Job ID = 14520597 SRX = SRX11781075 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-01-15T10:25:20 prefetch.2.10.7: 1) Downloading 'SRR15481018'... 2022-01-15T10:25:20 prefetch.2.10.7: Downloading via HTTPS... 2022-01-15T10:25:43 prefetch.2.10.7: HTTPS download succeed 2022-01-15T10:25:44 prefetch.2.10.7: 'SRR15481018' is valid 2022-01-15T10:25:44 prefetch.2.10.7: 1) 'SRR15481018' was downloaded successfully 2022-01-15T10:25:44 prefetch.2.10.7: 'SRR15481018' has 0 unresolved dependencies Read 6481257 spots for SRR15481018/SRR15481018.sra Written 6481257 spots for SRR15481018/SRR15481018.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: 00:05:34 6481257 reads; of these: 6481257 (100.00%) were paired; of these: 984499 (15.19%) aligned concordantly 0 times 4691113 (72.38%) aligned concordantly exactly 1 time 805645 (12.43%) aligned concordantly >1 times ---- 984499 pairs aligned concordantly 0 times; of these: 69148 (7.02%) aligned discordantly 1 time ---- 915351 pairs aligned 0 times concordantly or discordantly; of these: 1830702 mates make up the pairs; of these: 1275771 (69.69%) aligned 0 times 456596 (24.94%) aligned exactly 1 time 98335 (5.37%) aligned >1 times 90.16% overall alignment rate Time searching: 00:05:34 Overall time: 00:05:34 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] 498942 / 5565433 = 0.0897 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 19:35:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781075/SRX11781075.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781075/SRX11781075.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781075/SRX11781075.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781075/SRX11781075.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 19:35:57: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:35:57: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:36:03: 1000000 INFO @ Sat, 15 Jan 2022 19:36:08: 2000000 INFO @ Sat, 15 Jan 2022 19:36:13: 3000000 INFO @ Sat, 15 Jan 2022 19:36:18: 4000000 INFO @ Sat, 15 Jan 2022 19:36:23: 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 19:36:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781075/SRX11781075.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781075/SRX11781075.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781075/SRX11781075.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781075/SRX11781075.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 19:36:27: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:36:27: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:36:29: 6000000 INFO @ Sat, 15 Jan 2022 19:36:33: 1000000 INFO @ Sat, 15 Jan 2022 19:36:34: 7000000 INFO @ Sat, 15 Jan 2022 19:36:39: 2000000 INFO @ Sat, 15 Jan 2022 19:36:40: 8000000 INFO @ Sat, 15 Jan 2022 19:36:45: 3000000 INFO @ Sat, 15 Jan 2022 19:36:46: 9000000 INFO @ Sat, 15 Jan 2022 19:36:51: 4000000 INFO @ Sat, 15 Jan 2022 19:36:52: 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 19:36:56: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 19:36:56: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 19:36:56: #1 total tags in treatment: 5000377 INFO @ Sat, 15 Jan 2022 19:36:56: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:36:56: #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 19:36:56: #1 tags after filtering in treatment: 3272065 INFO @ Sat, 15 Jan 2022 19:36:56: #1 Redundant rate of treatment: 0.35 INFO @ Sat, 15 Jan 2022 19:36:56: #1 finished! INFO @ Sat, 15 Jan 2022 19:36:56: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:36:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:36:56: #2 number of paired peaks: 165 WARNING @ Sat, 15 Jan 2022 19:36:56: Fewer paired peaks (165) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 165 pairs to build model! INFO @ Sat, 15 Jan 2022 19:36:56: start model_add_line... INFO @ Sat, 15 Jan 2022 19:36:56: start X-correlation... INFO @ Sat, 15 Jan 2022 19:36:56: end of X-cor INFO @ Sat, 15 Jan 2022 19:36:56: #2 finished! INFO @ Sat, 15 Jan 2022 19:36:56: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 19:36:56: #2 alternative fragment length(s) may be 0,46,99,151,183,219,247,252,255,258,307,324,346,365,368,421,456,497,522,542,577,591 bps INFO @ Sat, 15 Jan 2022 19:36:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781075/SRX11781075.05_model.r WARNING @ Sat, 15 Jan 2022 19:36:56: #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 19:36:56: #2 You may need to consider one of the other alternative d(s): 0,46,99,151,183,219,247,252,255,258,307,324,346,365,368,421,456,497,522,542,577,591 WARNING @ Sat, 15 Jan 2022 19:36:56: #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 19:36:56: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:36:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:36:56: 5000000 INFO @ Sat, 15 Jan 2022 19:36:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781075/SRX11781075.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781075/SRX11781075.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781075/SRX11781075.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781075/SRX11781075.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 19:36:57: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:36:57: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:37:03: 6000000 INFO @ Sat, 15 Jan 2022 19:37:04: 1000000 INFO @ Sat, 15 Jan 2022 19:37:09: 7000000 INFO @ Sat, 15 Jan 2022 19:37:11: 2000000 INFO @ Sat, 15 Jan 2022 19:37:15: 8000000 INFO @ Sat, 15 Jan 2022 19:37:18: 3000000 INFO @ Sat, 15 Jan 2022 19:37:22: 9000000 INFO @ Sat, 15 Jan 2022 19:37:24: 4000000 INFO @ Sat, 15 Jan 2022 19:37:28: 10000000 INFO @ Sat, 15 Jan 2022 19:37:31: 5000000 INFO @ Sat, 15 Jan 2022 19:37:32: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 19:37:32: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 19:37:32: #1 total tags in treatment: 5000377 INFO @ Sat, 15 Jan 2022 19:37:32: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:37:32: #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 19:37:33: #1 tags after filtering in treatment: 3272065 INFO @ Sat, 15 Jan 2022 19:37:33: #1 Redundant rate of treatment: 0.35 INFO @ Sat, 15 Jan 2022 19:37:33: #1 finished! INFO @ Sat, 15 Jan 2022 19:37:33: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:37:33: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:37:33: #2 number of paired peaks: 165 WARNING @ Sat, 15 Jan 2022 19:37:33: Fewer paired peaks (165) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 165 pairs to build model! INFO @ Sat, 15 Jan 2022 19:37:33: start model_add_line... INFO @ Sat, 15 Jan 2022 19:37:33: start X-correlation... INFO @ Sat, 15 Jan 2022 19:37:33: end of X-cor INFO @ Sat, 15 Jan 2022 19:37:33: #2 finished! INFO @ Sat, 15 Jan 2022 19:37:33: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 19:37:33: #2 alternative fragment length(s) may be 0,46,99,151,183,219,247,252,255,258,307,324,346,365,368,421,456,497,522,542,577,591 bps INFO @ Sat, 15 Jan 2022 19:37:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781075/SRX11781075.10_model.r WARNING @ Sat, 15 Jan 2022 19:37:33: #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 19:37:33: #2 You may need to consider one of the other alternative d(s): 0,46,99,151,183,219,247,252,255,258,307,324,346,365,368,421,456,497,522,542,577,591 WARNING @ Sat, 15 Jan 2022 19:37:33: #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 19:37:33: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:37:33: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 19:37:38: 6000000 BigWig に変換しました。 /var/spool/uge/at149/job_scripts/14520597: line 297: 76893 Terminated MACS $i /var/spool/uge/at149/job_scripts/14520597: line 297: 78005 Terminated MACS $i /var/spool/uge/at149/job_scripts/14520597: line 297: 78119 Terminated MACS $i ls: cannot access SRX11781075.05.bed: No such file or directory mv: cannot stat ‘SRX11781075.05.bed’: No such file or directory mv: cannot stat ‘SRX11781075.05.bb’: No such file or directory ls: cannot access SRX11781075.10.bed: No such file or directory mv: cannot stat ‘SRX11781075.10.bed’: No such file or directory mv: cannot stat ‘SRX11781075.10.bb’: No such file or directory ls: cannot access SRX11781075.20.bed: No such file or directory mv: cannot stat ‘SRX11781075.20.bed’: No such file or directory mv: cannot stat ‘SRX11781075.20.bb’: No such file or directory