Job ID = 14521038 SRX = SRX8245461 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 14039228 spots for SRR11684672/SRR11684672.sra Written 14039228 spots for SRR11684672/SRR11684672.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: 00:10:40 14039228 reads; of these: 14039228 (100.00%) were paired; of these: 6174914 (43.98%) aligned concordantly 0 times 6887546 (49.06%) aligned concordantly exactly 1 time 976768 (6.96%) aligned concordantly >1 times ---- 6174914 pairs aligned concordantly 0 times; of these: 19346 (0.31%) aligned discordantly 1 time ---- 6155568 pairs aligned 0 times concordantly or discordantly; of these: 12311136 mates make up the pairs; of these: 7357964 (59.77%) aligned 0 times 4251956 (34.54%) aligned exactly 1 time 701216 (5.70%) aligned >1 times 73.79% overall alignment rate Time searching: 00:10:40 Overall time: 00:10:40 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 12 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] 575561 / 7882467 = 0.0730 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 20:40:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245461/SRX8245461.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245461/SRX8245461.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245461/SRX8245461.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245461/SRX8245461.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 20:40:21: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:40:21: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:40:32: 1000000 INFO @ Sat, 15 Jan 2022 20:40:42: 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 20:40:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245461/SRX8245461.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245461/SRX8245461.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245461/SRX8245461.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245461/SRX8245461.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 20:40:49: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:40:49: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:40:53: 3000000 INFO @ Sat, 15 Jan 2022 20:40:58: 1000000 INFO @ Sat, 15 Jan 2022 20:41:03: 4000000 INFO @ Sat, 15 Jan 2022 20:41:06: 2000000 INFO @ Sat, 15 Jan 2022 20:41:14: 5000000 INFO @ Sat, 15 Jan 2022 20:41:15: 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 20:41:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245461/SRX8245461.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245461/SRX8245461.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245461/SRX8245461.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245461/SRX8245461.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 20:41:19: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:41:19: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:41:23: 4000000 INFO @ Sat, 15 Jan 2022 20:41:25: 6000000 INFO @ Sat, 15 Jan 2022 20:41:29: 1000000 INFO @ Sat, 15 Jan 2022 20:41:31: 5000000 INFO @ Sat, 15 Jan 2022 20:41:36: 7000000 INFO @ Sat, 15 Jan 2022 20:41:39: 2000000 INFO @ Sat, 15 Jan 2022 20:41:39: 6000000 INFO @ Sat, 15 Jan 2022 20:41:47: 8000000 INFO @ Sat, 15 Jan 2022 20:41:47: 7000000 INFO @ Sat, 15 Jan 2022 20:41:48: 3000000 INFO @ Sat, 15 Jan 2022 20:41:55: 8000000 INFO @ Sat, 15 Jan 2022 20:41:57: 4000000 INFO @ Sat, 15 Jan 2022 20:41:59: 9000000 INFO @ Sat, 15 Jan 2022 20:42:03: 9000000 INFO @ Sat, 15 Jan 2022 20:42:07: 5000000 INFO @ Sat, 15 Jan 2022 20:42:11: 10000000 INFO @ Sat, 15 Jan 2022 20:42:11: 10000000 INFO @ Sat, 15 Jan 2022 20:42:16: 6000000 INFO @ Sat, 15 Jan 2022 20:42:20: 11000000 INFO @ Sat, 15 Jan 2022 20:42:25: 11000000 INFO @ Sat, 15 Jan 2022 20:42:25: 7000000 INFO @ Sat, 15 Jan 2022 20:42:28: 12000000 INFO @ Sat, 15 Jan 2022 20:42:35: 8000000 INFO @ Sat, 15 Jan 2022 20:42:37: 13000000 INFO @ Sat, 15 Jan 2022 20:42:38: 12000000 INFO @ Sat, 15 Jan 2022 20:42:45: 9000000 INFO @ Sat, 15 Jan 2022 20:42:45: 14000000 INFO @ Sat, 15 Jan 2022 20:42:51: 13000000 INFO @ Sat, 15 Jan 2022 20:42:53: 15000000 INFO @ Sat, 15 Jan 2022 20:42:54: 10000000 INFO @ Sat, 15 Jan 2022 20:43:02: 16000000 INFO @ Sat, 15 Jan 2022 20:43:05: 11000000 INFO @ Sat, 15 Jan 2022 20:43:05: 14000000 INFO @ Sat, 15 Jan 2022 20:43:10: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:43:15: 12000000 INFO @ Sat, 15 Jan 2022 20:43:19: 15000000 INFO @ Sat, 15 Jan 2022 20:43:19: 18000000 INFO @ Sat, 15 Jan 2022 20:43:24: 13000000 INFO @ Sat, 15 Jan 2022 20:43:27: 19000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:43:32: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:43:32: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:43:32: #1 total tags in treatment: 7289592 INFO @ Sat, 15 Jan 2022 20:43:32: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:43:32: #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 20:43:32: #1 tags after filtering in treatment: 4120987 INFO @ Sat, 15 Jan 2022 20:43:32: #1 Redundant rate of treatment: 0.43 INFO @ Sat, 15 Jan 2022 20:43:32: #1 finished! INFO @ Sat, 15 Jan 2022 20:43:32: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:43:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:43:32: 16000000 INFO @ Sat, 15 Jan 2022 20:43:32: #2 number of paired peaks: 162 WARNING @ Sat, 15 Jan 2022 20:43:32: Fewer paired peaks (162) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 162 pairs to build model! INFO @ Sat, 15 Jan 2022 20:43:32: start model_add_line... INFO @ Sat, 15 Jan 2022 20:43:32: start X-correlation... INFO @ Sat, 15 Jan 2022 20:43:33: end of X-cor INFO @ Sat, 15 Jan 2022 20:43:33: #2 finished! INFO @ Sat, 15 Jan 2022 20:43:33: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 20:43:33: #2 alternative fragment length(s) may be 0,25,53,124,199,224,253,268,294,343,361,379,418,444,488,501,545,567,578 bps INFO @ Sat, 15 Jan 2022 20:43:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245461/SRX8245461.10_model.r WARNING @ Sat, 15 Jan 2022 20:43:33: #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 20:43:33: #2 You may need to consider one of the other alternative d(s): 0,25,53,124,199,224,253,268,294,343,361,379,418,444,488,501,545,567,578 WARNING @ Sat, 15 Jan 2022 20:43:33: #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 20:43:33: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:43:33: #3 Pre-compute pvalue-qvalue table... /var/spool/uge/at074/job_scripts/14521038: line 297: 54194 Terminated MACS $i /var/spool/uge/at074/job_scripts/14521038: line 297: 54303 Terminated MACS $i /var/spool/uge/at074/job_scripts/14521038: line 297: 54441 Terminated MACS $i ls: cannot access SRX8245461.05.bed: No such file or directory mv: cannot stat ‘SRX8245461.05.bed’: No such file or directory mv: cannot stat ‘SRX8245461.05.bb’: No such file or directory ls: cannot access SRX8245461.10.bed: No such file or directory mv: cannot stat ‘SRX8245461.10.bed’: No such file or directory mv: cannot stat ‘SRX8245461.10.bb’: No such file or directory ls: cannot access SRX8245461.20.bed: No such file or directory mv: cannot stat ‘SRX8245461.20.bed’: No such file or directory mv: cannot stat ‘SRX8245461.20.bb’: No such file or directory