Job ID = 14520824 SRX = SRX8245531 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 8641502 spots for SRR11684742/SRR11684742.sra Written 8641502 spots for SRR11684742/SRR11684742.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: 00:00:01 Multiseed full-index search: 00:10:09 8641502 reads; of these: 8641502 (100.00%) were paired; of these: 4778314 (55.29%) aligned concordantly 0 times 3532102 (40.87%) aligned concordantly exactly 1 time 331086 (3.83%) aligned concordantly >1 times ---- 4778314 pairs aligned concordantly 0 times; of these: 21546 (0.45%) aligned discordantly 1 time ---- 4756768 pairs aligned 0 times concordantly or discordantly; of these: 9513536 mates make up the pairs; of these: 5212424 (54.79%) aligned 0 times 3870992 (40.69%) aligned exactly 1 time 430120 (4.52%) aligned >1 times 69.84% overall alignment rate Time searching: 00:10:10 Overall time: 00:10:10 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] 81792 / 3884060 = 0.0211 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 20:14:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245531/SRX8245531.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245531/SRX8245531.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245531/SRX8245531.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245531/SRX8245531.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 20:14:30: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:14:30: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:14:40: 1000000 INFO @ Sat, 15 Jan 2022 20:14:51: 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 20:15:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245531/SRX8245531.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245531/SRX8245531.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245531/SRX8245531.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245531/SRX8245531.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 20:15:00: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:15:00: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:15:01: 3000000 INFO @ Sat, 15 Jan 2022 20:15:10: 1000000 INFO @ Sat, 15 Jan 2022 20:15:12: 4000000 INFO @ Sat, 15 Jan 2022 20:15:19: 2000000 INFO @ Sat, 15 Jan 2022 20:15:23: 5000000 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 20:15:29: 3000000 INFO @ Sat, 15 Jan 2022 20:15:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245531/SRX8245531.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245531/SRX8245531.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245531/SRX8245531.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245531/SRX8245531.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 20:15:30: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:15:30: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:15:34: 6000000 INFO @ Sat, 15 Jan 2022 20:15:38: 4000000 INFO @ Sat, 15 Jan 2022 20:15:41: 1000000 INFO @ Sat, 15 Jan 2022 20:15:46: 7000000 INFO @ Sat, 15 Jan 2022 20:15:48: 5000000 INFO @ Sat, 15 Jan 2022 20:15:53: 2000000 INFO @ Sat, 15 Jan 2022 20:15:57: 8000000 INFO @ Sat, 15 Jan 2022 20:15:58: 6000000 INFO @ Sat, 15 Jan 2022 20:16:04: 3000000 INFO @ Sat, 15 Jan 2022 20:16:08: 7000000 INFO @ Sat, 15 Jan 2022 20:16:08: 9000000 INFO @ Sat, 15 Jan 2022 20:16:16: 4000000 INFO @ Sat, 15 Jan 2022 20:16:18: 8000000 INFO @ Sat, 15 Jan 2022 20:16:19: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:16:27: 5000000 INFO @ Sat, 15 Jan 2022 20:16:28: 9000000 INFO @ Sat, 15 Jan 2022 20:16:31: 11000000 INFO @ Sat, 15 Jan 2022 20:16:37: 10000000 INFO @ Sat, 15 Jan 2022 20:16:39: 6000000 INFO @ Sat, 15 Jan 2022 20:16:41: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:16:41: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:16:41: #1 total tags in treatment: 3781586 INFO @ Sat, 15 Jan 2022 20:16:41: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:16:41: #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 20:16:41: #1 tags after filtering in treatment: 2741993 INFO @ Sat, 15 Jan 2022 20:16:41: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 15 Jan 2022 20:16:41: #1 finished! INFO @ Sat, 15 Jan 2022 20:16:41: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:16:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:16:41: #2 number of paired peaks: 168 WARNING @ Sat, 15 Jan 2022 20:16:41: 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 20:16:41: start model_add_line... INFO @ Sat, 15 Jan 2022 20:16:41: start X-correlation... INFO @ Sat, 15 Jan 2022 20:16:41: end of X-cor INFO @ Sat, 15 Jan 2022 20:16:41: #2 finished! INFO @ Sat, 15 Jan 2022 20:16:41: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 20:16:41: #2 alternative fragment length(s) may be 0,16,48,82,116,166,185,233,269,287,302,321,351,413,476,547,578 bps INFO @ Sat, 15 Jan 2022 20:16:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245531/SRX8245531.05_model.r WARNING @ Sat, 15 Jan 2022 20:16:41: #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 20:16:41: #2 You may need to consider one of the other alternative d(s): 0,16,48,82,116,166,185,233,269,287,302,321,351,413,476,547,578 WARNING @ Sat, 15 Jan 2022 20:16:41: #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 20:16:41: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:16:41: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 /var/spool/uge/at073/job_scripts/14520824: line 297: 29461 Terminated MACS $i /var/spool/uge/at073/job_scripts/14520824: line 297: 29647 Terminated MACS $i /var/spool/uge/at073/job_scripts/14520824: line 297: 29815 Terminated MACS $i ls: cannot access SRX8245531.05.bed: No such file or directory mv: cannot stat ‘SRX8245531.05.bed’: No such file or directory mv: cannot stat ‘SRX8245531.05.bb’: No such file or directory ls: cannot access SRX8245531.10.bed: No such file or directory mv: cannot stat ‘SRX8245531.10.bed’: No such file or directory mv: cannot stat ‘SRX8245531.10.bb’: No such file or directory ls: cannot access SRX8245531.20.bed: No such file or directory mv: cannot stat ‘SRX8245531.20.bed’: No such file or directory mv: cannot stat ‘SRX8245531.20.bb’: No such file or directory