Job ID = 14520759 SRX = SRX8245510 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 7716501 spots for SRR11684721/SRR11684721.sra Written 7716501 spots for SRR11684721/SRR11684721.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: 00:04:12 7716501 reads; of these: 7716501 (100.00%) were paired; of these: 4379660 (56.76%) aligned concordantly 0 times 3037770 (39.37%) aligned concordantly exactly 1 time 299071 (3.88%) aligned concordantly >1 times ---- 4379660 pairs aligned concordantly 0 times; of these: 25103 (0.57%) aligned discordantly 1 time ---- 4354557 pairs aligned 0 times concordantly or discordantly; of these: 8709114 mates make up the pairs; of these: 4829474 (55.45%) aligned 0 times 3479971 (39.96%) aligned exactly 1 time 399669 (4.59%) aligned >1 times 68.71% overall alignment rate Time searching: 00:04:12 Overall time: 00:04:12 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] 64883 / 3361368 = 0.0193 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 19:57:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245510/SRX8245510.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245510/SRX8245510.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245510/SRX8245510.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245510/SRX8245510.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 19:57:40: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:57:40: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:57:45: 1000000 INFO @ Sat, 15 Jan 2022 19:57:49: 2000000 INFO @ Sat, 15 Jan 2022 19:57:54: 3000000 INFO @ Sat, 15 Jan 2022 19:57:58: 4000000 INFO @ Sat, 15 Jan 2022 19:58:03: 5000000 INFO @ Sat, 15 Jan 2022 19:58:08: 6000000 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 19:58:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245510/SRX8245510.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245510/SRX8245510.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245510/SRX8245510.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245510/SRX8245510.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 19:58:10: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:58:10: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:58:13: 7000000 INFO @ Sat, 15 Jan 2022 19:58:15: 1000000 INFO @ Sat, 15 Jan 2022 19:58:18: 8000000 INFO @ Sat, 15 Jan 2022 19:58:20: 2000000 INFO @ Sat, 15 Jan 2022 19:58:23: 9000000 INFO @ Sat, 15 Jan 2022 19:58:25: 3000000 INFO @ Sat, 15 Jan 2022 19:58:28: 10000000 INFO @ Sat, 15 Jan 2022 19:58:30: 4000000 INFO @ Sat, 15 Jan 2022 19:58:31: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 19:58:31: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 19:58:31: #1 total tags in treatment: 3272134 INFO @ Sat, 15 Jan 2022 19:58:31: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:58:31: #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 19:58:31: #1 tags after filtering in treatment: 2428059 INFO @ Sat, 15 Jan 2022 19:58:31: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 15 Jan 2022 19:58:31: #1 finished! INFO @ Sat, 15 Jan 2022 19:58:31: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:58:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:58:31: #2 number of paired peaks: 172 WARNING @ Sat, 15 Jan 2022 19:58:31: Fewer paired peaks (172) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 172 pairs to build model! INFO @ Sat, 15 Jan 2022 19:58:31: start model_add_line... INFO @ Sat, 15 Jan 2022 19:58:31: start X-correlation... INFO @ Sat, 15 Jan 2022 19:58:31: end of X-cor INFO @ Sat, 15 Jan 2022 19:58:31: #2 finished! INFO @ Sat, 15 Jan 2022 19:58:31: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 19:58:31: #2 alternative fragment length(s) may be 0,36,60,66,86,111,138,159,189,219,235,255,297,410,443,467,470,493,540,543,565,585 bps INFO @ Sat, 15 Jan 2022 19:58:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245510/SRX8245510.05_model.r WARNING @ Sat, 15 Jan 2022 19:58:31: #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 19:58:31: #2 You may need to consider one of the other alternative d(s): 0,36,60,66,86,111,138,159,189,219,235,255,297,410,443,467,470,493,540,543,565,585 WARNING @ Sat, 15 Jan 2022 19:58:31: #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 19:58:31: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:58:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:58:35: 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 19:58:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245510/SRX8245510.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245510/SRX8245510.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245510/SRX8245510.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245510/SRX8245510.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 19:58:40: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:58:40: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:58:40: 6000000 INFO @ Sat, 15 Jan 2022 19:58:45: 1000000 INFO @ Sat, 15 Jan 2022 19:58:46: 7000000 INFO @ Sat, 15 Jan 2022 19:58:50: 2000000 INFO @ Sat, 15 Jan 2022 19:58:51: 8000000 INFO @ Sat, 15 Jan 2022 19:58:56: 3000000 INFO @ Sat, 15 Jan 2022 19:58:56: 9000000 INFO @ Sat, 15 Jan 2022 19:59:01: 4000000 INFO @ Sat, 15 Jan 2022 19:59:01: 10000000 INFO @ Sat, 15 Jan 2022 19:59:03: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 19:59:03: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 19:59:03: #1 total tags in treatment: 3272134 INFO @ Sat, 15 Jan 2022 19:59:03: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:59:03: #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 19:59:04: #1 tags after filtering in treatment: 2428059 INFO @ Sat, 15 Jan 2022 19:59:04: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 15 Jan 2022 19:59:04: #1 finished! INFO @ Sat, 15 Jan 2022 19:59:04: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:59:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:59:04: #2 number of paired peaks: 172 WARNING @ Sat, 15 Jan 2022 19:59:04: Fewer paired peaks (172) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 172 pairs to build model! INFO @ Sat, 15 Jan 2022 19:59:04: start model_add_line... INFO @ Sat, 15 Jan 2022 19:59:04: start X-correlation... INFO @ Sat, 15 Jan 2022 19:59:04: end of X-cor INFO @ Sat, 15 Jan 2022 19:59:04: #2 finished! INFO @ Sat, 15 Jan 2022 19:59:04: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 19:59:04: #2 alternative fragment length(s) may be 0,36,60,66,86,111,138,159,189,219,235,255,297,410,443,467,470,493,540,543,565,585 bps INFO @ Sat, 15 Jan 2022 19:59:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245510/SRX8245510.10_model.r WARNING @ Sat, 15 Jan 2022 19:59:04: #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 19:59:04: #2 You may need to consider one of the other alternative d(s): 0,36,60,66,86,111,138,159,189,219,235,255,297,410,443,467,470,493,540,543,565,585 WARNING @ Sat, 15 Jan 2022 19:59:04: #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 19:59:04: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:59:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:59:06: 5000000 INFO @ Sat, 15 Jan 2022 19:59:11: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 19:59:16: 7000000 INFO @ Sat, 15 Jan 2022 19:59:21: 8000000 BigWig に変換しました。 /var/spool/uge/at140/job_scripts/14520759: line 297: 1270 Terminated MACS $i /var/spool/uge/at140/job_scripts/14520759: line 297: 2373 Terminated MACS $i /var/spool/uge/at140/job_scripts/14520759: line 297: 2469 Terminated MACS $i ls: cannot access SRX8245510.05.bed: No such file or directory mv: cannot stat ‘SRX8245510.05.bed’: No such file or directory mv: cannot stat ‘SRX8245510.05.bb’: No such file or directory ls: cannot access SRX8245510.10.bed: No such file or directory mv: cannot stat ‘SRX8245510.10.bed’: No such file or directory mv: cannot stat ‘SRX8245510.10.bb’: No such file or directory ls: cannot access SRX8245510.20.bed: No such file or directory mv: cannot stat ‘SRX8245510.20.bed’: No such file or directory mv: cannot stat ‘SRX8245510.20.bb’: No such file or directory