Job ID = 5791763 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 2,569,507 reads read : 5,139,014 reads written : 5,139,014 rm: cannot remove ‘[DSE]RR*’: No such file or directory 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: 00:01:38 2569507 reads; of these: 2569507 (100.00%) were paired; of these: 490522 (19.09%) aligned concordantly 0 times 1848258 (71.93%) aligned concordantly exactly 1 time 230727 (8.98%) aligned concordantly >1 times ---- 490522 pairs aligned concordantly 0 times; of these: 62910 (12.83%) aligned discordantly 1 time ---- 427612 pairs aligned 0 times concordantly or discordantly; of these: 855224 mates make up the pairs; of these: 810865 (94.81%) aligned 0 times 22871 (2.67%) aligned exactly 1 time 21488 (2.51%) aligned >1 times 84.22% overall alignment rate Time searching: 00:01:38 Overall time: 00:01:38 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_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] 47342 / 2139571 = 0.0221 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Apr 2020 10:46:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7741028/SRX7741028.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7741028/SRX7741028.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7741028/SRX7741028.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7741028/SRX7741028.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 @ Wed, 22 Apr 2020 10:46:00: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:46:00: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:46:05: 1000000 INFO @ Wed, 22 Apr 2020 10:46:10: 2000000 INFO @ Wed, 22 Apr 2020 10:46:15: 3000000 INFO @ Wed, 22 Apr 2020 10:46:20: 4000000 INFO @ Wed, 22 Apr 2020 10:46:21: #1 tag size is determined as 80 bps INFO @ Wed, 22 Apr 2020 10:46:21: #1 tag size = 80 INFO @ Wed, 22 Apr 2020 10:46:21: #1 total tags in treatment: 2032501 INFO @ Wed, 22 Apr 2020 10:46:21: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:46:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 10:46:21: #1 tags after filtering in treatment: 1831710 INFO @ Wed, 22 Apr 2020 10:46:21: #1 Redundant rate of treatment: 0.10 INFO @ Wed, 22 Apr 2020 10:46:21: #1 finished! INFO @ Wed, 22 Apr 2020 10:46:21: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:46:21: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:46:21: #2 number of paired peaks: 184 WARNING @ Wed, 22 Apr 2020 10:46:21: Fewer paired peaks (184) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 184 pairs to build model! INFO @ Wed, 22 Apr 2020 10:46:21: start model_add_line... INFO @ Wed, 22 Apr 2020 10:46:21: start X-correlation... INFO @ Wed, 22 Apr 2020 10:46:21: end of X-cor INFO @ Wed, 22 Apr 2020 10:46:21: #2 finished! INFO @ Wed, 22 Apr 2020 10:46:21: #2 predicted fragment length is 0 bps INFO @ Wed, 22 Apr 2020 10:46:21: #2 alternative fragment length(s) may be 0,26,48,72,89,125,128,149,151,161,183,223,256,275,298,320,340,373,393,415,435,467,474,508,523,561 bps INFO @ Wed, 22 Apr 2020 10:46:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7741028/SRX7741028.05_model.r WARNING @ Wed, 22 Apr 2020 10:46:21: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 10:46:21: #2 You may need to consider one of the other alternative d(s): 0,26,48,72,89,125,128,149,151,161,183,223,256,275,298,320,340,373,393,415,435,467,474,508,523,561 WARNING @ Wed, 22 Apr 2020 10:46:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 10:46:21: #3 Call peaks... INFO @ Wed, 22 Apr 2020 10:46:21: #3 Pre-compute pvalue-qvalue table... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Apr 2020 10:46:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7741028/SRX7741028.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7741028/SRX7741028.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7741028/SRX7741028.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7741028/SRX7741028.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 @ Wed, 22 Apr 2020 10:46:30: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:46:30: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:46:35: 1000000 INFO @ Wed, 22 Apr 2020 10:46:40: 2000000 INFO @ Wed, 22 Apr 2020 10:46:45: 3000000 INFO @ Wed, 22 Apr 2020 10:46:50: 4000000 INFO @ Wed, 22 Apr 2020 10:46:51: #1 tag size is determined as 80 bps INFO @ Wed, 22 Apr 2020 10:46:51: #1 tag size = 80 INFO @ Wed, 22 Apr 2020 10:46:51: #1 total tags in treatment: 2032501 INFO @ Wed, 22 Apr 2020 10:46:51: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:46:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 10:46:51: #1 tags after filtering in treatment: 1831710 INFO @ Wed, 22 Apr 2020 10:46:51: #1 Redundant rate of treatment: 0.10 INFO @ Wed, 22 Apr 2020 10:46:51: #1 finished! INFO @ Wed, 22 Apr 2020 10:46:51: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:46:51: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:46:51: #2 number of paired peaks: 184 WARNING @ Wed, 22 Apr 2020 10:46:51: Fewer paired peaks (184) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 184 pairs to build model! INFO @ Wed, 22 Apr 2020 10:46:51: start model_add_line... INFO @ Wed, 22 Apr 2020 10:46:51: start X-correlation... INFO @ Wed, 22 Apr 2020 10:46:51: end of X-cor INFO @ Wed, 22 Apr 2020 10:46:51: #2 finished! INFO @ Wed, 22 Apr 2020 10:46:51: #2 predicted fragment length is 0 bps INFO @ Wed, 22 Apr 2020 10:46:51: #2 alternative fragment length(s) may be 0,26,48,72,89,125,128,149,151,161,183,223,256,275,298,320,340,373,393,415,435,467,474,508,523,561 bps INFO @ Wed, 22 Apr 2020 10:46:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7741028/SRX7741028.10_model.r WARNING @ Wed, 22 Apr 2020 10:46:51: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 10:46:51: #2 You may need to consider one of the other alternative d(s): 0,26,48,72,89,125,128,149,151,161,183,223,256,275,298,320,340,373,393,415,435,467,474,508,523,561 WARNING @ Wed, 22 Apr 2020 10:46:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 10:46:51: #3 Call peaks... INFO @ Wed, 22 Apr 2020 10:46:51: #3 Pre-compute pvalue-qvalue table... BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Apr 2020 10:47:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7741028/SRX7741028.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7741028/SRX7741028.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7741028/SRX7741028.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7741028/SRX7741028.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 @ Wed, 22 Apr 2020 10:47:00: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:47:00: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:47:05: 1000000 INFO @ Wed, 22 Apr 2020 10:47:10: 2000000 INFO @ Wed, 22 Apr 2020 10:47:15: 3000000 INFO @ Wed, 22 Apr 2020 10:47:20: 4000000 INFO @ Wed, 22 Apr 2020 10:47:21: #1 tag size is determined as 80 bps INFO @ Wed, 22 Apr 2020 10:47:21: #1 tag size = 80 INFO @ Wed, 22 Apr 2020 10:47:21: #1 total tags in treatment: 2032501 INFO @ Wed, 22 Apr 2020 10:47:21: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:47:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 10:47:21: #1 tags after filtering in treatment: 1831710 INFO @ Wed, 22 Apr 2020 10:47:21: #1 Redundant rate of treatment: 0.10 INFO @ Wed, 22 Apr 2020 10:47:21: #1 finished! INFO @ Wed, 22 Apr 2020 10:47:21: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:47:21: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:47:21: #2 number of paired peaks: 184 WARNING @ Wed, 22 Apr 2020 10:47:21: Fewer paired peaks (184) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 184 pairs to build model! INFO @ Wed, 22 Apr 2020 10:47:21: start model_add_line... INFO @ Wed, 22 Apr 2020 10:47:21: start X-correlation... INFO @ Wed, 22 Apr 2020 10:47:21: end of X-cor INFO @ Wed, 22 Apr 2020 10:47:21: #2 finished! INFO @ Wed, 22 Apr 2020 10:47:21: #2 predicted fragment length is 0 bps INFO @ Wed, 22 Apr 2020 10:47:21: #2 alternative fragment length(s) may be 0,26,48,72,89,125,128,149,151,161,183,223,256,275,298,320,340,373,393,415,435,467,474,508,523,561 bps INFO @ Wed, 22 Apr 2020 10:47:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7741028/SRX7741028.20_model.r WARNING @ Wed, 22 Apr 2020 10:47:21: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 10:47:21: #2 You may need to consider one of the other alternative d(s): 0,26,48,72,89,125,128,149,151,161,183,223,256,275,298,320,340,373,393,415,435,467,474,508,523,561 WARNING @ Wed, 22 Apr 2020 10:47:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 10:47:21: #3 Call peaks... INFO @ Wed, 22 Apr 2020 10:47:21: #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/at160/job_scripts/5791763: line 336: 64432 Terminated MACS $i /var/spool/uge/at160/job_scripts/5791763: line 336: 102270 Terminated MACS $i /var/spool/uge/at160/job_scripts/5791763: line 336: 11277 Terminated MACS $i ls: cannot access SRX7741028.05.bed: No such file or directory mv: cannot stat ‘SRX7741028.05.bed’: No such file or directory mv: cannot stat ‘SRX7741028.05.bb’: No such file or directory ls: cannot access SRX7741028.10.bed: No such file or directory mv: cannot stat ‘SRX7741028.10.bed’: No such file or directory mv: cannot stat ‘SRX7741028.10.bb’: No such file or directory ls: cannot access SRX7741028.20.bed: No such file or directory mv: cannot stat ‘SRX7741028.20.bed’: No such file or directory mv: cannot stat ‘SRX7741028.20.bb’: No such file or directory