Job ID = 14520748 SRX = SRX8245509 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 9380521 spots for SRR11684720/SRR11684720.sra Written 9380521 spots for SRR11684720/SRR11684720.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: 00:06:35 9380521 reads; of these: 9380521 (100.00%) were paired; of these: 5200501 (55.44%) aligned concordantly 0 times 3832875 (40.86%) aligned concordantly exactly 1 time 347145 (3.70%) aligned concordantly >1 times ---- 5200501 pairs aligned concordantly 0 times; of these: 115209 (2.22%) aligned discordantly 1 time ---- 5085292 pairs aligned 0 times concordantly or discordantly; of these: 10170584 mates make up the pairs; of these: 6586439 (64.76%) aligned 0 times 3195532 (31.42%) aligned exactly 1 time 388613 (3.82%) aligned >1 times 64.89% overall alignment rate Time searching: 00:06:35 Overall time: 00:06:35 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] 324248 / 4294463 = 0.0755 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 19:57:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245509/SRX8245509.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245509/SRX8245509.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245509/SRX8245509.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245509/SRX8245509.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 19:57:34: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:57:34: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:57:42: 1000000 INFO @ Sat, 15 Jan 2022 19:57:50: 2000000 INFO @ Sat, 15 Jan 2022 19:57:57: 3000000 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 19:58:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245509/SRX8245509.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245509/SRX8245509.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245509/SRX8245509.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245509/SRX8245509.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 19:58:04: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:58:04: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:58:04: 4000000 INFO @ Sat, 15 Jan 2022 19:58:11: 1000000 INFO @ Sat, 15 Jan 2022 19:58:11: 5000000 INFO @ Sat, 15 Jan 2022 19:58:18: 2000000 INFO @ Sat, 15 Jan 2022 19:58:19: 6000000 INFO @ Sat, 15 Jan 2022 19:58:25: 3000000 INFO @ Sat, 15 Jan 2022 19:58:26: 7000000 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 19:58:31: 4000000 INFO @ Sat, 15 Jan 2022 19:58:33: 8000000 INFO @ Sat, 15 Jan 2022 19:58:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245509/SRX8245509.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245509/SRX8245509.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245509/SRX8245509.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245509/SRX8245509.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 19:58:34: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:58:34: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:58:38: 5000000 INFO @ Sat, 15 Jan 2022 19:58:41: 9000000 INFO @ Sat, 15 Jan 2022 19:58:41: 1000000 INFO @ Sat, 15 Jan 2022 19:58:45: 6000000 INFO @ Sat, 15 Jan 2022 19:58:48: 10000000 INFO @ Sat, 15 Jan 2022 19:58:48: 2000000 INFO @ Sat, 15 Jan 2022 19:58:52: 7000000 INFO @ Sat, 15 Jan 2022 19:58:55: 3000000 INFO @ Sat, 15 Jan 2022 19:58:56: 11000000 INFO @ Sat, 15 Jan 2022 19:58:59: 8000000 INFO @ Sat, 15 Jan 2022 19:59:00: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 19:59:00: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 19:59:00: #1 total tags in treatment: 3859297 INFO @ Sat, 15 Jan 2022 19:59:00: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:59:00: #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 19:59:00: #1 tags after filtering in treatment: 2636531 INFO @ Sat, 15 Jan 2022 19:59:00: #1 Redundant rate of treatment: 0.32 INFO @ Sat, 15 Jan 2022 19:59:00: #1 finished! INFO @ Sat, 15 Jan 2022 19:59:00: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:59:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:59:00: #2 number of paired peaks: 172 WARNING @ Sat, 15 Jan 2022 19:59:00: 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 19:59:00: start model_add_line... INFO @ Sat, 15 Jan 2022 19:59:00: start X-correlation... INFO @ Sat, 15 Jan 2022 19:59:00: end of X-cor INFO @ Sat, 15 Jan 2022 19:59:00: #2 finished! INFO @ Sat, 15 Jan 2022 19:59:00: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 19:59:00: #2 alternative fragment length(s) may be 0,15,42,60,92,97,123,144,172,191,218,239,281,286,316,373,384,417,469,528,557,563,571,589,591 bps INFO @ Sat, 15 Jan 2022 19:59:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245509/SRX8245509.05_model.r WARNING @ Sat, 15 Jan 2022 19:59:00: #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 19:59:00: #2 You may need to consider one of the other alternative d(s): 0,15,42,60,92,97,123,144,172,191,218,239,281,286,316,373,384,417,469,528,557,563,571,589,591 WARNING @ Sat, 15 Jan 2022 19:59:00: #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 19:59:00: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:59:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:59:02: 4000000 INFO @ Sat, 15 Jan 2022 19:59:06: 9000000 INFO @ Sat, 15 Jan 2022 19:59:09: 5000000 INFO @ Sat, 15 Jan 2022 19:59:12: 10000000 INFO @ Sat, 15 Jan 2022 19:59:15: 6000000 INFO @ Sat, 15 Jan 2022 19:59:19: 11000000 INFO @ Sat, 15 Jan 2022 19:59:23: 7000000 INFO @ Sat, 15 Jan 2022 19:59:23: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 19:59:23: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 19:59:23: #1 total tags in treatment: 3859297 INFO @ Sat, 15 Jan 2022 19:59:23: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:59:23: #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 19:59:23: #1 tags after filtering in treatment: 2636531 INFO @ Sat, 15 Jan 2022 19:59:23: #1 Redundant rate of treatment: 0.32 INFO @ Sat, 15 Jan 2022 19:59:23: #1 finished! INFO @ Sat, 15 Jan 2022 19:59:23: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:59:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:59:24: #2 number of paired peaks: 172 WARNING @ Sat, 15 Jan 2022 19:59:24: 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 19:59:24: start model_add_line... INFO @ Sat, 15 Jan 2022 19:59:24: start X-correlation... INFO @ Sat, 15 Jan 2022 19:59:24: end of X-cor INFO @ Sat, 15 Jan 2022 19:59:24: #2 finished! INFO @ Sat, 15 Jan 2022 19:59:24: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 19:59:24: #2 alternative fragment length(s) may be 0,15,42,60,92,97,123,144,172,191,218,239,281,286,316,373,384,417,469,528,557,563,571,589,591 bps INFO @ Sat, 15 Jan 2022 19:59:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245509/SRX8245509.10_model.r WARNING @ Sat, 15 Jan 2022 19:59:24: #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 19:59:24: #2 You may need to consider one of the other alternative d(s): 0,15,42,60,92,97,123,144,172,191,218,239,281,286,316,373,384,417,469,528,557,563,571,589,591 WARNING @ Sat, 15 Jan 2022 19:59:24: #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 19:59:24: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:59:24: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 19:59:29: 8000000 INFO @ Sat, 15 Jan 2022 19:59:36: 9000000 BigWig に変換しました。 /var/spool/uge/at085/job_scripts/14520748: line 297: 28453 Terminated MACS $i /var/spool/uge/at085/job_scripts/14520748: line 297: 28725 Terminated MACS $i /var/spool/uge/at085/job_scripts/14520748: line 297: 28843 Terminated MACS $i ls: cannot access SRX8245509.05.bed: No such file or directory mv: cannot stat ‘SRX8245509.05.bed’: No such file or directory mv: cannot stat ‘SRX8245509.05.bb’: No such file or directory ls: cannot access SRX8245509.10.bed: No such file or directory mv: cannot stat ‘SRX8245509.10.bed’: No such file or directory mv: cannot stat ‘SRX8245509.10.bb’: No such file or directory ls: cannot access SRX8245509.20.bed: No such file or directory mv: cannot stat ‘SRX8245509.20.bed’: No such file or directory mv: cannot stat ‘SRX8245509.20.bb’: No such file or directory