ Sat, 15 Jan 2022 20:09:59: 2000000 INFO @ Sat, 15 Jan 2022 20:10:04: 3000000 INFO @ Sat, 15 Jan 2022 20:10:08: 4000000 INFO @ Sat, 15 Jan 2022 20:10:13: 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 20:10:19: 6000000 INFO @ Sat, 15 Jan 2022 20:10:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245536/SRX8245536.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245536/SRX8245536.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245536/SRX8245536.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245536/SRX8245536.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 20:10:19: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:10:19: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:10:24: 7000000 INFO @ Sat, 15 Jan 2022 20:10:25: 1000000 INFO @ Sat, 15 Jan 2022 20:10:30: 8000000 INFO @ Sat, 15 Jan 2022 20:10:30: 2000000 INFO @ Sat, 15 Jan 2022 20:10:35: 9000000 INFO @ Sat, 15 Jan 2022 20:10:36: 3000000 INFO @ Sat, 15 Jan 2022 20:10:41: 10000000 INFO @ Sat, 15 Jan 2022 20:10:41: 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 20:10:46: 5000000 INFO @ Sat, 15 Jan 2022 20:10:46: 11000000 INFO @ Sat, 15 Jan 2022 20:10:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245536/SRX8245536.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245536/SRX8245536.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245536/SRX8245536.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245536/SRX8245536.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 20:10:49: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:10:49: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:10:52: 6000000 INFO @ Sat, 15 Jan 2022 20:10:53: 12000000 INFO @ Sat, 15 Jan 2022 20:10:55: 1000000 INFO @ Sat, 15 Jan 2022 20:10:58: 7000000 INFO @ Sat, 15 Jan 2022 20:10:59: 13000000 INFO @ Sat, 15 Jan 2022 20:11:00: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:11:00: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:11:00: #1 total tags in treatment: 4566449 INFO @ Sat, 15 Jan 2022 20:11:00: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:11:00: #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 20:11:00: #1 tags after filtering in treatment: 2880384 INFO @ Sat, 15 Jan 2022 20:11:00: #1 Redundant rate of treatment: 0.37 INFO @ Sat, 15 Jan 2022 20:11:00: #1 finished! INFO @ Sat, 15 Jan 2022 20:11:00: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:11:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:11:00: #2 number of paired peaks: 170 WARNING @ Sat, 15 Jan 2022 20:11:00: Fewer paired peaks (170) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 170 pairs to build model! INFO @ Sat, 15 Jan 2022 20:11:00: start model_add_line... INFO @ Sat, 15 Jan 2022 20:11:00: start X-correlation... INFO @ Sat, 15 Jan 2022 20:11:00: end of X-cor INFO @ Sat, 15 Jan 2022 20:11:00: #2 finished! INFO @ Sat, 15 Jan 2022 20:11:00: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 20:11:00: #2 alternative fragment length(s) may be 0,48,55,101,120,135,151,176,197,238,265,271,287,315,345,371,383,406,422,426,470,491,514,537,575 bps INFO @ Sat, 15 Jan 2022 20:11:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245536/SRX8245536.05_model.r WARNING @ Sat, 15 Jan 2022 20:11:00: #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 20:11:00: #2 You may need to consider one of the other alternative d(s): 0,48,55,101,120,135,151,176,197,238,265,271,287,315,345,371,383,406,422,426,470,491,514,537,575 WARNING @ Sat, 15 Jan 2022 20:11:00: #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 20:11:00: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:11:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:11:00: 2000000 INFO @ Sat, 15 Jan 2022 20:11:05: 8000000 INFO @ Sat, 15 Jan 2022 20:11:05: 3000000 INFO @ Sat, 15 Jan 2022 20:11:11: 4000000 INFO @ Sat, 15 Jan 2022 20:11:11: 9000000 INFO @ Sat, 15 Jan 2022 20:11:16: 5000000 INFO @ Sat, 15 Jan 2022 20:11:16: 10000000 INFO @ Sat, 15 Jan 2022 20:11:21: 6000000 INFO @ Sat, 15 Jan 2022 20:11:22: 11000000 INFO @ Sat, 15 Jan 2022 20:11:26: 7000000 INFO @ Sat, 15 Jan 2022 20:11:27: 12000000 INFO @ Sat, 15 Jan 2022 20:11:31: 8000000 INFO @ Sat, 15 Jan 2022 20:11:32: 13000000 INFO @ Sat, 15 Jan 2022 20:11:32: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:11:32: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:11:32: #1 total tags in treatment: 4566449 INFO @ Sat, 15 Jan 2022 20:11:32: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:11:32: #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 20:11:32: #1 tags after filtering in treatment: 2880384 INFO @ Sat, 15 Jan 2022 20:11:32: #1 Redundant rate of treatment: 0.37 INFO @ Sat, 15 Jan 2022 20:11:32: #1 finished! INFO @ Sat, 15 Jan 2022 20:11:32: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:11:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:11:32: #2 number of paired peaks: 170 WARNING @ Sat, 15 Jan 2022 20:11:32: Fewer paired peaks (170) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 170 pairs to build model! INFO @ Sat, 15 Jan 2022 20:11:32: start model_add_line... INFO @ Sat, 15 Jan 2022 20:11:32: start X-correlation... INFO @ Sat, 15 Jan 2022 20:11:32: end of X-cor INFO @ Sat, 15 Jan 2022 20:11:32: #2 finished! INFO @ Sat, 15 Jan 2022 20:11:32: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 20:11:32: #2 alternative fragment length(s) may be 0,48,55,101,120,135,151,176,197,238,265,271,287,315,345,371,383,406,422,426,470,491,514,537,575 bps INFO @ Sat, 15 Jan 2022 20:11:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245536/SRX8245536.10_model.r WARNING @ Sat, 15 Jan 2022 20:11:33: #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 20:11:33: #2 You may need to consider one of the other alternative d(s): 0,48,55,101,120,135,151,176,197,238,265,271,287,315,345,371,383,406,422,426,470,491,514,537,575 WARNING @ Sat, 15 Jan 2022 20:11:33: #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 20:11:33: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:11:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:11:36: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:11:41: 10000000 INFO @ Sat, 15 Jan 2022 20:11:45: 11000000 INFO @ Sat, 15 Jan 2022 20:11:50: 12000000 BigWig に変換しました。 /var/spool/uge/it019/job_scripts/14520829: line 297: 19499 Terminated MACS $i /var/spool/uge/it019/job_scripts/14520829: line 297: 20666 Terminated MACS $i /var/spool/uge/it019/job_scripts/14520829: line 297: 20784 Terminated MACS $i ls: cannot access SRX8245536.05.bed: No such file or directory mv: cannot stat ‘SRX8245536.05.bed’: No such file or directory mv: cannot stat ‘SRX8245536.05.bb’: No such file or directory ls: cannot access SRX8245536.10.bed: No such file or directory mv: cannot stat ‘SRX8245536.10.bed’: No such file or directory mv: cannot stat ‘SRX8245536.10.bb’: No such file or directory ls: cannot access SRX8245536.20.bed: No such file or directory mv: cannot stat ‘SRX8245536.20.bed’: No such file or directory mv: cannot stat ‘SRX8245536.20.bb’: No such file or directory