Job ID = 14521231 SRX = SRX8245386 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 7002853 spots for SRR11684597/SRR11684597.sra Written 7002853 spots for SRR11684597/SRR11684597.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: 00:03:58 7002853 reads; of these: 7002853 (100.00%) were paired; of these: 3511533 (50.14%) aligned concordantly 0 times 3010785 (42.99%) aligned concordantly exactly 1 time 480535 (6.86%) aligned concordantly >1 times ---- 3511533 pairs aligned concordantly 0 times; of these: 4858 (0.14%) aligned discordantly 1 time ---- 3506675 pairs aligned 0 times concordantly or discordantly; of these: 7013350 mates make up the pairs; of these: 4480255 (63.88%) aligned 0 times 2176686 (31.04%) aligned exactly 1 time 356409 (5.08%) aligned >1 times 68.01% overall alignment rate Time searching: 00:03:58 Overall time: 00:03:58 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_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] 154650 / 3495587 = 0.0442 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 20:47:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245386/SRX8245386.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245386/SRX8245386.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245386/SRX8245386.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245386/SRX8245386.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 20:47:57: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:47:57: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:48:03: 1000000 INFO @ Sat, 15 Jan 2022 20:48:10: 2000000 INFO @ Sat, 15 Jan 2022 20:48:16: 3000000 INFO @ Sat, 15 Jan 2022 20:48:22: 4000000 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 20:48:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245386/SRX8245386.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245386/SRX8245386.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245386/SRX8245386.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245386/SRX8245386.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 20:48:27: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:48:27: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:48:29: 5000000 INFO @ Sat, 15 Jan 2022 20:48:34: 1000000 INFO @ Sat, 15 Jan 2022 20:48:36: 6000000 INFO @ Sat, 15 Jan 2022 20:48:41: 2000000 INFO @ Sat, 15 Jan 2022 20:48:43: 7000000 INFO @ Sat, 15 Jan 2022 20:48:48: 3000000 INFO @ Sat, 15 Jan 2022 20:48:50: 8000000 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 20:48:55: 4000000 INFO @ Sat, 15 Jan 2022 20:48:57: 9000000 INFO @ Sat, 15 Jan 2022 20:48:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245386/SRX8245386.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245386/SRX8245386.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245386/SRX8245386.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245386/SRX8245386.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 20:48:57: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:48:57: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:48:58: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:48:58: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:48:58: #1 total tags in treatment: 3337504 INFO @ Sat, 15 Jan 2022 20:48:58: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:48:58: #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 20:48:58: #1 tags after filtering in treatment: 2345939 INFO @ Sat, 15 Jan 2022 20:48:58: #1 Redundant rate of treatment: 0.30 INFO @ Sat, 15 Jan 2022 20:48:58: #1 finished! INFO @ Sat, 15 Jan 2022 20:48:58: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:48:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:48:58: #2 number of paired peaks: 176 WARNING @ Sat, 15 Jan 2022 20:48:58: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Sat, 15 Jan 2022 20:48:58: start model_add_line... INFO @ Sat, 15 Jan 2022 20:48:58: start X-correlation... INFO @ Sat, 15 Jan 2022 20:48:58: end of X-cor INFO @ Sat, 15 Jan 2022 20:48:58: #2 finished! INFO @ Sat, 15 Jan 2022 20:48:58: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 20:48:58: #2 alternative fragment length(s) may be 0,12,89,125,151,167,188,212,228,250,511,572,595 bps INFO @ Sat, 15 Jan 2022 20:48:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245386/SRX8245386.05_model.r WARNING @ Sat, 15 Jan 2022 20:48:58: #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 20:48:58: #2 You may need to consider one of the other alternative d(s): 0,12,89,125,151,167,188,212,228,250,511,572,595 WARNING @ Sat, 15 Jan 2022 20:48:58: #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 20:48:58: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:48:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:49:02: 5000000 INFO @ Sat, 15 Jan 2022 20:49:04: 1000000 INFO @ Sat, 15 Jan 2022 20:49:10: 6000000 INFO @ Sat, 15 Jan 2022 20:49:11: 2000000 INFO @ Sat, 15 Jan 2022 20:49:17: 7000000 INFO @ Sat, 15 Jan 2022 20:49:18: 3000000 INFO @ Sat, 15 Jan 2022 20:49:24: 8000000 INFO @ Sat, 15 Jan 2022 20:49:24: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:49:31: 9000000 INFO @ Sat, 15 Jan 2022 20:49:31: 5000000 INFO @ Sat, 15 Jan 2022 20:49:33: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:49:33: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:49:33: #1 total tags in treatment: 3337504 INFO @ Sat, 15 Jan 2022 20:49:33: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:49:33: #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 20:49:33: #1 tags after filtering in treatment: 2345939 INFO @ Sat, 15 Jan 2022 20:49:33: #1 Redundant rate of treatment: 0.30 INFO @ Sat, 15 Jan 2022 20:49:33: #1 finished! INFO @ Sat, 15 Jan 2022 20:49:33: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:49:33: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:49:33: #2 number of paired peaks: 176 WARNING @ Sat, 15 Jan 2022 20:49:33: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Sat, 15 Jan 2022 20:49:33: start model_add_line... INFO @ Sat, 15 Jan 2022 20:49:33: start X-correlation... INFO @ Sat, 15 Jan 2022 20:49:33: end of X-cor INFO @ Sat, 15 Jan 2022 20:49:33: #2 finished! INFO @ Sat, 15 Jan 2022 20:49:33: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 20:49:33: #2 alternative fragment length(s) may be 0,12,89,125,151,167,188,212,228,250,511,572,595 bps INFO @ Sat, 15 Jan 2022 20:49:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245386/SRX8245386.10_model.r WARNING @ Sat, 15 Jan 2022 20:49:33: #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 20:49:33: #2 You may need to consider one of the other alternative d(s): 0,12,89,125,151,167,188,212,228,250,511,572,595 WARNING @ Sat, 15 Jan 2022 20:49:33: #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 20:49:33: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:49:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:49:37: 6000000 BigWig に変換しました。 /var/spool/uge/at157/job_scripts/14521231: line 297: 110265 Terminated MACS $i /var/spool/uge/at157/job_scripts/14521231: line 297: 111439 Terminated MACS $i /var/spool/uge/at157/job_scripts/14521231: line 297: 111713 Terminated MACS $i ls: cannot access SRX8245386.05.bed: No such file or directory mv: cannot stat ‘SRX8245386.05.bed’: No such file or directory mv: cannot stat ‘SRX8245386.05.bb’: No such file or directory ls: cannot access SRX8245386.10.bed: No such file or directory mv: cannot stat ‘SRX8245386.10.bed’: No such file or directory mv: cannot stat ‘SRX8245386.10.bb’: No such file or directory ls: cannot access SRX8245386.20.bed: No such file or directory mv: cannot stat ‘SRX8245386.20.bed’: No such file or directory mv: cannot stat ‘SRX8245386.20.bb’: No such file or directory