Job ID = 14521138 SRX = SRX8245364 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 12557061 spots for SRR11684575/SRR11684575.sra Written 12557061 spots for SRR11684575/SRR11684575.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: 00:14:08 12557061 reads; of these: 12557061 (100.00%) were paired; of these: 6027300 (48.00%) aligned concordantly 0 times 5688443 (45.30%) aligned concordantly exactly 1 time 841318 (6.70%) aligned concordantly >1 times ---- 6027300 pairs aligned concordantly 0 times; of these: 127465 (2.11%) aligned discordantly 1 time ---- 5899835 pairs aligned 0 times concordantly or discordantly; of these: 11799670 mates make up the pairs; of these: 6588441 (55.84%) aligned 0 times 4438748 (37.62%) aligned exactly 1 time 772481 (6.55%) aligned >1 times 73.77% overall alignment rate Time searching: 00:14:09 Overall time: 00:14:09 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] 299937 / 6656392 = 0.0451 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 20:54:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245364/SRX8245364.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245364/SRX8245364.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245364/SRX8245364.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245364/SRX8245364.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 20:54:36: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:54:36: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:54:46: 1000000 INFO @ Sat, 15 Jan 2022 20:54:55: 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 20:55:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245364/SRX8245364.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245364/SRX8245364.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245364/SRX8245364.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245364/SRX8245364.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 20:55:05: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:55:05: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:55:05: 3000000 INFO @ Sat, 15 Jan 2022 20:55:15: 4000000 INFO @ Sat, 15 Jan 2022 20:55:16: 1000000 INFO @ Sat, 15 Jan 2022 20:55:25: 5000000 INFO @ Sat, 15 Jan 2022 20:55:27: 2000000 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 20:55:35: 6000000 INFO @ Sat, 15 Jan 2022 20:55:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245364/SRX8245364.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245364/SRX8245364.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245364/SRX8245364.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245364/SRX8245364.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 20:55:35: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:55:35: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:55:38: 3000000 INFO @ Sat, 15 Jan 2022 20:55:46: 7000000 INFO @ Sat, 15 Jan 2022 20:55:46: 1000000 INFO @ Sat, 15 Jan 2022 20:55:49: 4000000 INFO @ Sat, 15 Jan 2022 20:55:56: 8000000 INFO @ Sat, 15 Jan 2022 20:55:58: 2000000 INFO @ Sat, 15 Jan 2022 20:56:01: 5000000 INFO @ Sat, 15 Jan 2022 20:56:06: 9000000 INFO @ Sat, 15 Jan 2022 20:56:09: 3000000 INFO @ Sat, 15 Jan 2022 20:56:11: 6000000 INFO @ Sat, 15 Jan 2022 20:56:17: 10000000 INFO @ Sat, 15 Jan 2022 20:56:19: 4000000 INFO @ Sat, 15 Jan 2022 20:56:22: 7000000 INFO @ Sat, 15 Jan 2022 20:56:27: 11000000 INFO @ Sat, 15 Jan 2022 20:56:30: 5000000 INFO @ Sat, 15 Jan 2022 20:56:33: 8000000 INFO @ Sat, 15 Jan 2022 20:56:37: 12000000 INFO @ Sat, 15 Jan 2022 20:56:40: 6000000 INFO @ Sat, 15 Jan 2022 20:56:43: 9000000 INFO @ Sat, 15 Jan 2022 20:56:47: 13000000 INFO @ Sat, 15 Jan 2022 20:56:50: 7000000 INFO @ Sat, 15 Jan 2022 20:56:54: 10000000 INFO @ Sat, 15 Jan 2022 20:56:58: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:57:00: 8000000 INFO @ Sat, 15 Jan 2022 20:57:05: 11000000 INFO @ Sat, 15 Jan 2022 20:57:07: 15000000 INFO @ Sat, 15 Jan 2022 20:57:10: 9000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:57:16: 12000000 INFO @ Sat, 15 Jan 2022 20:57:17: 16000000 INFO @ Sat, 15 Jan 2022 20:57:21: 10000000 INFO @ Sat, 15 Jan 2022 20:57:27: 17000000 INFO @ Sat, 15 Jan 2022 20:57:28: 13000000 INFO @ Sat, 15 Jan 2022 20:57:32: 11000000 INFO @ Sat, 15 Jan 2022 20:57:35: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:57:35: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:57:35: #1 total tags in treatment: 6231290 INFO @ Sat, 15 Jan 2022 20:57:35: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:57:35: #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 20:57:35: #1 tags after filtering in treatment: 3722446 INFO @ Sat, 15 Jan 2022 20:57:35: #1 Redundant rate of treatment: 0.40 INFO @ Sat, 15 Jan 2022 20:57:35: #1 finished! INFO @ Sat, 15 Jan 2022 20:57:35: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:57:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:57:36: #2 number of paired peaks: 166 WARNING @ Sat, 15 Jan 2022 20:57:36: Fewer paired peaks (166) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 166 pairs to build model! INFO @ Sat, 15 Jan 2022 20:57:36: start model_add_line... INFO @ Sat, 15 Jan 2022 20:57:36: start X-correlation... INFO @ Sat, 15 Jan 2022 20:57:36: end of X-cor INFO @ Sat, 15 Jan 2022 20:57:36: #2 finished! INFO @ Sat, 15 Jan 2022 20:57:36: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 20:57:36: #2 alternative fragment length(s) may be 0,16,20,51,63,102,138,213,253,280,334,363,379,383,427,449,475,525,549,570,583 bps INFO @ Sat, 15 Jan 2022 20:57:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245364/SRX8245364.05_model.r WARNING @ Sat, 15 Jan 2022 20:57:36: #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 20:57:36: #2 You may need to consider one of the other alternative d(s): 0,16,20,51,63,102,138,213,253,280,334,363,379,383,427,449,475,525,549,570,583 WARNING @ Sat, 15 Jan 2022 20:57:36: #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 20:57:36: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:57:36: #3 Pre-compute pvalue-qvalue table... /var/spool/uge/at074/job_scripts/14521138: line 297: 3724 Terminated MACS $i /var/spool/uge/at074/job_scripts/14521138: line 297: 3902 Terminated MACS $i /var/spool/uge/at074/job_scripts/14521138: line 297: 4069 Terminated MACS $i ls: cannot access SRX8245364.05.bed: No such file or directory mv: cannot stat ‘SRX8245364.05.bed’: No such file or directory mv: cannot stat ‘SRX8245364.05.bb’: No such file or directory ls: cannot access SRX8245364.10.bed: No such file or directory mv: cannot stat ‘SRX8245364.10.bed’: No such file or directory mv: cannot stat ‘SRX8245364.10.bb’: No such file or directory ls: cannot access SRX8245364.20.bed: No such file or directory mv: cannot stat ‘SRX8245364.20.bed’: No such file or directory mv: cannot stat ‘SRX8245364.20.bb’: No such file or directory