Job ID = 14520871 SRX = SRX8245549 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 11669242 spots for SRR11684760/SRR11684760.sra Written 11669242 spots for SRR11684760/SRR11684760.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: 00:06:44 11669242 reads; of these: 11669242 (100.00%) were paired; of these: 6025996 (51.64%) aligned concordantly 0 times 4996798 (42.82%) aligned concordantly exactly 1 time 646448 (5.54%) aligned concordantly >1 times ---- 6025996 pairs aligned concordantly 0 times; of these: 59255 (0.98%) aligned discordantly 1 time ---- 5966741 pairs aligned 0 times concordantly or discordantly; of these: 11933482 mates make up the pairs; of these: 6548204 (54.87%) aligned 0 times 4706607 (39.44%) aligned exactly 1 time 678671 (5.69%) aligned >1 times 71.94% overall alignment rate Time searching: 00:06:44 Overall time: 00:06:44 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] 127544 / 5701571 = 0.0224 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 20:21:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245549/SRX8245549.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245549/SRX8245549.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245549/SRX8245549.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245549/SRX8245549.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 20:21:05: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:21:05: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:21:10: 1000000 INFO @ Sat, 15 Jan 2022 20:21:15: 2000000 INFO @ Sat, 15 Jan 2022 20:21:20: 3000000 INFO @ Sat, 15 Jan 2022 20:21:26: 4000000 INFO @ Sat, 15 Jan 2022 20:21:31: 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 20:21:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245549/SRX8245549.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245549/SRX8245549.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245549/SRX8245549.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245549/SRX8245549.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 20:21:35: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:21:35: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:21:36: 6000000 INFO @ Sat, 15 Jan 2022 20:21:41: 1000000 INFO @ Sat, 15 Jan 2022 20:21:42: 7000000 INFO @ Sat, 15 Jan 2022 20:21:47: 2000000 INFO @ Sat, 15 Jan 2022 20:21:49: 8000000 INFO @ Sat, 15 Jan 2022 20:21:54: 3000000 INFO @ Sat, 15 Jan 2022 20:21:55: 9000000 INFO @ Sat, 15 Jan 2022 20:22:00: 4000000 INFO @ Sat, 15 Jan 2022 20:22:01: 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 20:22:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245549/SRX8245549.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245549/SRX8245549.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245549/SRX8245549.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245549/SRX8245549.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 20:22:05: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:22:05: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:22:06: 5000000 INFO @ Sat, 15 Jan 2022 20:22:08: 11000000 INFO @ Sat, 15 Jan 2022 20:22:12: 1000000 INFO @ Sat, 15 Jan 2022 20:22:13: 6000000 INFO @ Sat, 15 Jan 2022 20:22:15: 12000000 INFO @ Sat, 15 Jan 2022 20:22:19: 2000000 INFO @ Sat, 15 Jan 2022 20:22:19: 7000000 INFO @ Sat, 15 Jan 2022 20:22:21: 13000000 INFO @ Sat, 15 Jan 2022 20:22:25: 3000000 INFO @ Sat, 15 Jan 2022 20:22:26: 8000000 INFO @ Sat, 15 Jan 2022 20:22:28: 14000000 INFO @ Sat, 15 Jan 2022 20:22:32: 4000000 INFO @ Sat, 15 Jan 2022 20:22:33: 9000000 INFO @ Sat, 15 Jan 2022 20:22:35: 15000000 INFO @ Sat, 15 Jan 2022 20:22:39: 5000000 INFO @ Sat, 15 Jan 2022 20:22:40: 10000000 INFO @ Sat, 15 Jan 2022 20:22:42: 16000000 INFO @ Sat, 15 Jan 2022 20:22:45: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:22:45: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:22:45: #1 total tags in treatment: 5515983 INFO @ Sat, 15 Jan 2022 20:22:45: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:22:45: #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 20:22:45: #1 tags after filtering in treatment: 3848773 INFO @ Sat, 15 Jan 2022 20:22:45: #1 Redundant rate of treatment: 0.30 INFO @ Sat, 15 Jan 2022 20:22:45: #1 finished! INFO @ Sat, 15 Jan 2022 20:22:45: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:22:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:22:46: #2 number of paired peaks: 165 WARNING @ Sat, 15 Jan 2022 20:22:46: 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 20:22:46: start model_add_line... INFO @ Sat, 15 Jan 2022 20:22:46: 6000000 INFO @ Sat, 15 Jan 2022 20:22:46: start X-correlation... INFO @ Sat, 15 Jan 2022 20:22:46: end of X-cor INFO @ Sat, 15 Jan 2022 20:22:46: #2 finished! INFO @ Sat, 15 Jan 2022 20:22:46: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 20:22:46: #2 alternative fragment length(s) may be 0,21,54,85,104,118,128,176,214,229,262,285,302,319,345,405,435,475,501,529,550,593 bps INFO @ Sat, 15 Jan 2022 20:22:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245549/SRX8245549.05_model.r WARNING @ Sat, 15 Jan 2022 20:22:46: #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 20:22:46: #2 You may need to consider one of the other alternative d(s): 0,21,54,85,104,118,128,176,214,229,262,285,302,319,345,405,435,475,501,529,550,593 WARNING @ Sat, 15 Jan 2022 20:22:46: #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 20:22:46: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:22:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:22:46: 11000000 INFO @ Sat, 15 Jan 2022 20:22:52: 7000000 INFO @ Sat, 15 Jan 2022 20:22:53: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:22:59: 8000000 INFO @ Sat, 15 Jan 2022 20:22:59: 13000000 INFO @ Sat, 15 Jan 2022 20:23:05: 9000000 INFO @ Sat, 15 Jan 2022 20:23:06: 14000000 BigWig に変換しました。 /var/spool/uge/at150/job_scripts/14520871: line 297: 25598 Terminated MACS $i /var/spool/uge/at150/job_scripts/14520871: line 297: 25702 Terminated MACS $i /var/spool/uge/at150/job_scripts/14520871: line 297: 26802 Terminated MACS $i ls: cannot access SRX8245549.05.bed: No such file or directory mv: cannot stat ‘SRX8245549.05.bed’: No such file or directory mv: cannot stat ‘SRX8245549.05.bb’: No such file or directory ls: cannot access SRX8245549.10.bed: No such file or directory mv: cannot stat ‘SRX8245549.10.bed’: No such file or directory mv: cannot stat ‘SRX8245549.10.bb’: No such file or directory ls: cannot access SRX8245549.20.bed: No such file or directory mv: cannot stat ‘SRX8245549.20.bed’: No such file or directory mv: cannot stat ‘SRX8245549.20.bb’: No such file or directory