Job ID = 7105225 SRX = SRX6911531 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 7480327 spots for SRR10191142/SRR10191142.sra Written 7480327 spots for SRR10191142/SRR10191142.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: 00:08:22 7480327 reads; of these: 7480327 (100.00%) were paired; of these: 1911425 (25.55%) aligned concordantly 0 times 4275687 (57.16%) aligned concordantly exactly 1 time 1293215 (17.29%) aligned concordantly >1 times ---- 1911425 pairs aligned concordantly 0 times; of these: 787839 (41.22%) aligned discordantly 1 time ---- 1123586 pairs aligned 0 times concordantly or discordantly; of these: 2247172 mates make up the pairs; of these: 1108855 (49.34%) aligned 0 times 520314 (23.15%) aligned exactly 1 time 618003 (27.50%) aligned >1 times 92.59% overall alignment rate Time searching: 00:08:22 Overall time: 00:08:23 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] 479466 / 6354824 = 0.0754 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Jul 2020 12:53:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6911531/SRX6911531.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6911531/SRX6911531.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6911531/SRX6911531.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6911531/SRX6911531.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 @ Wed, 22 Jul 2020 12:53:14: #1 read tag files... INFO @ Wed, 22 Jul 2020 12:53:14: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 12:53:20: 1000000 INFO @ Wed, 22 Jul 2020 12:53:26: 2000000 INFO @ Wed, 22 Jul 2020 12:53:32: 3000000 INFO @ Wed, 22 Jul 2020 12:53:38: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Jul 2020 12:53:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6911531/SRX6911531.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6911531/SRX6911531.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6911531/SRX6911531.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6911531/SRX6911531.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 @ Wed, 22 Jul 2020 12:53:43: #1 read tag files... INFO @ Wed, 22 Jul 2020 12:53:43: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 12:53:44: 5000000 INFO @ Wed, 22 Jul 2020 12:53:51: 1000000 INFO @ Wed, 22 Jul 2020 12:53:51: 6000000 INFO @ Wed, 22 Jul 2020 12:53:57: 2000000 INFO @ Wed, 22 Jul 2020 12:53:58: 7000000 INFO @ Wed, 22 Jul 2020 12:54:04: 3000000 INFO @ Wed, 22 Jul 2020 12:54:05: 8000000 INFO @ Wed, 22 Jul 2020 12:54:11: 4000000 INFO @ Wed, 22 Jul 2020 12:54:11: 9000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Jul 2020 12:54:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6911531/SRX6911531.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6911531/SRX6911531.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6911531/SRX6911531.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6911531/SRX6911531.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 @ Wed, 22 Jul 2020 12:54:13: #1 read tag files... INFO @ Wed, 22 Jul 2020 12:54:13: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 12:54:18: 5000000 INFO @ Wed, 22 Jul 2020 12:54:18: 10000000 INFO @ Wed, 22 Jul 2020 12:54:20: 1000000 INFO @ Wed, 22 Jul 2020 12:54:25: 6000000 INFO @ Wed, 22 Jul 2020 12:54:25: 11000000 INFO @ Wed, 22 Jul 2020 12:54:27: 2000000 INFO @ Wed, 22 Jul 2020 12:54:31: 7000000 INFO @ Wed, 22 Jul 2020 12:54:32: 12000000 INFO @ Wed, 22 Jul 2020 12:54:34: 3000000 INFO @ Wed, 22 Jul 2020 12:54:38: #1 tag size is determined as 101 bps INFO @ Wed, 22 Jul 2020 12:54:38: #1 tag size = 101 INFO @ Wed, 22 Jul 2020 12:54:38: #1 total tags in treatment: 5123397 INFO @ Wed, 22 Jul 2020 12:54:38: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 12:54:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 12:54:38: 8000000 INFO @ Wed, 22 Jul 2020 12:54:38: #1 tags after filtering in treatment: 2985399 INFO @ Wed, 22 Jul 2020 12:54:38: #1 Redundant rate of treatment: 0.42 INFO @ Wed, 22 Jul 2020 12:54:38: #1 finished! INFO @ Wed, 22 Jul 2020 12:54:38: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 12:54:38: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 12:54:38: #2 number of paired peaks: 169 WARNING @ Wed, 22 Jul 2020 12:54:38: Fewer paired peaks (169) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 169 pairs to build model! INFO @ Wed, 22 Jul 2020 12:54:38: start model_add_line... INFO @ Wed, 22 Jul 2020 12:54:38: start X-correlation... INFO @ Wed, 22 Jul 2020 12:54:38: end of X-cor INFO @ Wed, 22 Jul 2020 12:54:38: #2 finished! INFO @ Wed, 22 Jul 2020 12:54:38: #2 predicted fragment length is 0 bps INFO @ Wed, 22 Jul 2020 12:54:38: #2 alternative fragment length(s) may be 0,90,113,144,163,208,244,281,284,318,361,402,429,462,482,528,545 bps INFO @ Wed, 22 Jul 2020 12:54:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6911531/SRX6911531.05_model.r WARNING @ Wed, 22 Jul 2020 12:54:39: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Jul 2020 12:54:39: #2 You may need to consider one of the other alternative d(s): 0,90,113,144,163,208,244,281,284,318,361,402,429,462,482,528,545 WARNING @ Wed, 22 Jul 2020 12:54:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Jul 2020 12:54:39: #3 Call peaks... INFO @ Wed, 22 Jul 2020 12:54:39: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 12:54:41: 4000000 INFO @ Wed, 22 Jul 2020 12:54:45: 9000000 INFO @ Wed, 22 Jul 2020 12:54:47: 5000000 INFO @ Wed, 22 Jul 2020 12:54:52: 10000000 INFO @ Wed, 22 Jul 2020 12:54:54: 6000000 INFO @ Wed, 22 Jul 2020 12:54:58: 11000000 INFO @ Wed, 22 Jul 2020 12:55:01: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Jul 2020 12:55:05: 12000000 INFO @ Wed, 22 Jul 2020 12:55:08: 8000000 INFO @ Wed, 22 Jul 2020 12:55:11: #1 tag size is determined as 101 bps INFO @ Wed, 22 Jul 2020 12:55:11: #1 tag size = 101 INFO @ Wed, 22 Jul 2020 12:55:11: #1 total tags in treatment: 5123397 INFO @ Wed, 22 Jul 2020 12:55:11: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 12:55:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 12:55:11: #1 tags after filtering in treatment: 2985399 INFO @ Wed, 22 Jul 2020 12:55:11: #1 Redundant rate of treatment: 0.42 INFO @ Wed, 22 Jul 2020 12:55:11: #1 finished! INFO @ Wed, 22 Jul 2020 12:55:11: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 12:55:11: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 12:55:12: #2 number of paired peaks: 169 WARNING @ Wed, 22 Jul 2020 12:55:12: Fewer paired peaks (169) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 169 pairs to build model! INFO @ Wed, 22 Jul 2020 12:55:12: start model_add_line... INFO @ Wed, 22 Jul 2020 12:55:12: start X-correlation... INFO @ Wed, 22 Jul 2020 12:55:12: end of X-cor INFO @ Wed, 22 Jul 2020 12:55:12: #2 finished! INFO @ Wed, 22 Jul 2020 12:55:12: #2 predicted fragment length is 0 bps INFO @ Wed, 22 Jul 2020 12:55:12: #2 alternative fragment length(s) may be 0,90,113,144,163,208,244,281,284,318,361,402,429,462,482,528,545 bps INFO @ Wed, 22 Jul 2020 12:55:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6911531/SRX6911531.10_model.r WARNING @ Wed, 22 Jul 2020 12:55:12: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Jul 2020 12:55:12: #2 You may need to consider one of the other alternative d(s): 0,90,113,144,163,208,244,281,284,318,361,402,429,462,482,528,545 WARNING @ Wed, 22 Jul 2020 12:55:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Jul 2020 12:55:12: #3 Call peaks... INFO @ Wed, 22 Jul 2020 12:55:12: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 /var/spool/uge/at146/job_scripts/7105225: line 297: 92219 Terminated MACS $i /var/spool/uge/at146/job_scripts/7105225: line 297: 93924 Terminated MACS $i /var/spool/uge/at146/job_scripts/7105225: line 297: 96789 Terminated MACS $i ls: cannot access SRX6911531.05.bed: No such file or directory mv: cannot stat ‘SRX6911531.05.bed’: No such file or directory mv: cannot stat ‘SRX6911531.05.bb’: No such file or directory ls: cannot access SRX6911531.10.bed: No such file or directory mv: cannot stat ‘SRX6911531.10.bed’: No such file or directory mv: cannot stat ‘SRX6911531.10.bb’: No such file or directory ls: cannot access SRX6911531.20.bed: No such file or directory mv: cannot stat ‘SRX6911531.20.bed’: No such file or directory mv: cannot stat ‘SRX6911531.20.bb’: No such file or directory