Job ID = 2009917 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 5,934,147 reads read : 11,868,294 reads written : 11,868,294 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: 00:05:52 5934147 reads; of these: 5934147 (100.00%) were paired; of these: 895555 (15.09%) aligned concordantly 0 times 4119530 (69.42%) aligned concordantly exactly 1 time 919062 (15.49%) aligned concordantly >1 times ---- 895555 pairs aligned concordantly 0 times; of these: 59298 (6.62%) aligned discordantly 1 time ---- 836257 pairs aligned 0 times concordantly or discordantly; of these: 1672514 mates make up the pairs; of these: 1527924 (91.35%) aligned 0 times 96548 (5.77%) aligned exactly 1 time 48042 (2.87%) aligned >1 times 87.13% overall alignment rate Time searching: 00:05:53 Overall time: 00:05:53 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] 172372 / 5082503 = 0.0339 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 20:57:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2339852/SRX2339852.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2339852/SRX2339852.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2339852/SRX2339852.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2339852/SRX2339852.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 20:57:56: #1 read tag files... INFO @ Fri, 05 Jul 2019 20:57:56: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 20:57:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2339852/SRX2339852.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2339852/SRX2339852.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2339852/SRX2339852.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2339852/SRX2339852.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 20:57:56: #1 read tag files... INFO @ Fri, 05 Jul 2019 20:57:56: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 20:57:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2339852/SRX2339852.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2339852/SRX2339852.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2339852/SRX2339852.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2339852/SRX2339852.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 20:57:56: #1 read tag files... INFO @ Fri, 05 Jul 2019 20:57:56: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 20:58:06: 1000000 INFO @ Fri, 05 Jul 2019 20:58:07: 1000000 INFO @ Fri, 05 Jul 2019 20:58:08: 1000000 INFO @ Fri, 05 Jul 2019 20:58:16: 2000000 INFO @ Fri, 05 Jul 2019 20:58:19: 2000000 INFO @ Fri, 05 Jul 2019 20:58:19: 2000000 INFO @ Fri, 05 Jul 2019 20:58:25: 3000000 INFO @ Fri, 05 Jul 2019 20:58:30: 3000000 INFO @ Fri, 05 Jul 2019 20:58:31: 3000000 INFO @ Fri, 05 Jul 2019 20:58:34: 4000000 INFO @ Fri, 05 Jul 2019 20:58:41: 4000000 INFO @ Fri, 05 Jul 2019 20:58:42: 4000000 INFO @ Fri, 05 Jul 2019 20:58:44: 5000000 INFO @ Fri, 05 Jul 2019 20:58:52: 5000000 INFO @ Fri, 05 Jul 2019 20:58:53: 5000000 INFO @ Fri, 05 Jul 2019 20:58:53: 6000000 INFO @ Fri, 05 Jul 2019 20:59:03: 7000000 INFO @ Fri, 05 Jul 2019 20:59:03: 6000000 INFO @ Fri, 05 Jul 2019 20:59:04: 6000000 INFO @ Fri, 05 Jul 2019 20:59:12: 8000000 INFO @ Fri, 05 Jul 2019 20:59:14: 7000000 INFO @ Fri, 05 Jul 2019 20:59:15: 7000000 INFO @ Fri, 05 Jul 2019 20:59:22: 9000000 INFO @ Fri, 05 Jul 2019 20:59:25: 8000000 INFO @ Fri, 05 Jul 2019 20:59:26: 8000000 INFO @ Fri, 05 Jul 2019 20:59:31: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 20:59:31: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 20:59:31: #1 total tags in treatment: 4866995 INFO @ Fri, 05 Jul 2019 20:59:31: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 20:59:31: #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 20:59:31: #1 tags after filtering in treatment: 3276690 INFO @ Fri, 05 Jul 2019 20:59:31: #1 Redundant rate of treatment: 0.33 INFO @ Fri, 05 Jul 2019 20:59:31: #1 finished! INFO @ Fri, 05 Jul 2019 20:59:31: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 20:59:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 20:59:31: #2 number of paired peaks: 172 WARNING @ Fri, 05 Jul 2019 20:59:31: Fewer paired peaks (172) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 172 pairs to build model! INFO @ Fri, 05 Jul 2019 20:59:31: start model_add_line... INFO @ Fri, 05 Jul 2019 20:59:31: start X-correlation... INFO @ Fri, 05 Jul 2019 20:59:31: end of X-cor INFO @ Fri, 05 Jul 2019 20:59:31: #2 finished! INFO @ Fri, 05 Jul 2019 20:59:31: #2 predicted fragment length is 0 bps INFO @ Fri, 05 Jul 2019 20:59:31: #2 alternative fragment length(s) may be 0,17,33,51,53,73,111,156,163,201,233,261,297,315,353,376,392,428,439,445,469,502,533,547,561,576,592 bps INFO @ Fri, 05 Jul 2019 20:59:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2339852/SRX2339852.10_model.r WARNING @ Fri, 05 Jul 2019 20:59:31: #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 20:59:31: #2 You may need to consider one of the other alternative d(s): 0,17,33,51,53,73,111,156,163,201,233,261,297,315,353,376,392,428,439,445,469,502,533,547,561,576,592 WARNING @ Fri, 05 Jul 2019 20:59:31: #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 20:59:31: #3 Call peaks... INFO @ Fri, 05 Jul 2019 20:59:31: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 20:59:36: 9000000 INFO @ Fri, 05 Jul 2019 20:59:37: 9000000 INFO @ Fri, 05 Jul 2019 20:59:46: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 20:59:46: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 20:59:46: #1 total tags in treatment: 4866995 INFO @ Fri, 05 Jul 2019 20:59:46: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 20:59:46: #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 20:59:46: #1 tags after filtering in treatment: 3276690 INFO @ Fri, 05 Jul 2019 20:59:46: #1 Redundant rate of treatment: 0.33 INFO @ Fri, 05 Jul 2019 20:59:46: #1 finished! INFO @ Fri, 05 Jul 2019 20:59:46: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 20:59:46: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 20:59:47: #2 number of paired peaks: 172 WARNING @ Fri, 05 Jul 2019 20:59:47: Fewer paired peaks (172) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 172 pairs to build model! INFO @ Fri, 05 Jul 2019 20:59:47: start model_add_line... INFO @ Fri, 05 Jul 2019 20:59:47: start X-correlation... INFO @ Fri, 05 Jul 2019 20:59:47: end of X-cor INFO @ Fri, 05 Jul 2019 20:59:47: #2 finished! INFO @ Fri, 05 Jul 2019 20:59:47: #2 predicted fragment length is 0 bps INFO @ Fri, 05 Jul 2019 20:59:47: #2 alternative fragment length(s) may be 0,17,33,51,53,73,111,156,163,201,233,261,297,315,353,376,392,428,439,445,469,502,533,547,561,576,592 bps INFO @ Fri, 05 Jul 2019 20:59:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2339852/SRX2339852.05_model.r WARNING @ Fri, 05 Jul 2019 20:59:47: #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 20:59:47: #2 You may need to consider one of the other alternative d(s): 0,17,33,51,53,73,111,156,163,201,233,261,297,315,353,376,392,428,439,445,469,502,533,547,561,576,592 WARNING @ Fri, 05 Jul 2019 20:59:47: #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 20:59:47: #3 Call peaks... INFO @ Fri, 05 Jul 2019 20:59:47: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 20:59:48: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 20:59:48: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 20:59:48: #1 total tags in treatment: 4866995 INFO @ Fri, 05 Jul 2019 20:59:48: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 20:59:48: #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 20:59:48: #1 tags after filtering in treatment: 3276690 INFO @ Fri, 05 Jul 2019 20:59:48: #1 Redundant rate of treatment: 0.33 INFO @ Fri, 05 Jul 2019 20:59:48: #1 finished! INFO @ Fri, 05 Jul 2019 20:59:48: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 20:59:48: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 20:59:48: #2 number of paired peaks: 172 WARNING @ Fri, 05 Jul 2019 20:59:48: Fewer paired peaks (172) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 172 pairs to build model! INFO @ Fri, 05 Jul 2019 20:59:48: start model_add_line... INFO @ Fri, 05 Jul 2019 20:59:48: start X-correlation... INFO @ Fri, 05 Jul 2019 20:59:48: end of X-cor INFO @ Fri, 05 Jul 2019 20:59:48: #2 finished! INFO @ Fri, 05 Jul 2019 20:59:48: #2 predicted fragment length is 0 bps INFO @ Fri, 05 Jul 2019 20:59:48: #2 alternative fragment length(s) may be 0,17,33,51,53,73,111,156,163,201,233,261,297,315,353,376,392,428,439,445,469,502,533,547,561,576,592 bps INFO @ Fri, 05 Jul 2019 20:59:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2339852/SRX2339852.20_model.r WARNING @ Fri, 05 Jul 2019 20:59:48: #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 20:59:48: #2 You may need to consider one of the other alternative d(s): 0,17,33,51,53,73,111,156,163,201,233,261,297,315,353,376,392,428,439,445,469,502,533,547,561,576,592 WARNING @ Fri, 05 Jul 2019 20:59:48: #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 20:59:48: #3 Call peaks... INFO @ Fri, 05 Jul 2019 20:59:48: #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 SRX2339852.05.bed: No such file or directory mv: cannot stat ‘SRX2339852.05.bed’: No such file or directory /var/spool/uge/at103/job_scripts/2009917: line 335: 2549 Terminated MACS $i /var/spool/uge/at103/job_scripts/2009917: line 335: 2563 Terminated MACS $i /var/spool/uge/at103/job_scripts/2009917: line 335: 2578 Terminated MACS $i mv: cannot stat ‘SRX2339852.05.bb’: No such file or directory ls: cannot access SRX2339852.10.bed: No such file or directory mv: cannot stat ‘SRX2339852.10.bed’: No such file or directory mv: cannot stat ‘SRX2339852.10.bb’: No such file or directory ls: cannot access SRX2339852.20.bed: No such file or directory mv: cannot stat ‘SRX2339852.20.bed’: No such file or directory mv: cannot stat ‘SRX2339852.20.bb’: No such file or directory