Job ID = 14521147 SRX = SRX8245369 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 11412960 spots for SRR11684580/SRR11684580.sra Written 11412960 spots for SRR11684580/SRR11684580.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: 00:06:52 11412960 reads; of these: 11412960 (100.00%) were paired; of these: 5640236 (49.42%) aligned concordantly 0 times 4803379 (42.09%) aligned concordantly exactly 1 time 969345 (8.49%) aligned concordantly >1 times ---- 5640236 pairs aligned concordantly 0 times; of these: 88043 (1.56%) aligned discordantly 1 time ---- 5552193 pairs aligned 0 times concordantly or discordantly; of these: 11104386 mates make up the pairs; of these: 6874839 (61.91%) aligned 0 times 3457687 (31.14%) aligned exactly 1 time 771860 (6.95%) aligned >1 times 69.88% overall alignment rate Time searching: 00:06:52 Overall time: 00:06:52 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] 382854 / 5860059 = 0.0653 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 20:43:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245369/SRX8245369.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245369/SRX8245369.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245369/SRX8245369.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245369/SRX8245369.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 20:43:47: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:43:47: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:43:52: 1000000 INFO @ Sat, 15 Jan 2022 20:43:58: 2000000 INFO @ Sat, 15 Jan 2022 20:44:03: 3000000 INFO @ Sat, 15 Jan 2022 20:44:09: 4000000 INFO @ Sat, 15 Jan 2022 20:44:14: 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 20:44:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245369/SRX8245369.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245369/SRX8245369.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245369/SRX8245369.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245369/SRX8245369.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 20:44:17: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:44:17: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:44:19: 6000000 INFO @ Sat, 15 Jan 2022 20:44:23: 1000000 INFO @ Sat, 15 Jan 2022 20:44:25: 7000000 INFO @ Sat, 15 Jan 2022 20:44:28: 2000000 INFO @ Sat, 15 Jan 2022 20:44:30: 8000000 INFO @ Sat, 15 Jan 2022 20:44:34: 3000000 INFO @ Sat, 15 Jan 2022 20:44:36: 9000000 INFO @ Sat, 15 Jan 2022 20:44:39: 4000000 INFO @ Sat, 15 Jan 2022 20:44:42: 10000000 INFO @ Sat, 15 Jan 2022 20:44:44: 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 20:44:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245369/SRX8245369.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245369/SRX8245369.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245369/SRX8245369.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245369/SRX8245369.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 20:44:47: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:44:47: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:44:47: 11000000 INFO @ Sat, 15 Jan 2022 20:44:50: 6000000 INFO @ Sat, 15 Jan 2022 20:44:53: 1000000 INFO @ Sat, 15 Jan 2022 20:44:53: 12000000 INFO @ Sat, 15 Jan 2022 20:44:55: 7000000 INFO @ Sat, 15 Jan 2022 20:44:58: 2000000 INFO @ Sat, 15 Jan 2022 20:44:58: 13000000 INFO @ Sat, 15 Jan 2022 20:45:01: 8000000 INFO @ Sat, 15 Jan 2022 20:45:04: 3000000 INFO @ Sat, 15 Jan 2022 20:45:04: 14000000 INFO @ Sat, 15 Jan 2022 20:45:06: 9000000 INFO @ Sat, 15 Jan 2022 20:45:09: 4000000 INFO @ Sat, 15 Jan 2022 20:45:10: 15000000 INFO @ Sat, 15 Jan 2022 20:45:11: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:45:11: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:45:11: #1 total tags in treatment: 5392009 INFO @ Sat, 15 Jan 2022 20:45:11: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:45:11: #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 20:45:11: #1 tags after filtering in treatment: 3503684 INFO @ Sat, 15 Jan 2022 20:45:11: #1 Redundant rate of treatment: 0.35 INFO @ Sat, 15 Jan 2022 20:45:11: #1 finished! INFO @ Sat, 15 Jan 2022 20:45:11: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:45:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:45:11: #2 number of paired peaks: 177 WARNING @ Sat, 15 Jan 2022 20:45:11: Fewer paired peaks (177) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 177 pairs to build model! INFO @ Sat, 15 Jan 2022 20:45:11: start model_add_line... INFO @ Sat, 15 Jan 2022 20:45:11: start X-correlation... INFO @ Sat, 15 Jan 2022 20:45:11: end of X-cor INFO @ Sat, 15 Jan 2022 20:45:11: #2 finished! INFO @ Sat, 15 Jan 2022 20:45:11: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 20:45:11: #2 alternative fragment length(s) may be 0,61,84,105,124,137,159,183,206,245,279,304,359,387,432,467,490,510,529,542,559,569,592 bps INFO @ Sat, 15 Jan 2022 20:45:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245369/SRX8245369.05_model.r WARNING @ Sat, 15 Jan 2022 20:45:11: #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 20:45:11: #2 You may need to consider one of the other alternative d(s): 0,61,84,105,124,137,159,183,206,245,279,304,359,387,432,467,490,510,529,542,559,569,592 WARNING @ Sat, 15 Jan 2022 20:45:11: #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 20:45:11: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:45:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:45:12: 10000000 INFO @ Sat, 15 Jan 2022 20:45:14: 5000000 INFO @ Sat, 15 Jan 2022 20:45:17: 11000000 INFO @ Sat, 15 Jan 2022 20:45:20: 6000000 INFO @ Sat, 15 Jan 2022 20:45:23: 12000000 INFO @ Sat, 15 Jan 2022 20:45:25: 7000000 INFO @ Sat, 15 Jan 2022 20:45:28: 13000000 INFO @ Sat, 15 Jan 2022 20:45:30: 8000000 INFO @ Sat, 15 Jan 2022 20:45:34: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:45:36: 9000000 INFO @ Sat, 15 Jan 2022 20:45:39: 15000000 INFO @ Sat, 15 Jan 2022 20:45:40: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:45:40: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:45:40: #1 total tags in treatment: 5392009 INFO @ Sat, 15 Jan 2022 20:45:40: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:45:40: #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 20:45:40: #1 tags after filtering in treatment: 3503684 INFO @ Sat, 15 Jan 2022 20:45:40: #1 Redundant rate of treatment: 0.35 INFO @ Sat, 15 Jan 2022 20:45:40: #1 finished! INFO @ Sat, 15 Jan 2022 20:45:40: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:45:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:45:41: #2 number of paired peaks: 177 WARNING @ Sat, 15 Jan 2022 20:45:41: Fewer paired peaks (177) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 177 pairs to build model! INFO @ Sat, 15 Jan 2022 20:45:41: start model_add_line... INFO @ Sat, 15 Jan 2022 20:45:41: start X-correlation... INFO @ Sat, 15 Jan 2022 20:45:41: end of X-cor INFO @ Sat, 15 Jan 2022 20:45:41: #2 finished! INFO @ Sat, 15 Jan 2022 20:45:41: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 20:45:41: #2 alternative fragment length(s) may be 0,61,84,105,124,137,159,183,206,245,279,304,359,387,432,467,490,510,529,542,559,569,592 bps INFO @ Sat, 15 Jan 2022 20:45:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245369/SRX8245369.10_model.r WARNING @ Sat, 15 Jan 2022 20:45:41: #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 20:45:41: #2 You may need to consider one of the other alternative d(s): 0,61,84,105,124,137,159,183,206,245,279,304,359,387,432,467,490,510,529,542,559,569,592 WARNING @ Sat, 15 Jan 2022 20:45:41: #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 20:45:41: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:45:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:45:41: 10000000 BigWig に変換しました。 /var/spool/uge/at141/job_scripts/14521147: line 297: 126649 Terminated MACS $i /var/spool/uge/at141/job_scripts/14521147: line 297: 128816 Terminated MACS $i /var/spool/uge/at141/job_scripts/14521147: line 297: 129057 Terminated MACS $i ls: cannot access SRX8245369.05.bed: No such file or directory mv: cannot stat ‘SRX8245369.05.bed’: No such file or directory mv: cannot stat ‘SRX8245369.05.bb’: No such file or directory ls: cannot access SRX8245369.10.bed: No such file or directory mv: cannot stat ‘SRX8245369.10.bed’: No such file or directory mv: cannot stat ‘SRX8245369.10.bb’: No such file or directory ls: cannot access SRX8245369.20.bed: No such file or directory mv: cannot stat ‘SRX8245369.20.bed’: No such file or directory mv: cannot stat ‘SRX8245369.20.bb’: No such file or directory