Job ID = 14522129 SRX = SRX9786304 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 8587611 spots for SRR13362168/SRR13362168.sra Written 8587611 spots for SRR13362168/SRR13362168.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: 00:10:05 8587611 reads; of these: 8587611 (100.00%) were paired; of these: 1662220 (19.36%) aligned concordantly 0 times 6430303 (74.88%) aligned concordantly exactly 1 time 495088 (5.77%) aligned concordantly >1 times ---- 1662220 pairs aligned concordantly 0 times; of these: 197325 (11.87%) aligned discordantly 1 time ---- 1464895 pairs aligned 0 times concordantly or discordantly; of these: 2929790 mates make up the pairs; of these: 1901163 (64.89%) aligned 0 times 907607 (30.98%) aligned exactly 1 time 121020 (4.13%) aligned >1 times 88.93% overall alignment rate Time searching: 00:10:05 Overall time: 00:10:05 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] 544851 / 7122016 = 0.0765 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 22:32:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9786304/SRX9786304.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9786304/SRX9786304.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9786304/SRX9786304.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9786304/SRX9786304.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 22:32:49: #1 read tag files... INFO @ Sat, 15 Jan 2022 22:32:49: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 22:32:56: 1000000 INFO @ Sat, 15 Jan 2022 22:33:03: 2000000 INFO @ Sat, 15 Jan 2022 22:33:11: 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 22:33:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9786304/SRX9786304.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9786304/SRX9786304.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9786304/SRX9786304.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9786304/SRX9786304.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 22:33:19: #1 read tag files... INFO @ Sat, 15 Jan 2022 22:33:19: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 22:33:20: 4000000 INFO @ Sat, 15 Jan 2022 22:33:28: 1000000 INFO @ Sat, 15 Jan 2022 22:33:28: 5000000 INFO @ Sat, 15 Jan 2022 22:33:36: 6000000 INFO @ Sat, 15 Jan 2022 22:33:37: 2000000 INFO @ Sat, 15 Jan 2022 22:33:44: 7000000 INFO @ Sat, 15 Jan 2022 22:33:45: 3000000 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 22:33:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9786304/SRX9786304.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9786304/SRX9786304.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9786304/SRX9786304.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9786304/SRX9786304.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 22:33:49: #1 read tag files... INFO @ Sat, 15 Jan 2022 22:33:49: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 22:33:52: 8000000 INFO @ Sat, 15 Jan 2022 22:33:54: 4000000 INFO @ Sat, 15 Jan 2022 22:33:58: 1000000 INFO @ Sat, 15 Jan 2022 22:34:00: 9000000 INFO @ Sat, 15 Jan 2022 22:34:03: 5000000 INFO @ Sat, 15 Jan 2022 22:34:06: 2000000 INFO @ Sat, 15 Jan 2022 22:34:08: 10000000 INFO @ Sat, 15 Jan 2022 22:34:11: 6000000 INFO @ Sat, 15 Jan 2022 22:34:14: 3000000 INFO @ Sat, 15 Jan 2022 22:34:17: 11000000 INFO @ Sat, 15 Jan 2022 22:34:20: 7000000 INFO @ Sat, 15 Jan 2022 22:34:22: 4000000 INFO @ Sat, 15 Jan 2022 22:34:25: 12000000 INFO @ Sat, 15 Jan 2022 22:34:29: 8000000 INFO @ Sat, 15 Jan 2022 22:34:30: 5000000 INFO @ Sat, 15 Jan 2022 22:34:33: 13000000 INFO @ Sat, 15 Jan 2022 22:34:37: 9000000 INFO @ Sat, 15 Jan 2022 22:34:38: 6000000 INFO @ Sat, 15 Jan 2022 22:34:41: 14000000 INFO @ Sat, 15 Jan 2022 22:34:43: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 22:34:43: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 22:34:43: #1 total tags in treatment: 6386684 INFO @ Sat, 15 Jan 2022 22:34:43: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 22:34:43: #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 22:34:43: #1 tags after filtering in treatment: 3592664 INFO @ Sat, 15 Jan 2022 22:34:43: #1 Redundant rate of treatment: 0.44 INFO @ Sat, 15 Jan 2022 22:34:43: #1 finished! INFO @ Sat, 15 Jan 2022 22:34:43: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 22:34:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 22:34:43: #2 number of paired peaks: 171 WARNING @ Sat, 15 Jan 2022 22:34:43: Fewer paired peaks (171) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 171 pairs to build model! INFO @ Sat, 15 Jan 2022 22:34:43: start model_add_line... INFO @ Sat, 15 Jan 2022 22:34:43: start X-correlation... INFO @ Sat, 15 Jan 2022 22:34:43: end of X-cor INFO @ Sat, 15 Jan 2022 22:34:43: #2 finished! INFO @ Sat, 15 Jan 2022 22:34:43: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 22:34:43: #2 alternative fragment length(s) may be 0,13,40,69,120,150,167,186,212,231,254,289,310,340,361,389,417,472,490,504,535,554,574 bps INFO @ Sat, 15 Jan 2022 22:34:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX9786304/SRX9786304.05_model.r WARNING @ Sat, 15 Jan 2022 22:34:43: #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 22:34:43: #2 You may need to consider one of the other alternative d(s): 0,13,40,69,120,150,167,186,212,231,254,289,310,340,361,389,417,472,490,504,535,554,574 WARNING @ Sat, 15 Jan 2022 22:34:43: #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 22:34:43: #3 Call peaks... INFO @ Sat, 15 Jan 2022 22:34:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 22:34:46: 7000000 INFO @ Sat, 15 Jan 2022 22:34:46: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 22:34:54: 8000000 INFO @ Sat, 15 Jan 2022 22:34:55: 11000000 INFO @ Sat, 15 Jan 2022 22:35:01: 9000000 BigWig に変換しました。 /var/spool/uge/it020/job_scripts/14522129: line 297: 5473 Terminated MACS $i /var/spool/uge/it020/job_scripts/14522129: line 297: 5615 Terminated MACS $i /var/spool/uge/it020/job_scripts/14522129: line 297: 6552 Terminated MACS $i ls: cannot access SRX9786304.05.bed: No such file or directory mv: cannot stat ‘SRX9786304.05.bed’: No such file or directory mv: cannot stat ‘SRX9786304.05.bb’: No such file or directory ls: cannot access SRX9786304.10.bed: No such file or directory mv: cannot stat ‘SRX9786304.10.bed’: No such file or directory mv: cannot stat ‘SRX9786304.10.bb’: No such file or directory ls: cannot access SRX9786304.20.bed: No such file or directory mv: cannot stat ‘SRX9786304.20.bed’: No such file or directory mv: cannot stat ‘SRX9786304.20.bb’: No such file or directory