Job ID = 14520766 SRX = SRX8245517 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 34366356 spots for SRR11684728/SRR11684728.sra Written 34366356 spots for SRR11684728/SRR11684728.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: 00:14:54 34366356 reads; of these: 34366356 (100.00%) were paired; of these: 22836018 (66.45%) aligned concordantly 0 times 10392783 (30.24%) aligned concordantly exactly 1 time 1137555 (3.31%) aligned concordantly >1 times ---- 22836018 pairs aligned concordantly 0 times; of these: 83429 (0.37%) aligned discordantly 1 time ---- 22752589 pairs aligned 0 times concordantly or discordantly; of these: 45505178 mates make up the pairs; of these: 33870039 (74.43%) aligned 0 times 10240523 (22.50%) aligned exactly 1 time 1394616 (3.06%) aligned >1 times 50.72% overall alignment rate Time searching: 00:14:54 Overall time: 00:14:54 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 16 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] 2741703 / 11611970 = 0.2361 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 21:11:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245517/SRX8245517.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245517/SRX8245517.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245517/SRX8245517.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245517/SRX8245517.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 21:11:38: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:11:38: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:11:44: 1000000 INFO @ Sat, 15 Jan 2022 21:11:50: 2000000 INFO @ Sat, 15 Jan 2022 21:11:55: 3000000 INFO @ Sat, 15 Jan 2022 21:12:01: 4000000 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 21:12:07: 5000000 INFO @ Sat, 15 Jan 2022 21:12:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245517/SRX8245517.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245517/SRX8245517.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245517/SRX8245517.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245517/SRX8245517.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 21:12:08: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:12:08: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:12:12: 6000000 INFO @ Sat, 15 Jan 2022 21:12:13: 1000000 INFO @ Sat, 15 Jan 2022 21:12:18: 7000000 INFO @ Sat, 15 Jan 2022 21:12:18: 2000000 INFO @ Sat, 15 Jan 2022 21:12:23: 3000000 INFO @ Sat, 15 Jan 2022 21:12:24: 8000000 INFO @ Sat, 15 Jan 2022 21:12:28: 4000000 INFO @ Sat, 15 Jan 2022 21:12:29: 9000000 INFO @ Sat, 15 Jan 2022 21:12:33: 5000000 INFO @ Sat, 15 Jan 2022 21:12:35: 10000000 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 21:12:38: 6000000 INFO @ Sat, 15 Jan 2022 21:12:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245517/SRX8245517.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245517/SRX8245517.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245517/SRX8245517.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245517/SRX8245517.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 21:12:38: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:12:38: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:12:40: 11000000 INFO @ Sat, 15 Jan 2022 21:12:43: 7000000 INFO @ Sat, 15 Jan 2022 21:12:43: 1000000 INFO @ Sat, 15 Jan 2022 21:12:46: 12000000 INFO @ Sat, 15 Jan 2022 21:12:48: 8000000 INFO @ Sat, 15 Jan 2022 21:12:48: 2000000 INFO @ Sat, 15 Jan 2022 21:12:51: 13000000 INFO @ Sat, 15 Jan 2022 21:12:52: 9000000 INFO @ Sat, 15 Jan 2022 21:12:53: 3000000 INFO @ Sat, 15 Jan 2022 21:12:57: 14000000 INFO @ Sat, 15 Jan 2022 21:12:57: 10000000 INFO @ Sat, 15 Jan 2022 21:12:58: 4000000 INFO @ Sat, 15 Jan 2022 21:13:02: 11000000 INFO @ Sat, 15 Jan 2022 21:13:03: 15000000 INFO @ Sat, 15 Jan 2022 21:13:03: 5000000 INFO @ Sat, 15 Jan 2022 21:13:07: 12000000 INFO @ Sat, 15 Jan 2022 21:13:08: 6000000 INFO @ Sat, 15 Jan 2022 21:13:08: 16000000 INFO @ Sat, 15 Jan 2022 21:13:11: 13000000 INFO @ Sat, 15 Jan 2022 21:13:13: 7000000 INFO @ Sat, 15 Jan 2022 21:13:14: 17000000 INFO @ Sat, 15 Jan 2022 21:13:17: 14000000 INFO @ Sat, 15 Jan 2022 21:13:18: 8000000 INFO @ Sat, 15 Jan 2022 21:13:20: 18000000 INFO @ Sat, 15 Jan 2022 21:13:22: 15000000 INFO @ Sat, 15 Jan 2022 21:13:23: 9000000 INFO @ Sat, 15 Jan 2022 21:13:26: 19000000 INFO @ Sat, 15 Jan 2022 21:13:27: 16000000 INFO @ Sat, 15 Jan 2022 21:13:27: 10000000 INFO @ Sat, 15 Jan 2022 21:13:31: 17000000 INFO @ Sat, 15 Jan 2022 21:13:32: 20000000 INFO @ Sat, 15 Jan 2022 21:13:32: 11000000 INFO @ Sat, 15 Jan 2022 21:13:36: 18000000 INFO @ Sat, 15 Jan 2022 21:13:37: 12000000 INFO @ Sat, 15 Jan 2022 21:13:38: 21000000 INFO @ Sat, 15 Jan 2022 21:13:41: 19000000 INFO @ Sat, 15 Jan 2022 21:13:42: 13000000 INFO @ Sat, 15 Jan 2022 21:13:44: 22000000 INFO @ Sat, 15 Jan 2022 21:13:46: 20000000 INFO @ Sat, 15 Jan 2022 21:13:46: 14000000 INFO @ Sat, 15 Jan 2022 21:13:50: 23000000 INFO @ Sat, 15 Jan 2022 21:13:51: 15000000 INFO @ Sat, 15 Jan 2022 21:13:51: 21000000 INFO @ Sat, 15 Jan 2022 21:13:56: 24000000 INFO @ Sat, 15 Jan 2022 21:13:56: 16000000 INFO @ Sat, 15 Jan 2022 21:13:56: 22000000 INFO @ Sat, 15 Jan 2022 21:14:01: 17000000 INFO @ Sat, 15 Jan 2022 21:14:01: 23000000 INFO @ Sat, 15 Jan 2022 21:14:02: 25000000 INFO @ Sat, 15 Jan 2022 21:14:06: 18000000 INFO @ Sat, 15 Jan 2022 21:14:06: 24000000 INFO @ Sat, 15 Jan 2022 21:14:07: 26000000 INFO @ Sat, 15 Jan 2022 21:14:11: 19000000 INFO @ Sat, 15 Jan 2022 21:14:11: 25000000 INFO @ Sat, 15 Jan 2022 21:14:13: 27000000 INFO @ Sat, 15 Jan 2022 21:14:16: 20000000 INFO @ Sat, 15 Jan 2022 21:14:16: 26000000 INFO @ Sat, 15 Jan 2022 21:14:19: 28000000 INFO @ Sat, 15 Jan 2022 21:14:21: 21000000 INFO @ Sat, 15 Jan 2022 21:14:21: 27000000 INFO @ Sat, 15 Jan 2022 21:14:24: 29000000 INFO @ Sat, 15 Jan 2022 21:14:26: 22000000 INFO @ Sat, 15 Jan 2022 21:14:26: 28000000 INFO @ Sat, 15 Jan 2022 21:14:27: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 21:14:27: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 21:14:27: #1 total tags in treatment: 8794169 INFO @ Sat, 15 Jan 2022 21:14:27: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:14:27: #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 21:14:27: #1 tags after filtering in treatment: 4316590 INFO @ Sat, 15 Jan 2022 21:14:27: #1 Redundant rate of treatment: 0.51 INFO @ Sat, 15 Jan 2022 21:14:27: #1 finished! INFO @ Sat, 15 Jan 2022 21:14:27: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:14:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:14:27: #2 number of paired peaks: 160 WARNING @ Sat, 15 Jan 2022 21:14:27: Fewer paired peaks (160) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 160 pairs to build model! INFO @ Sat, 15 Jan 2022 21:14:27: start model_add_line... INFO @ Sat, 15 Jan 2022 21:14:27: start X-correlation... INFO @ Sat, 15 Jan 2022 21:14:27: end of X-cor INFO @ Sat, 15 Jan 2022 21:14:27: #2 finished! INFO @ Sat, 15 Jan 2022 21:14:27: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 21:14:27: #2 alternative fragment length(s) may be 0,23,49,95,130,189,241,303,346,363,378,427,432,435,443,467,475,491,547,568,579 bps INFO @ Sat, 15 Jan 2022 21:14:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245517/SRX8245517.05_model.r WARNING @ Sat, 15 Jan 2022 21:14:27: #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 21:14:27: #2 You may need to consider one of the other alternative d(s): 0,23,49,95,130,189,241,303,346,363,378,427,432,435,443,467,475,491,547,568,579 WARNING @ Sat, 15 Jan 2022 21:14:27: #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 21:14:27: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:14:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:14:31: 23000000 INFO @ Sat, 15 Jan 2022 21:14:31: 29000000 INFO @ Sat, 15 Jan 2022 21:14:33: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 21:14:33: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 21:14:33: #1 total tags in treatment: 8794169 INFO @ Sat, 15 Jan 2022 21:14:33: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:14:33: #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 21:14:33: #1 tags after filtering in treatment: 4316590 INFO @ Sat, 15 Jan 2022 21:14:33: #1 Redundant rate of treatment: 0.51 INFO @ Sat, 15 Jan 2022 21:14:33: #1 finished! INFO @ Sat, 15 Jan 2022 21:14:33: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:14:33: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:14:33: #2 number of paired peaks: 160 WARNING @ Sat, 15 Jan 2022 21:14:33: Fewer paired peaks (160) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 160 pairs to build model! INFO @ Sat, 15 Jan 2022 21:14:33: start model_add_line... INFO @ Sat, 15 Jan 2022 21:14:34: start X-correlation... INFO @ Sat, 15 Jan 2022 21:14:34: end of X-cor INFO @ Sat, 15 Jan 2022 21:14:34: #2 finished! INFO @ Sat, 15 Jan 2022 21:14:34: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 21:14:34: #2 alternative fragment length(s) may be 0,23,49,95,130,189,241,303,346,363,378,427,432,435,443,467,475,491,547,568,579 bps INFO @ Sat, 15 Jan 2022 21:14:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245517/SRX8245517.10_model.r WARNING @ Sat, 15 Jan 2022 21:14:34: #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 21:14:34: #2 You may need to consider one of the other alternative d(s): 0,23,49,95,130,189,241,303,346,363,378,427,432,435,443,467,475,491,547,568,579 WARNING @ Sat, 15 Jan 2022 21:14:34: #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 21:14:34: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:14:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:14:36: 24000000 INFO @ Sat, 15 Jan 2022 21:14:41: 25000000 INFO @ Sat, 15 Jan 2022 21:14:46: 26000000 INFO @ Sat, 15 Jan 2022 21:14:51: 27000000 INFO @ Sat, 15 Jan 2022 21:14:56: 28000000 INFO @ Sat, 15 Jan 2022 21:15:01: 29000000 INFO @ Sat, 15 Jan 2022 21:15:03: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 21:15:03: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 21:15:03: #1 total tags in treatment: 8794169 INFO @ Sat, 15 Jan 2022 21:15:03: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:15:03: #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 21:15:03: #1 tags after filtering in treatment: 4316590 INFO @ Sat, 15 Jan 2022 21:15:03: #1 Redundant rate of treatment: 0.51 INFO @ Sat, 15 Jan 2022 21:15:03: #1 finished! INFO @ Sat, 15 Jan 2022 21:15:03: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:15:03: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:15:03: #2 number of paired peaks: 160 WARNING @ Sat, 15 Jan 2022 21:15:03: Fewer paired peaks (160) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 160 pairs to build model! INFO @ Sat, 15 Jan 2022 21:15:03: start model_add_line... INFO @ Sat, 15 Jan 2022 21:15:03: start X-correlation... INFO @ Sat, 15 Jan 2022 21:15:03: end of X-cor INFO @ Sat, 15 Jan 2022 21:15:03: #2 finished! INFO @ Sat, 15 Jan 2022 21:15:03: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 21:15:03: #2 alternative fragment length(s) may be 0,23,49,95,130,189,241,303,346,363,378,427,432,435,443,467,475,491,547,568,579 bps INFO @ Sat, 15 Jan 2022 21:15:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245517/SRX8245517.20_model.r WARNING @ Sat, 15 Jan 2022 21:15:03: #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 21:15:03: #2 You may need to consider one of the other alternative d(s): 0,23,49,95,130,189,241,303,346,363,378,427,432,435,443,467,475,491,547,568,579 WARNING @ Sat, 15 Jan 2022 21:15:03: #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 21:15:03: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:15:03: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 /var/spool/uge/at163/job_scripts/14520766: line 297: 92295 Terminated MACS $i /var/spool/uge/at163/job_scripts/14520766: line 297: 93972 Terminated MACS $i /var/spool/uge/at163/job_scripts/14520766: line 297: 94670 Terminated MACS $i ls: cannot access SRX8245517.05.bed: No such file or directory mv: cannot stat ‘SRX8245517.05.bed’: No such file or directory mv: cannot stat ‘SRX8245517.05.bb’: No such file or directory ls: cannot access SRX8245517.10.bed: No such file or directory mv: cannot stat ‘SRX8245517.10.bed’: No such file or directory mv: cannot stat ‘SRX8245517.10.bb’: No such file or directory ls: cannot access SRX8245517.20.bed: No such file or directory mv: cannot stat ‘SRX8245517.20.bed’: No such file or directory mv: cannot stat ‘SRX8245517.20.bb’: No such file or directory