Job ID = 14520867 SRX = SRX8245546 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 8948101 spots for SRR11684757/SRR11684757.sra Written 8948101 spots for SRR11684757/SRR11684757.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: 00:05:13 8948101 reads; of these: 8948101 (100.00%) were paired; of these: 4792700 (53.56%) aligned concordantly 0 times 3662028 (40.93%) aligned concordantly exactly 1 time 493373 (5.51%) aligned concordantly >1 times ---- 4792700 pairs aligned concordantly 0 times; of these: 19808 (0.41%) aligned discordantly 1 time ---- 4772892 pairs aligned 0 times concordantly or discordantly; of these: 9545784 mates make up the pairs; of these: 5217255 (54.66%) aligned 0 times 3775845 (39.56%) aligned exactly 1 time 552684 (5.79%) aligned >1 times 70.85% overall alignment rate Time searching: 00:05:13 Overall time: 00:05:13 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] 83288 / 4174546 = 0.0200 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 20:12:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245546/SRX8245546.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245546/SRX8245546.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245546/SRX8245546.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245546/SRX8245546.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 20:12:13: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:12:13: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:12:17: 1000000 INFO @ Sat, 15 Jan 2022 20:12:21: 2000000 INFO @ Sat, 15 Jan 2022 20:12:25: 3000000 INFO @ Sat, 15 Jan 2022 20:12:29: 4000000 INFO @ Sat, 15 Jan 2022 20:12:33: 5000000 INFO @ Sat, 15 Jan 2022 20:12:37: 6000000 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 20:12:42: 7000000 INFO @ Sat, 15 Jan 2022 20:12:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245546/SRX8245546.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245546/SRX8245546.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245546/SRX8245546.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245546/SRX8245546.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 20:12:43: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:12:43: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:12:46: 8000000 INFO @ Sat, 15 Jan 2022 20:12:47: 1000000 INFO @ Sat, 15 Jan 2022 20:12:50: 9000000 INFO @ Sat, 15 Jan 2022 20:12:51: 2000000 INFO @ Sat, 15 Jan 2022 20:12:54: 10000000 INFO @ Sat, 15 Jan 2022 20:12:56: 3000000 INFO @ Sat, 15 Jan 2022 20:12:58: 11000000 INFO @ Sat, 15 Jan 2022 20:13:00: 4000000 INFO @ Sat, 15 Jan 2022 20:13:03: 12000000 INFO @ Sat, 15 Jan 2022 20:13:04: 5000000 INFO @ Sat, 15 Jan 2022 20:13:05: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:13:05: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:13:05: #1 total tags in treatment: 4072250 INFO @ Sat, 15 Jan 2022 20:13:05: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:13:05: #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 20:13:05: #1 tags after filtering in treatment: 2912618 INFO @ Sat, 15 Jan 2022 20:13:05: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 15 Jan 2022 20:13:05: #1 finished! INFO @ Sat, 15 Jan 2022 20:13:05: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:13:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:13:05: #2 number of paired peaks: 168 WARNING @ Sat, 15 Jan 2022 20:13:05: 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 20:13:05: start model_add_line... INFO @ Sat, 15 Jan 2022 20:13:05: start X-correlation... INFO @ Sat, 15 Jan 2022 20:13:05: end of X-cor INFO @ Sat, 15 Jan 2022 20:13:05: #2 finished! INFO @ Sat, 15 Jan 2022 20:13:05: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 20:13:05: #2 alternative fragment length(s) may be 0,44,99,121,139,152,157,169,203,231,274,301,316,325,411,427,451,498,515,545,582,590 bps INFO @ Sat, 15 Jan 2022 20:13:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245546/SRX8245546.05_model.r WARNING @ Sat, 15 Jan 2022 20:13:05: #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 20:13:05: #2 You may need to consider one of the other alternative d(s): 0,44,99,121,139,152,157,169,203,231,274,301,316,325,411,427,451,498,515,545,582,590 WARNING @ Sat, 15 Jan 2022 20:13:05: #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 20:13:05: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:13:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:13:08: 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 20:13:12: 7000000 INFO @ Sat, 15 Jan 2022 20:13:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245546/SRX8245546.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245546/SRX8245546.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245546/SRX8245546.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245546/SRX8245546.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 20:13:13: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:13:13: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:13:16: 8000000 INFO @ Sat, 15 Jan 2022 20:13:18: 1000000 INFO @ Sat, 15 Jan 2022 20:13:21: 9000000 INFO @ Sat, 15 Jan 2022 20:13:23: 2000000 INFO @ Sat, 15 Jan 2022 20:13:25: 10000000 INFO @ Sat, 15 Jan 2022 20:13:28: 3000000 INFO @ Sat, 15 Jan 2022 20:13:29: 11000000 INFO @ Sat, 15 Jan 2022 20:13:33: 4000000 INFO @ Sat, 15 Jan 2022 20:13:33: 12000000 INFO @ Sat, 15 Jan 2022 20:13:36: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:13:36: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:13:36: #1 total tags in treatment: 4072250 INFO @ Sat, 15 Jan 2022 20:13:36: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:13:36: #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 20:13:36: #1 tags after filtering in treatment: 2912618 INFO @ Sat, 15 Jan 2022 20:13:36: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 15 Jan 2022 20:13:36: #1 finished! INFO @ Sat, 15 Jan 2022 20:13:36: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:13:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:13:36: #2 number of paired peaks: 168 WARNING @ Sat, 15 Jan 2022 20:13:36: 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 20:13:36: start model_add_line... INFO @ Sat, 15 Jan 2022 20:13:36: start X-correlation... INFO @ Sat, 15 Jan 2022 20:13:36: end of X-cor INFO @ Sat, 15 Jan 2022 20:13:36: #2 finished! INFO @ Sat, 15 Jan 2022 20:13:36: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 20:13:36: #2 alternative fragment length(s) may be 0,44,99,121,139,152,157,169,203,231,274,301,316,325,411,427,451,498,515,545,582,590 bps INFO @ Sat, 15 Jan 2022 20:13:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245546/SRX8245546.10_model.r WARNING @ Sat, 15 Jan 2022 20:13:36: #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 20:13:36: #2 You may need to consider one of the other alternative d(s): 0,44,99,121,139,152,157,169,203,231,274,301,316,325,411,427,451,498,515,545,582,590 WARNING @ Sat, 15 Jan 2022 20:13:36: #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 20:13:36: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:13:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:13:38: 5000000 INFO @ Sat, 15 Jan 2022 20:13:43: 6000000 INFO @ Sat, 15 Jan 2022 20:13:48: 7000000 INFO @ Sat, 15 Jan 2022 20:13:53: 8000000 INFO @ Sat, 15 Jan 2022 20:13:57: 9000000 INFO @ Sat, 15 Jan 2022 20:14:02: 10000000 INFO @ Sat, 15 Jan 2022 20:14:07: 11000000 INFO @ Sat, 15 Jan 2022 20:14:12: 12000000 INFO @ Sat, 15 Jan 2022 20:14:14: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:14:14: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:14:14: #1 total tags in treatment: 4072250 INFO @ Sat, 15 Jan 2022 20:14:14: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:14:14: #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 20:14:14: #1 tags after filtering in treatment: 2912618 INFO @ Sat, 15 Jan 2022 20:14:14: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 15 Jan 2022 20:14:14: #1 finished! INFO @ Sat, 15 Jan 2022 20:14:14: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:14:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:14:14: #2 number of paired peaks: 168 WARNING @ Sat, 15 Jan 2022 20:14:14: 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 20:14:14: start model_add_line... INFO @ Sat, 15 Jan 2022 20:14:14: start X-correlation... INFO @ Sat, 15 Jan 2022 20:14:14: end of X-cor INFO @ Sat, 15 Jan 2022 20:14:14: #2 finished! INFO @ Sat, 15 Jan 2022 20:14:14: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 20:14:14: #2 alternative fragment length(s) may be 0,44,99,121,139,152,157,169,203,231,274,301,316,325,411,427,451,498,515,545,582,590 bps INFO @ Sat, 15 Jan 2022 20:14:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245546/SRX8245546.20_model.r WARNING @ Sat, 15 Jan 2022 20:14:14: #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 20:14:14: #2 You may need to consider one of the other alternative d(s): 0,44,99,121,139,152,157,169,203,231,274,301,316,325,411,427,451,498,515,545,582,590 WARNING @ Sat, 15 Jan 2022 20:14:14: #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 20:14:14: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:14:14: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 /var/spool/uge/at149/job_scripts/14520867: line 297: 20178 Terminated MACS $i /var/spool/uge/at149/job_scripts/14520867: line 297: 20294 Terminated MACS $i /var/spool/uge/at149/job_scripts/14520867: line 297: 20390 Terminated MACS $i ls: cannot access SRX8245546.05.bed: No such file or directory mv: cannot stat ‘SRX8245546.05.bed’: No such file or directory mv: cannot stat ‘SRX8245546.05.bb’: No such file or directory ls: cannot access SRX8245546.10.bed: No such file or directory mv: cannot stat ‘SRX8245546.10.bed’: No such file or directory mv: cannot stat ‘SRX8245546.10.bb’: No such file or directory ls: cannot access SRX8245546.20.bed: No such file or directory mv: cannot stat ‘SRX8245546.20.bed’: No such file or directory mv: cannot stat ‘SRX8245546.20.bb’: No such file or directory