Job ID = 7104820 SRX = SRX6911527 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 16860171 spots for SRR10191170/SRR10191170.sra Written 16860171 spots for SRR10191170/SRR10191170.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: 00:15:17 16860171 reads; of these: 16860171 (100.00%) were paired; of these: 5903410 (35.01%) aligned concordantly 0 times 9517725 (56.45%) aligned concordantly exactly 1 time 1439036 (8.54%) aligned concordantly >1 times ---- 5903410 pairs aligned concordantly 0 times; of these: 599414 (10.15%) aligned discordantly 1 time ---- 5303996 pairs aligned 0 times concordantly or discordantly; of these: 10607992 mates make up the pairs; of these: 10032567 (94.58%) aligned 0 times 329266 (3.10%) aligned exactly 1 time 246159 (2.32%) aligned >1 times 70.25% overall alignment rate Time searching: 00:15:17 Overall time: 00:15:17 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 12 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] 1302928 / 11554263 = 0.1128 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 Jul 2020 12:56:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6911527/SRX6911527.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6911527/SRX6911527.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6911527/SRX6911527.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6911527/SRX6911527.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 Jul 2020 12:56:34: #1 read tag files... INFO @ Wed, 22 Jul 2020 12:56:34: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 12:56:40: 1000000 INFO @ Wed, 22 Jul 2020 12:56:46: 2000000 INFO @ Wed, 22 Jul 2020 12:56:53: 3000000 INFO @ Wed, 22 Jul 2020 12:56:59: 4000000 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 Jul 2020 12:57:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6911527/SRX6911527.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6911527/SRX6911527.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6911527/SRX6911527.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6911527/SRX6911527.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 Jul 2020 12:57:03: #1 read tag files... INFO @ Wed, 22 Jul 2020 12:57:03: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 12:57:06: 5000000 INFO @ Wed, 22 Jul 2020 12:57:10: 1000000 INFO @ Wed, 22 Jul 2020 12:57:13: 6000000 INFO @ Wed, 22 Jul 2020 12:57:18: 2000000 INFO @ Wed, 22 Jul 2020 12:57:20: 7000000 INFO @ Wed, 22 Jul 2020 12:57:25: 3000000 INFO @ Wed, 22 Jul 2020 12:57:27: 8000000 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 Jul 2020 12:57:32: 4000000 INFO @ Wed, 22 Jul 2020 12:57:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6911527/SRX6911527.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6911527/SRX6911527.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6911527/SRX6911527.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6911527/SRX6911527.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 Jul 2020 12:57:33: #1 read tag files... INFO @ Wed, 22 Jul 2020 12:57:33: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 12:57:34: 9000000 INFO @ Wed, 22 Jul 2020 12:57:40: 5000000 INFO @ Wed, 22 Jul 2020 12:57:41: 1000000 INFO @ Wed, 22 Jul 2020 12:57:42: 10000000 INFO @ Wed, 22 Jul 2020 12:57:47: 6000000 INFO @ Wed, 22 Jul 2020 12:57:48: 2000000 INFO @ Wed, 22 Jul 2020 12:57:49: 11000000 INFO @ Wed, 22 Jul 2020 12:57:54: 7000000 INFO @ Wed, 22 Jul 2020 12:57:56: 3000000 INFO @ Wed, 22 Jul 2020 12:57:56: 12000000 INFO @ Wed, 22 Jul 2020 12:58:01: 8000000 INFO @ Wed, 22 Jul 2020 12:58:03: 4000000 INFO @ Wed, 22 Jul 2020 12:58:04: 13000000 INFO @ Wed, 22 Jul 2020 12:58:09: 9000000 INFO @ Wed, 22 Jul 2020 12:58:10: 5000000 INFO @ Wed, 22 Jul 2020 12:58:11: 14000000 INFO @ Wed, 22 Jul 2020 12:58:16: 10000000 INFO @ Wed, 22 Jul 2020 12:58:18: 6000000 INFO @ Wed, 22 Jul 2020 12:58:18: 15000000 INFO @ Wed, 22 Jul 2020 12:58:23: 11000000 INFO @ Wed, 22 Jul 2020 12:58:25: 7000000 INFO @ Wed, 22 Jul 2020 12:58:26: 16000000 INFO @ Wed, 22 Jul 2020 12:58:30: 12000000 INFO @ Wed, 22 Jul 2020 12:58:32: 8000000 INFO @ Wed, 22 Jul 2020 12:58:33: 17000000 INFO @ Wed, 22 Jul 2020 12:58:38: 13000000 INFO @ Wed, 22 Jul 2020 12:58:39: 9000000 INFO @ Wed, 22 Jul 2020 12:58:40: 18000000 INFO @ Wed, 22 Jul 2020 12:58:45: 14000000 INFO @ Wed, 22 Jul 2020 12:58:47: 10000000 INFO @ Wed, 22 Jul 2020 12:58:48: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Jul 2020 12:58:52: 15000000 INFO @ Wed, 22 Jul 2020 12:58:54: 11000000 INFO @ Wed, 22 Jul 2020 12:58:55: 20000000 BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 12:58:59: 16000000 INFO @ Wed, 22 Jul 2020 12:59:01: 12000000 INFO @ Wed, 22 Jul 2020 12:59:02: 21000000 INFO @ Wed, 22 Jul 2020 12:59:03: #1 tag size is determined as 101 bps INFO @ Wed, 22 Jul 2020 12:59:03: #1 tag size = 101 INFO @ Wed, 22 Jul 2020 12:59:03: #1 total tags in treatment: 9694650 INFO @ Wed, 22 Jul 2020 12:59:03: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 12:59:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 12:59:03: #1 tags after filtering in treatment: 4140519 INFO @ Wed, 22 Jul 2020 12:59:03: #1 Redundant rate of treatment: 0.57 INFO @ Wed, 22 Jul 2020 12:59:03: #1 finished! INFO @ Wed, 22 Jul 2020 12:59:03: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 12:59:03: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 12:59:03: #2 number of paired peaks: 160 WARNING @ Wed, 22 Jul 2020 12:59:03: Fewer paired peaks (160) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 160 pairs to build model! INFO @ Wed, 22 Jul 2020 12:59:03: start model_add_line... INFO @ Wed, 22 Jul 2020 12:59:03: start X-correlation... INFO @ Wed, 22 Jul 2020 12:59:03: end of X-cor INFO @ Wed, 22 Jul 2020 12:59:03: #2 finished! INFO @ Wed, 22 Jul 2020 12:59:03: #2 predicted fragment length is 0 bps INFO @ Wed, 22 Jul 2020 12:59:03: #2 alternative fragment length(s) may be 0,64,88,156,172,179,185,206,242,257,275,290,322,351,362,412,433,466,481,512,527,531,540,555,587 bps INFO @ Wed, 22 Jul 2020 12:59:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6911527/SRX6911527.05_model.r WARNING @ Wed, 22 Jul 2020 12:59:03: #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 Jul 2020 12:59:03: #2 You may need to consider one of the other alternative d(s): 0,64,88,156,172,179,185,206,242,257,275,290,322,351,362,412,433,466,481,512,527,531,540,555,587 WARNING @ Wed, 22 Jul 2020 12:59:03: #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 Jul 2020 12:59:03: #3 Call peaks... INFO @ Wed, 22 Jul 2020 12:59:03: #3 Pre-compute pvalue-qvalue table... /var/spool/uge/at145/job_scripts/7104820: line 297: 4448 Terminated MACS $i /var/spool/uge/at145/job_scripts/7104820: line 297: 23812 Terminated MACS $i /var/spool/uge/at145/job_scripts/7104820: line 297: 46888 Terminated MACS $i ls: cannot access SRX6911527.05.bed: No such file or directory mv: cannot stat ‘SRX6911527.05.bed’: No such file or directory mv: cannot stat ‘SRX6911527.05.bb’: No such file or directory ls: cannot access SRX6911527.10.bed: No such file or directory mv: cannot stat ‘SRX6911527.10.bed’: No such file or directory mv: cannot stat ‘SRX6911527.10.bb’: No such file or directory ls: cannot access SRX6911527.20.bed: No such file or directory mv: cannot stat ‘SRX6911527.20.bed’: No such file or directory mv: cannot stat ‘SRX6911527.20.bb’: No such file or directory