Job ID = 2010546 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 7,977,954 reads read : 15,955,908 reads written : 15,955,908 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: 00:05:41 7977954 reads; of these: 7977954 (100.00%) were paired; of these: 1948934 (24.43%) aligned concordantly 0 times 4862052 (60.94%) aligned concordantly exactly 1 time 1166968 (14.63%) aligned concordantly >1 times ---- 1948934 pairs aligned concordantly 0 times; of these: 351175 (18.02%) aligned discordantly 1 time ---- 1597759 pairs aligned 0 times concordantly or discordantly; of these: 3195518 mates make up the pairs; of these: 2774220 (86.82%) aligned 0 times 204130 (6.39%) aligned exactly 1 time 217168 (6.80%) aligned >1 times 82.61% overall alignment rate Time searching: 00:05:41 Overall time: 00:05:41 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] 162598 / 6327136 = 0.0257 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Fri, 05 Jul 2019 23:12:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381248/SRX381248.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381248/SRX381248.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381248/SRX381248.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381248/SRX381248.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 @ Fri, 05 Jul 2019 23:12:27: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:12:27: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:12:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381248/SRX381248.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381248/SRX381248.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381248/SRX381248.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381248/SRX381248.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 @ Fri, 05 Jul 2019 23:12:28: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:12:28: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:12:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381248/SRX381248.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381248/SRX381248.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381248/SRX381248.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381248/SRX381248.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 @ Fri, 05 Jul 2019 23:12:29: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:12:29: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:12:36: 1000000 INFO @ Fri, 05 Jul 2019 23:12:37: 1000000 INFO @ Fri, 05 Jul 2019 23:12:37: 1000000 INFO @ Fri, 05 Jul 2019 23:12:42: 2000000 INFO @ Fri, 05 Jul 2019 23:12:43: 2000000 INFO @ Fri, 05 Jul 2019 23:12:45: 2000000 INFO @ Fri, 05 Jul 2019 23:12:50: 3000000 INFO @ Fri, 05 Jul 2019 23:12:51: 3000000 INFO @ Fri, 05 Jul 2019 23:12:53: 3000000 INFO @ Fri, 05 Jul 2019 23:12:57: 4000000 INFO @ Fri, 05 Jul 2019 23:12:58: 4000000 INFO @ Fri, 05 Jul 2019 23:13:01: 4000000 INFO @ Fri, 05 Jul 2019 23:13:05: 5000000 INFO @ Fri, 05 Jul 2019 23:13:05: 5000000 INFO @ Fri, 05 Jul 2019 23:13:08: 5000000 INFO @ Fri, 05 Jul 2019 23:13:12: 6000000 INFO @ Fri, 05 Jul 2019 23:13:12: 6000000 INFO @ Fri, 05 Jul 2019 23:13:16: 6000000 INFO @ Fri, 05 Jul 2019 23:13:18: 7000000 INFO @ Fri, 05 Jul 2019 23:13:19: 7000000 INFO @ Fri, 05 Jul 2019 23:13:23: 7000000 INFO @ Fri, 05 Jul 2019 23:13:25: 8000000 INFO @ Fri, 05 Jul 2019 23:13:26: 8000000 INFO @ Fri, 05 Jul 2019 23:13:30: 8000000 INFO @ Fri, 05 Jul 2019 23:13:32: 9000000 INFO @ Fri, 05 Jul 2019 23:13:32: 9000000 INFO @ Fri, 05 Jul 2019 23:13:38: 9000000 INFO @ Fri, 05 Jul 2019 23:13:39: 10000000 INFO @ Fri, 05 Jul 2019 23:13:39: 10000000 INFO @ Fri, 05 Jul 2019 23:13:45: 10000000 INFO @ Fri, 05 Jul 2019 23:13:46: 11000000 INFO @ Fri, 05 Jul 2019 23:13:46: 11000000 INFO @ Fri, 05 Jul 2019 23:13:52: 12000000 INFO @ Fri, 05 Jul 2019 23:13:53: 11000000 INFO @ Fri, 05 Jul 2019 23:13:53: 12000000 INFO @ Fri, 05 Jul 2019 23:13:58: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:13:58: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:13:58: #1 total tags in treatment: 5873353 INFO @ Fri, 05 Jul 2019 23:13:58: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:13:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 23:13:58: #1 tags after filtering in treatment: 4139190 INFO @ Fri, 05 Jul 2019 23:13:58: #1 Redundant rate of treatment: 0.30 INFO @ Fri, 05 Jul 2019 23:13:58: #1 finished! INFO @ Fri, 05 Jul 2019 23:13:58: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:13:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:13:59: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:13:59: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:13:59: #1 total tags in treatment: 5873353 INFO @ Fri, 05 Jul 2019 23:13:59: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:13:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 23:13:59: #1 tags after filtering in treatment: 4139190 INFO @ Fri, 05 Jul 2019 23:13:59: #1 Redundant rate of treatment: 0.30 INFO @ Fri, 05 Jul 2019 23:13:59: #1 finished! INFO @ Fri, 05 Jul 2019 23:13:59: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:13:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:13:59: #2 number of paired peaks: 165 WARNING @ Fri, 05 Jul 2019 23:13:59: Fewer paired peaks (165) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 165 pairs to build model! INFO @ Fri, 05 Jul 2019 23:13:59: start model_add_line... INFO @ Fri, 05 Jul 2019 23:13:59: start X-correlation... INFO @ Fri, 05 Jul 2019 23:13:59: end of X-cor INFO @ Fri, 05 Jul 2019 23:13:59: #2 finished! INFO @ Fri, 05 Jul 2019 23:13:59: #2 predicted fragment length is 0 bps INFO @ Fri, 05 Jul 2019 23:13:59: #2 alternative fragment length(s) may be 0,76,102,124,143,160,192,214,254,271,308,314,328,373,389,407,447,477,484,493,498,518,529,532,573,593 bps INFO @ Fri, 05 Jul 2019 23:13:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381248/SRX381248.10_model.r WARNING @ Fri, 05 Jul 2019 23:13:59: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 23:13:59: #2 You may need to consider one of the other alternative d(s): 0,76,102,124,143,160,192,214,254,271,308,314,328,373,389,407,447,477,484,493,498,518,529,532,573,593 WARNING @ Fri, 05 Jul 2019 23:13:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 23:13:59: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:13:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 23:13:59: #2 number of paired peaks: 165 WARNING @ Fri, 05 Jul 2019 23:13:59: Fewer paired peaks (165) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 165 pairs to build model! INFO @ Fri, 05 Jul 2019 23:13:59: start model_add_line... INFO @ Fri, 05 Jul 2019 23:13:59: start X-correlation... INFO @ Fri, 05 Jul 2019 23:13:59: end of X-cor INFO @ Fri, 05 Jul 2019 23:13:59: #2 finished! INFO @ Fri, 05 Jul 2019 23:13:59: #2 predicted fragment length is 0 bps INFO @ Fri, 05 Jul 2019 23:13:59: #2 alternative fragment length(s) may be 0,76,102,124,143,160,192,214,254,271,308,314,328,373,389,407,447,477,484,493,498,518,529,532,573,593 bps INFO @ Fri, 05 Jul 2019 23:13:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381248/SRX381248.20_model.r WARNING @ Fri, 05 Jul 2019 23:13:59: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 23:13:59: #2 You may need to consider one of the other alternative d(s): 0,76,102,124,143,160,192,214,254,271,308,314,328,373,389,407,447,477,484,493,498,518,529,532,573,593 WARNING @ Fri, 05 Jul 2019 23:13:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 23:13:59: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:13:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 23:14:00: 12000000 INFO @ Fri, 05 Jul 2019 23:14:06: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:14:06: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:14:06: #1 total tags in treatment: 5873353 INFO @ Fri, 05 Jul 2019 23:14:06: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:14:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 23:14:06: #1 tags after filtering in treatment: 4139190 INFO @ Fri, 05 Jul 2019 23:14:06: #1 Redundant rate of treatment: 0.30 INFO @ Fri, 05 Jul 2019 23:14:06: #1 finished! INFO @ Fri, 05 Jul 2019 23:14:06: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:14:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:14:07: #2 number of paired peaks: 165 WARNING @ Fri, 05 Jul 2019 23:14:07: Fewer paired peaks (165) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 165 pairs to build model! INFO @ Fri, 05 Jul 2019 23:14:07: start model_add_line... INFO @ Fri, 05 Jul 2019 23:14:07: start X-correlation... INFO @ Fri, 05 Jul 2019 23:14:07: end of X-cor INFO @ Fri, 05 Jul 2019 23:14:07: #2 finished! INFO @ Fri, 05 Jul 2019 23:14:07: #2 predicted fragment length is 0 bps INFO @ Fri, 05 Jul 2019 23:14:07: #2 alternative fragment length(s) may be 0,76,102,124,143,160,192,214,254,271,308,314,328,373,389,407,447,477,484,493,498,518,529,532,573,593 bps INFO @ Fri, 05 Jul 2019 23:14:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381248/SRX381248.05_model.r WARNING @ Fri, 05 Jul 2019 23:14:07: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 23:14:07: #2 You may need to consider one of the other alternative d(s): 0,76,102,124,143,160,192,214,254,271,308,314,328,373,389,407,447,477,484,493,498,518,529,532,573,593 WARNING @ Fri, 05 Jul 2019 23:14:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 23:14:07: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:14:07: #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。 ls: cannot access SRX381248.05.bed: No such file or directory mv: cannot stat ‘SRX381248.05.bed’: No such file or directory /var/spool/uge/at094/job_scripts/2010546: line 335: 60028 Terminated MACS $i /var/spool/uge/at094/job_scripts/2010546: line 335: 60043 Terminated MACS $i /var/spool/uge/at094/job_scripts/2010546: line 335: 60057 Terminated MACS $i mv: cannot stat ‘SRX381248.05.bb’: No such file or directory ls: cannot access SRX381248.10.bed: No such file or directory mv: cannot stat ‘SRX381248.10.bed’: No such file or directory mv: cannot stat ‘SRX381248.10.bb’: No such file or directory ls: cannot access SRX381248.20.bed: No such file or directory mv: cannot stat ‘SRX381248.20.bed’: No such file or directory mv: cannot stat ‘SRX381248.20.bb’: No such file or directory