Job ID = 2010548 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 5,863,003 reads read : 11,726,006 reads written : 11,726,006 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: 00:04:22 5863003 reads; of these: 5863003 (100.00%) were paired; of these: 1854400 (31.63%) aligned concordantly 0 times 3136104 (53.49%) aligned concordantly exactly 1 time 872499 (14.88%) aligned concordantly >1 times ---- 1854400 pairs aligned concordantly 0 times; of these: 210618 (11.36%) aligned discordantly 1 time ---- 1643782 pairs aligned 0 times concordantly or discordantly; of these: 3287564 mates make up the pairs; of these: 3031860 (92.22%) aligned 0 times 106392 (3.24%) aligned exactly 1 time 149312 (4.54%) aligned >1 times 74.14% overall alignment rate Time searching: 00:04:22 Overall time: 00:04:22 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] 263715 / 4187962 = 0.0630 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 23:07:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381249/SRX381249.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381249/SRX381249.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381249/SRX381249.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381249/SRX381249.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 23:07:58: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:07:58: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:07:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381249/SRX381249.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381249/SRX381249.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381249/SRX381249.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381249/SRX381249.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 23:07:59: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:07:59: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:08:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381249/SRX381249.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381249/SRX381249.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381249/SRX381249.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381249/SRX381249.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 23:08:00: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:08:00: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:08:05: 1000000 INFO @ Fri, 05 Jul 2019 23:08:07: 1000000 INFO @ Fri, 05 Jul 2019 23:08:09: 1000000 INFO @ Fri, 05 Jul 2019 23:08:11: 2000000 INFO @ Fri, 05 Jul 2019 23:08:15: 2000000 INFO @ Fri, 05 Jul 2019 23:08:18: 2000000 INFO @ Fri, 05 Jul 2019 23:08:18: 3000000 INFO @ Fri, 05 Jul 2019 23:08:23: 3000000 INFO @ Fri, 05 Jul 2019 23:08:25: 4000000 INFO @ Fri, 05 Jul 2019 23:08:27: 3000000 INFO @ Fri, 05 Jul 2019 23:08:31: 4000000 INFO @ Fri, 05 Jul 2019 23:08:31: 5000000 INFO @ Fri, 05 Jul 2019 23:08:35: 4000000 INFO @ Fri, 05 Jul 2019 23:08:38: 6000000 INFO @ Fri, 05 Jul 2019 23:08:39: 5000000 INFO @ Fri, 05 Jul 2019 23:08:44: 7000000 INFO @ Fri, 05 Jul 2019 23:08:44: 5000000 INFO @ Fri, 05 Jul 2019 23:08:47: 6000000 INFO @ Fri, 05 Jul 2019 23:08:51: 8000000 INFO @ Fri, 05 Jul 2019 23:08:52: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:08:52: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:08:52: #1 total tags in treatment: 3759678 INFO @ Fri, 05 Jul 2019 23:08:52: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:08:52: #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 23:08:52: #1 tags after filtering in treatment: 1575219 INFO @ Fri, 05 Jul 2019 23:08:52: #1 Redundant rate of treatment: 0.58 INFO @ Fri, 05 Jul 2019 23:08:52: #1 finished! INFO @ Fri, 05 Jul 2019 23:08:52: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:08:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:08:52: #2 number of paired peaks: 1189 INFO @ Fri, 05 Jul 2019 23:08:52: start model_add_line... INFO @ Fri, 05 Jul 2019 23:08:52: start X-correlation... INFO @ Fri, 05 Jul 2019 23:08:52: end of X-cor INFO @ Fri, 05 Jul 2019 23:08:52: #2 finished! INFO @ Fri, 05 Jul 2019 23:08:52: #2 predicted fragment length is 0 bps INFO @ Fri, 05 Jul 2019 23:08:52: #2 alternative fragment length(s) may be 0,11,25,51,70,76,89,113,137,159,598 bps INFO @ Fri, 05 Jul 2019 23:08:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381249/SRX381249.05_model.r WARNING @ Fri, 05 Jul 2019 23:08:53: #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 23:08:53: #2 You may need to consider one of the other alternative d(s): 0,11,25,51,70,76,89,113,137,159,598 WARNING @ Fri, 05 Jul 2019 23:08:53: #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 23:08:53: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:08:53: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 23:08:53: 6000000 INFO @ Fri, 05 Jul 2019 23:08:55: 7000000 INFO @ Fri, 05 Jul 2019 23:09:02: 7000000 INFO @ Fri, 05 Jul 2019 23:09:03: 8000000 INFO @ Fri, 05 Jul 2019 23:09:04: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:09:04: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:09:04: #1 total tags in treatment: 3759678 INFO @ Fri, 05 Jul 2019 23:09:04: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:09:04: #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 23:09:04: #1 tags after filtering in treatment: 1575219 INFO @ Fri, 05 Jul 2019 23:09:04: #1 Redundant rate of treatment: 0.58 INFO @ Fri, 05 Jul 2019 23:09:04: #1 finished! INFO @ Fri, 05 Jul 2019 23:09:04: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:09:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:09:04: #2 number of paired peaks: 1189 INFO @ Fri, 05 Jul 2019 23:09:04: start model_add_line... INFO @ Fri, 05 Jul 2019 23:09:04: start X-correlation... INFO @ Fri, 05 Jul 2019 23:09:04: end of X-cor INFO @ Fri, 05 Jul 2019 23:09:04: #2 finished! INFO @ Fri, 05 Jul 2019 23:09:04: #2 predicted fragment length is 0 bps INFO @ Fri, 05 Jul 2019 23:09:04: #2 alternative fragment length(s) may be 0,11,25,51,70,76,89,113,137,159,598 bps INFO @ Fri, 05 Jul 2019 23:09:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381249/SRX381249.10_model.r WARNING @ Fri, 05 Jul 2019 23:09:04: #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 23:09:04: #2 You may need to consider one of the other alternative d(s): 0,11,25,51,70,76,89,113,137,159,598 WARNING @ Fri, 05 Jul 2019 23:09:04: #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 23:09:04: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:09:04: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 23:09:11: 8000000 INFO @ Fri, 05 Jul 2019 23:09:12: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:09:12: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:09:12: #1 total tags in treatment: 3759678 INFO @ Fri, 05 Jul 2019 23:09:12: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:09:12: #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 23:09:12: #1 tags after filtering in treatment: 1575219 INFO @ Fri, 05 Jul 2019 23:09:12: #1 Redundant rate of treatment: 0.58 INFO @ Fri, 05 Jul 2019 23:09:12: #1 finished! INFO @ Fri, 05 Jul 2019 23:09:12: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:09:12: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:09:13: #2 number of paired peaks: 1189 INFO @ Fri, 05 Jul 2019 23:09:13: start model_add_line... INFO @ Fri, 05 Jul 2019 23:09:13: start X-correlation... INFO @ Fri, 05 Jul 2019 23:09:13: end of X-cor INFO @ Fri, 05 Jul 2019 23:09:13: #2 finished! INFO @ Fri, 05 Jul 2019 23:09:13: #2 predicted fragment length is 0 bps INFO @ Fri, 05 Jul 2019 23:09:13: #2 alternative fragment length(s) may be 0,11,25,51,70,76,89,113,137,159,598 bps INFO @ Fri, 05 Jul 2019 23:09:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381249/SRX381249.20_model.r WARNING @ Fri, 05 Jul 2019 23:09:39: #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 23:09:39: #2 You may need to consider one of the other alternative d(s): 0,11,25,51,70,76,89,113,137,159,598 WARNING @ Fri, 05 Jul 2019 23:09:39: #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 23:09:39: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:09:39: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 ls: cannot access SRX381249.05.bed: No such file or directory mv: cannot stat ‘SRX381249.05.bed’: No such file or directory /var/spool/uge/at096/job_scripts/2010548: line 335: 6872 Terminated MACS $i /var/spool/uge/at096/job_scripts/2010548: line 335: 6903 Terminated MACS $i /var/spool/uge/at096/job_scripts/2010548: line 335: 6986 Terminated MACS $i mv: cannot stat ‘SRX381249.05.bb’: No such file or directory ls: cannot access SRX381249.10.bed: No such file or directory mv: cannot stat ‘SRX381249.10.bed’: No such file or directory mv: cannot stat ‘SRX381249.10.bb’: No such file or directory ls: cannot access SRX381249.20.bed: No such file or directory mv: cannot stat ‘SRX381249.20.bed’: No such file or directory mv: cannot stat ‘SRX381249.20.bb’: No such file or directory