Job ID = 14521097 SRX = SRX8245357 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 10442471 spots for SRR11684568/SRR11684568.sra Written 10442471 spots for SRR11684568/SRR11684568.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: 00:05:35 10442471 reads; of these: 10442471 (100.00%) were paired; of these: 4731846 (45.31%) aligned concordantly 0 times 4817398 (46.13%) aligned concordantly exactly 1 time 893227 (8.55%) aligned concordantly >1 times ---- 4731846 pairs aligned concordantly 0 times; of these: 141778 (3.00%) aligned discordantly 1 time ---- 4590068 pairs aligned 0 times concordantly or discordantly; of these: 9180136 mates make up the pairs; of these: 6131795 (66.79%) aligned 0 times 2486386 (27.08%) aligned exactly 1 time 561955 (6.12%) aligned >1 times 70.64% overall alignment rate Time searching: 00:05:35 Overall time: 00:05:35 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] 833828 / 5851696 = 0.1425 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 20:36:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245357/SRX8245357.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245357/SRX8245357.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245357/SRX8245357.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245357/SRX8245357.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 20:36:33: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:36:33: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:36:38: 1000000 INFO @ Sat, 15 Jan 2022 20:36:43: 2000000 INFO @ Sat, 15 Jan 2022 20:36:48: 3000000 INFO @ Sat, 15 Jan 2022 20:36:53: 4000000 INFO @ Sat, 15 Jan 2022 20:36:58: 5000000 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 20:37:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245357/SRX8245357.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245357/SRX8245357.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245357/SRX8245357.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245357/SRX8245357.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 20:37:03: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:37:03: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:37:04: 6000000 INFO @ Sat, 15 Jan 2022 20:37:07: 1000000 INFO @ Sat, 15 Jan 2022 20:37:09: 7000000 INFO @ Sat, 15 Jan 2022 20:37:12: 2000000 INFO @ Sat, 15 Jan 2022 20:37:14: 8000000 INFO @ Sat, 15 Jan 2022 20:37:17: 3000000 INFO @ Sat, 15 Jan 2022 20:37:20: 9000000 INFO @ Sat, 15 Jan 2022 20:37:21: 4000000 INFO @ Sat, 15 Jan 2022 20:37:26: 10000000 INFO @ Sat, 15 Jan 2022 20:37:26: 5000000 INFO @ Sat, 15 Jan 2022 20:37:31: 6000000 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 20:37:31: 11000000 INFO @ Sat, 15 Jan 2022 20:37:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245357/SRX8245357.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245357/SRX8245357.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245357/SRX8245357.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245357/SRX8245357.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 20:37:33: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:37:33: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:37:35: 7000000 INFO @ Sat, 15 Jan 2022 20:37:37: 12000000 INFO @ Sat, 15 Jan 2022 20:37:38: 1000000 INFO @ Sat, 15 Jan 2022 20:37:40: 8000000 INFO @ Sat, 15 Jan 2022 20:37:43: 2000000 INFO @ Sat, 15 Jan 2022 20:37:43: 13000000 INFO @ Sat, 15 Jan 2022 20:37:43: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:37:43: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:37:43: #1 total tags in treatment: 4888399 INFO @ Sat, 15 Jan 2022 20:37:43: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:37:43: #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 20:37:43: #1 tags after filtering in treatment: 3195753 INFO @ Sat, 15 Jan 2022 20:37:43: #1 Redundant rate of treatment: 0.35 INFO @ Sat, 15 Jan 2022 20:37:43: #1 finished! INFO @ Sat, 15 Jan 2022 20:37:43: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:37:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:37:44: #2 number of paired peaks: 167 WARNING @ Sat, 15 Jan 2022 20:37:44: Fewer paired peaks (167) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 167 pairs to build model! INFO @ Sat, 15 Jan 2022 20:37:44: start model_add_line... INFO @ Sat, 15 Jan 2022 20:37:44: start X-correlation... INFO @ Sat, 15 Jan 2022 20:37:44: end of X-cor INFO @ Sat, 15 Jan 2022 20:37:44: #2 finished! INFO @ Sat, 15 Jan 2022 20:37:44: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 20:37:44: #2 alternative fragment length(s) may be 0,20,54,102,123,136,182,194,210,237,265,293,312,342,373,401,405,420,440,480,497,516,536,548,574 bps INFO @ Sat, 15 Jan 2022 20:37:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245357/SRX8245357.05_model.r WARNING @ Sat, 15 Jan 2022 20:37:44: #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 20:37:44: #2 You may need to consider one of the other alternative d(s): 0,20,54,102,123,136,182,194,210,237,265,293,312,342,373,401,405,420,440,480,497,516,536,548,574 WARNING @ Sat, 15 Jan 2022 20:37:44: #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 20:37:44: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:37:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:37:45: 9000000 INFO @ Sat, 15 Jan 2022 20:37:47: 3000000 INFO @ Sat, 15 Jan 2022 20:37:50: 10000000 INFO @ Sat, 15 Jan 2022 20:37:52: 4000000 INFO @ Sat, 15 Jan 2022 20:37:54: 11000000 INFO @ Sat, 15 Jan 2022 20:37:56: 5000000 INFO @ Sat, 15 Jan 2022 20:37:59: 12000000 INFO @ Sat, 15 Jan 2022 20:38:01: 6000000 INFO @ Sat, 15 Jan 2022 20:38:04: 13000000 INFO @ Sat, 15 Jan 2022 20:38:04: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:38:04: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:38:04: #1 total tags in treatment: 4888399 INFO @ Sat, 15 Jan 2022 20:38:04: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:38:04: #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 20:38:04: #1 tags after filtering in treatment: 3195753 INFO @ Sat, 15 Jan 2022 20:38:04: #1 Redundant rate of treatment: 0.35 INFO @ Sat, 15 Jan 2022 20:38:04: #1 finished! INFO @ Sat, 15 Jan 2022 20:38:04: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:38:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:38:05: #2 number of paired peaks: 167 WARNING @ Sat, 15 Jan 2022 20:38:05: Fewer paired peaks (167) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 167 pairs to build model! INFO @ Sat, 15 Jan 2022 20:38:05: start model_add_line... INFO @ Sat, 15 Jan 2022 20:38:05: start X-correlation... INFO @ Sat, 15 Jan 2022 20:38:05: end of X-cor INFO @ Sat, 15 Jan 2022 20:38:05: #2 finished! INFO @ Sat, 15 Jan 2022 20:38:05: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 20:38:05: #2 alternative fragment length(s) may be 0,20,54,102,123,136,182,194,210,237,265,293,312,342,373,401,405,420,440,480,497,516,536,548,574 bps INFO @ Sat, 15 Jan 2022 20:38:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245357/SRX8245357.10_model.r WARNING @ Sat, 15 Jan 2022 20:38:05: #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 20:38:05: #2 You may need to consider one of the other alternative d(s): 0,20,54,102,123,136,182,194,210,237,265,293,312,342,373,401,405,420,440,480,497,516,536,548,574 WARNING @ Sat, 15 Jan 2022 20:38:05: #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 20:38:05: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:38:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:38:06: 7000000 INFO @ Sat, 15 Jan 2022 20:38:10: 8000000 INFO @ Sat, 15 Jan 2022 20:38:15: 9000000 INFO @ Sat, 15 Jan 2022 20:38:20: 10000000 INFO @ Sat, 15 Jan 2022 20:38:24: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:38:29: 12000000 INFO @ Sat, 15 Jan 2022 20:38:33: 13000000 INFO @ Sat, 15 Jan 2022 20:38:34: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:38:34: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:38:34: #1 total tags in treatment: 4888399 INFO @ Sat, 15 Jan 2022 20:38:34: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:38:34: #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 20:38:34: #1 tags after filtering in treatment: 3195753 INFO @ Sat, 15 Jan 2022 20:38:34: #1 Redundant rate of treatment: 0.35 INFO @ Sat, 15 Jan 2022 20:38:34: #1 finished! INFO @ Sat, 15 Jan 2022 20:38:34: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:38:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:38:34: #2 number of paired peaks: 167 WARNING @ Sat, 15 Jan 2022 20:38:34: Fewer paired peaks (167) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 167 pairs to build model! INFO @ Sat, 15 Jan 2022 20:38:34: start model_add_line... INFO @ Sat, 15 Jan 2022 20:38:34: start X-correlation... INFO @ Sat, 15 Jan 2022 20:38:34: end of X-cor INFO @ Sat, 15 Jan 2022 20:38:34: #2 finished! INFO @ Sat, 15 Jan 2022 20:38:34: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 20:38:34: #2 alternative fragment length(s) may be 0,20,54,102,123,136,182,194,210,237,265,293,312,342,373,401,405,420,440,480,497,516,536,548,574 bps INFO @ Sat, 15 Jan 2022 20:38:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245357/SRX8245357.20_model.r WARNING @ Sat, 15 Jan 2022 20:38:34: #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 20:38:34: #2 You may need to consider one of the other alternative d(s): 0,20,54,102,123,136,182,194,210,237,265,293,312,342,373,401,405,420,440,480,497,516,536,548,574 WARNING @ Sat, 15 Jan 2022 20:38:34: #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 20:38:34: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:38:34: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 /var/spool/uge/at163/job_scripts/14521097: line 297: 29675 Terminated MACS $i /var/spool/uge/at163/job_scripts/14521097: line 297: 29850 Terminated MACS $i /var/spool/uge/at163/job_scripts/14521097: line 297: 31281 Terminated MACS $i ls: cannot access SRX8245357.05.bed: No such file or directory mv: cannot stat ‘SRX8245357.05.bed’: No such file or directory mv: cannot stat ‘SRX8245357.05.bb’: No such file or directory ls: cannot access SRX8245357.10.bed: No such file or directory mv: cannot stat ‘SRX8245357.10.bed’: No such file or directory mv: cannot stat ‘SRX8245357.10.bb’: No such file or directory ls: cannot access SRX8245357.20.bed: No such file or directory mv: cannot stat ‘SRX8245357.20.bed’: No such file or directory mv: cannot stat ‘SRX8245357.20.bb’: No such file or directory