Job ID = 14521135 SRX = SRX8245361 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 12034945 spots for SRR11684572/SRR11684572.sra Written 12034945 spots for SRR11684572/SRR11684572.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: 00:06:03 12034945 reads; of these: 12034945 (100.00%) were paired; of these: 6014956 (49.98%) aligned concordantly 0 times 5189262 (43.12%) aligned concordantly exactly 1 time 830727 (6.90%) aligned concordantly >1 times ---- 6014956 pairs aligned concordantly 0 times; of these: 140410 (2.33%) aligned discordantly 1 time ---- 5874546 pairs aligned 0 times concordantly or discordantly; of these: 11749092 mates make up the pairs; of these: 7537142 (64.15%) aligned 0 times 3534487 (30.08%) aligned exactly 1 time 677463 (5.77%) aligned >1 times 68.69% overall alignment rate Time searching: 00:06:03 Overall time: 00:06:03 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] 467328 / 6159603 = 0.0759 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 20:46:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245361/SRX8245361.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245361/SRX8245361.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245361/SRX8245361.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245361/SRX8245361.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 20:46:05: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:46:05: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:46:11: 1000000 INFO @ Sat, 15 Jan 2022 20:46:16: 2000000 INFO @ Sat, 15 Jan 2022 20:46:21: 3000000 INFO @ Sat, 15 Jan 2022 20:46:26: 4000000 INFO @ Sat, 15 Jan 2022 20:46:31: 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 20:46:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245361/SRX8245361.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245361/SRX8245361.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245361/SRX8245361.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245361/SRX8245361.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 20:46:35: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:46:35: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:46:36: 6000000 INFO @ Sat, 15 Jan 2022 20:46:42: 1000000 INFO @ Sat, 15 Jan 2022 20:46:42: 7000000 INFO @ Sat, 15 Jan 2022 20:46:48: 8000000 INFO @ Sat, 15 Jan 2022 20:46:49: 2000000 INFO @ Sat, 15 Jan 2022 20:46:54: 9000000 INFO @ Sat, 15 Jan 2022 20:46:55: 3000000 INFO @ Sat, 15 Jan 2022 20:47:00: 10000000 INFO @ Sat, 15 Jan 2022 20:47:02: 4000000 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 20:47:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245361/SRX8245361.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245361/SRX8245361.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245361/SRX8245361.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245361/SRX8245361.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 20:47:05: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:47:05: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:47:07: 11000000 INFO @ Sat, 15 Jan 2022 20:47:09: 5000000 INFO @ Sat, 15 Jan 2022 20:47:12: 1000000 INFO @ Sat, 15 Jan 2022 20:47:13: 12000000 INFO @ Sat, 15 Jan 2022 20:47:15: 6000000 INFO @ Sat, 15 Jan 2022 20:47:18: 2000000 INFO @ Sat, 15 Jan 2022 20:47:19: 13000000 INFO @ Sat, 15 Jan 2022 20:47:21: 7000000 INFO @ Sat, 15 Jan 2022 20:47:24: 3000000 INFO @ Sat, 15 Jan 2022 20:47:25: 14000000 INFO @ Sat, 15 Jan 2022 20:47:27: 8000000 INFO @ Sat, 15 Jan 2022 20:47:30: 4000000 INFO @ Sat, 15 Jan 2022 20:47:31: 15000000 INFO @ Sat, 15 Jan 2022 20:47:33: 9000000 INFO @ Sat, 15 Jan 2022 20:47:35: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:47:35: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:47:35: #1 total tags in treatment: 5557189 INFO @ Sat, 15 Jan 2022 20:47:35: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:47:35: #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 20:47:35: #1 tags after filtering in treatment: 3518367 INFO @ Sat, 15 Jan 2022 20:47:35: #1 Redundant rate of treatment: 0.37 INFO @ Sat, 15 Jan 2022 20:47:35: #1 finished! INFO @ Sat, 15 Jan 2022 20:47:35: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:47:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:47:35: #2 number of paired peaks: 168 WARNING @ Sat, 15 Jan 2022 20:47:35: Fewer paired peaks (168) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 168 pairs to build model! INFO @ Sat, 15 Jan 2022 20:47:35: start model_add_line... INFO @ Sat, 15 Jan 2022 20:47:35: start X-correlation... INFO @ Sat, 15 Jan 2022 20:47:35: end of X-cor INFO @ Sat, 15 Jan 2022 20:47:35: #2 finished! INFO @ Sat, 15 Jan 2022 20:47:35: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 20:47:35: #2 alternative fragment length(s) may be 0,58,78,117,123,136,203,248,291,316,365,424,429,457,470,505,525,551,581 bps INFO @ Sat, 15 Jan 2022 20:47:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245361/SRX8245361.05_model.r WARNING @ Sat, 15 Jan 2022 20:47:35: #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 20:47:35: #2 You may need to consider one of the other alternative d(s): 0,58,78,117,123,136,203,248,291,316,365,424,429,457,470,505,525,551,581 WARNING @ Sat, 15 Jan 2022 20:47:35: #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 20:47:35: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:47:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:47:36: 5000000 INFO @ Sat, 15 Jan 2022 20:47:40: 10000000 INFO @ Sat, 15 Jan 2022 20:47:42: 6000000 INFO @ Sat, 15 Jan 2022 20:47:46: 11000000 INFO @ Sat, 15 Jan 2022 20:47:48: 7000000 INFO @ Sat, 15 Jan 2022 20:47:52: 12000000 INFO @ Sat, 15 Jan 2022 20:47:54: 8000000 INFO @ Sat, 15 Jan 2022 20:47:58: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:48:00: 9000000 INFO @ Sat, 15 Jan 2022 20:48:04: 14000000 INFO @ Sat, 15 Jan 2022 20:48:06: 10000000 INFO @ Sat, 15 Jan 2022 20:48:10: 15000000 BigWig に変換しました。 /var/spool/uge/at143/job_scripts/14521135: line 297: 8719 Terminated MACS $i /var/spool/uge/at143/job_scripts/14521135: line 297: 8871 Terminated MACS $i /var/spool/uge/at143/job_scripts/14521135: line 297: 9004 Terminated MACS $i ls: cannot access SRX8245361.05.bed: No such file or directory mv: cannot stat ‘SRX8245361.05.bed’: No such file or directory mv: cannot stat ‘SRX8245361.05.bb’: No such file or directory ls: cannot access SRX8245361.10.bed: No such file or directory mv: cannot stat ‘SRX8245361.10.bed’: No such file or directory mv: cannot stat ‘SRX8245361.10.bb’: No such file or directory ls: cannot access SRX8245361.20.bed: No such file or directory mv: cannot stat ‘SRX8245361.20.bed’: No such file or directory mv: cannot stat ‘SRX8245361.20.bb’: No such file or directory