Job ID = 14519809 SRX = SRX9786272 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 11319055 spots for SRR13362136/SRR13362136.sra Written 11319055 spots for SRR13362136/SRR13362136.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: 00:09:11 11319055 reads; of these: 11319055 (100.00%) were paired; of these: 5563473 (49.15%) aligned concordantly 0 times 5119168 (45.23%) aligned concordantly exactly 1 time 636414 (5.62%) aligned concordantly >1 times ---- 5563473 pairs aligned concordantly 0 times; of these: 97296 (1.75%) aligned discordantly 1 time ---- 5466177 pairs aligned 0 times concordantly or discordantly; of these: 10932354 mates make up the pairs; of these: 6966546 (63.72%) aligned 0 times 3452368 (31.58%) aligned exactly 1 time 513440 (4.70%) aligned >1 times 69.23% overall alignment rate Time searching: 00:09:11 Overall time: 00:09:11 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] 350640 / 5851933 = 0.0599 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 18:04:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9786272/SRX9786272.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9786272/SRX9786272.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9786272/SRX9786272.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9786272/SRX9786272.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 18:04:36: #1 read tag files... INFO @ Sat, 15 Jan 2022 18:04:36: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 18:04:45: 1000000 INFO @ Sat, 15 Jan 2022 18:04:54: 2000000 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 18:05:03: 3000000 INFO @ Sat, 15 Jan 2022 18:05:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9786272/SRX9786272.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9786272/SRX9786272.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9786272/SRX9786272.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9786272/SRX9786272.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 18:05:06: #1 read tag files... INFO @ Sat, 15 Jan 2022 18:05:06: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 18:05:13: 4000000 INFO @ Sat, 15 Jan 2022 18:05:15: 1000000 INFO @ Sat, 15 Jan 2022 18:05:22: 5000000 INFO @ Sat, 15 Jan 2022 18:05:23: 2000000 INFO @ Sat, 15 Jan 2022 18:05:31: 6000000 INFO @ Sat, 15 Jan 2022 18:05:32: 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 18:05:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9786272/SRX9786272.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9786272/SRX9786272.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9786272/SRX9786272.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9786272/SRX9786272.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 18:05:36: #1 read tag files... INFO @ Sat, 15 Jan 2022 18:05:36: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 18:05:40: 7000000 INFO @ Sat, 15 Jan 2022 18:05:41: 4000000 INFO @ Sat, 15 Jan 2022 18:05:45: 1000000 INFO @ Sat, 15 Jan 2022 18:05:49: 8000000 INFO @ Sat, 15 Jan 2022 18:05:50: 5000000 INFO @ Sat, 15 Jan 2022 18:05:54: 2000000 INFO @ Sat, 15 Jan 2022 18:05:59: 9000000 INFO @ Sat, 15 Jan 2022 18:05:59: 6000000 INFO @ Sat, 15 Jan 2022 18:06:03: 3000000 INFO @ Sat, 15 Jan 2022 18:06:08: 10000000 INFO @ Sat, 15 Jan 2022 18:06:09: 7000000 INFO @ Sat, 15 Jan 2022 18:06:13: 4000000 INFO @ Sat, 15 Jan 2022 18:06:19: 11000000 INFO @ Sat, 15 Jan 2022 18:06:19: 8000000 INFO @ Sat, 15 Jan 2022 18:06:22: 5000000 INFO @ Sat, 15 Jan 2022 18:06:29: 9000000 INFO @ Sat, 15 Jan 2022 18:06:29: 12000000 INFO @ Sat, 15 Jan 2022 18:06:31: 6000000 INFO @ Sat, 15 Jan 2022 18:06:38: 10000000 INFO @ Sat, 15 Jan 2022 18:06:40: 13000000 INFO @ Sat, 15 Jan 2022 18:06:41: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 18:06:48: 11000000 INFO @ Sat, 15 Jan 2022 18:06:49: 14000000 INFO @ Sat, 15 Jan 2022 18:06:51: 8000000 INFO @ Sat, 15 Jan 2022 18:06:58: 12000000 INFO @ Sat, 15 Jan 2022 18:06:59: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 18:06:59: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 18:06:59: #1 total tags in treatment: 5407203 INFO @ Sat, 15 Jan 2022 18:06:59: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 18:06:59: #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 18:06:59: #1 tags after filtering in treatment: 4014856 INFO @ Sat, 15 Jan 2022 18:06:59: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 15 Jan 2022 18:06:59: #1 finished! INFO @ Sat, 15 Jan 2022 18:06:59: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 18:06:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 18:07:00: #2 number of paired peaks: 151 WARNING @ Sat, 15 Jan 2022 18:07:00: Fewer paired peaks (151) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 151 pairs to build model! INFO @ Sat, 15 Jan 2022 18:07:00: start model_add_line... INFO @ Sat, 15 Jan 2022 18:07:00: start X-correlation... INFO @ Sat, 15 Jan 2022 18:07:00: end of X-cor INFO @ Sat, 15 Jan 2022 18:07:00: #2 finished! INFO @ Sat, 15 Jan 2022 18:07:00: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 18:07:00: #2 alternative fragment length(s) may be 0,13,39,72,96,100,109,134,150,204,247,289,303,319,354,381,405,419,444,451,494,509,524,553 bps INFO @ Sat, 15 Jan 2022 18:07:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX9786272/SRX9786272.05_model.r WARNING @ Sat, 15 Jan 2022 18:07:00: #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 18:07:00: #2 You may need to consider one of the other alternative d(s): 0,13,39,72,96,100,109,134,150,204,247,289,303,319,354,381,405,419,444,451,494,509,524,553 WARNING @ Sat, 15 Jan 2022 18:07:00: #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 18:07:00: #3 Call peaks... INFO @ Sat, 15 Jan 2022 18:07:00: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 /var/spool/uge/at073/job_scripts/14519809: line 297: 17124 Terminated MACS $i /var/spool/uge/at073/job_scripts/14519809: line 297: 17288 Terminated MACS $i /var/spool/uge/at073/job_scripts/14519809: line 297: 17452 Terminated MACS $i ls: cannot access SRX9786272.05.bed: No such file or directory mv: cannot stat ‘SRX9786272.05.bed’: No such file or directory mv: cannot stat ‘SRX9786272.05.bb’: No such file or directory ls: cannot access SRX9786272.10.bed: No such file or directory mv: cannot stat ‘SRX9786272.10.bed’: No such file or directory mv: cannot stat ‘SRX9786272.10.bb’: No such file or directory ls: cannot access SRX9786272.20.bed: No such file or directory mv: cannot stat ‘SRX9786272.20.bed’: No such file or directory mv: cannot stat ‘SRX9786272.20.bb’: No such file or directory