Job ID = 7103007 SRX = SRX6911523 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 16310095 spots for SRR10191166/SRR10191166.sra Written 16310095 spots for SRR10191166/SRR10191166.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: 00:14:51 16310095 reads; of these: 16310095 (100.00%) were paired; of these: 5170660 (31.70%) aligned concordantly 0 times 9537530 (58.48%) aligned concordantly exactly 1 time 1601905 (9.82%) aligned concordantly >1 times ---- 5170660 pairs aligned concordantly 0 times; of these: 579474 (11.21%) aligned discordantly 1 time ---- 4591186 pairs aligned 0 times concordantly or discordantly; of these: 9182372 mates make up the pairs; of these: 8406819 (91.55%) aligned 0 times 506567 (5.52%) aligned exactly 1 time 268986 (2.93%) aligned >1 times 74.23% overall alignment rate Time searching: 00:14:51 Overall time: 00:14:51 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] 964176 / 11716010 = 0.0823 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 12:42:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6911523/SRX6911523.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6911523/SRX6911523.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6911523/SRX6911523.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6911523/SRX6911523.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 12:42:36: #1 read tag files... INFO @ Wed, 22 Jul 2020 12:42:36: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 12:42:43: 1000000 INFO @ Wed, 22 Jul 2020 12:42:49: 2000000 INFO @ Wed, 22 Jul 2020 12:42:55: 3000000 INFO @ Wed, 22 Jul 2020 12:43:01: 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 12:43:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6911523/SRX6911523.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6911523/SRX6911523.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6911523/SRX6911523.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6911523/SRX6911523.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 12:43:06: #1 read tag files... INFO @ Wed, 22 Jul 2020 12:43:06: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 12:43:08: 5000000 INFO @ Wed, 22 Jul 2020 12:43:15: 1000000 INFO @ Wed, 22 Jul 2020 12:43:15: 6000000 INFO @ Wed, 22 Jul 2020 12:43:23: 7000000 INFO @ Wed, 22 Jul 2020 12:43:24: 2000000 INFO @ Wed, 22 Jul 2020 12:43:30: 8000000 INFO @ Wed, 22 Jul 2020 12:43:32: 3000000 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 12:43:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6911523/SRX6911523.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6911523/SRX6911523.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6911523/SRX6911523.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6911523/SRX6911523.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 12:43:37: #1 read tag files... INFO @ Wed, 22 Jul 2020 12:43:37: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 12:43:38: 9000000 INFO @ Wed, 22 Jul 2020 12:43:41: 4000000 INFO @ Wed, 22 Jul 2020 12:43:45: 1000000 INFO @ Wed, 22 Jul 2020 12:43:46: 10000000 INFO @ Wed, 22 Jul 2020 12:43:49: 5000000 INFO @ Wed, 22 Jul 2020 12:43:54: 11000000 INFO @ Wed, 22 Jul 2020 12:43:54: 2000000 INFO @ Wed, 22 Jul 2020 12:43:58: 6000000 INFO @ Wed, 22 Jul 2020 12:44:02: 12000000 INFO @ Wed, 22 Jul 2020 12:44:03: 3000000 INFO @ Wed, 22 Jul 2020 12:44:07: 7000000 INFO @ Wed, 22 Jul 2020 12:44:09: 13000000 INFO @ Wed, 22 Jul 2020 12:44:12: 4000000 INFO @ Wed, 22 Jul 2020 12:44:15: 8000000 INFO @ Wed, 22 Jul 2020 12:44:17: 14000000 INFO @ Wed, 22 Jul 2020 12:44:20: 5000000 INFO @ Wed, 22 Jul 2020 12:44:24: 9000000 INFO @ Wed, 22 Jul 2020 12:44:25: 15000000 INFO @ Wed, 22 Jul 2020 12:44:29: 6000000 INFO @ Wed, 22 Jul 2020 12:44:32: 10000000 INFO @ Wed, 22 Jul 2020 12:44:33: 16000000 INFO @ Wed, 22 Jul 2020 12:44:37: 7000000 INFO @ Wed, 22 Jul 2020 12:44:40: 17000000 INFO @ Wed, 22 Jul 2020 12:44:41: 11000000 INFO @ Wed, 22 Jul 2020 12:44:46: 8000000 INFO @ Wed, 22 Jul 2020 12:44:48: 18000000 INFO @ Wed, 22 Jul 2020 12:44:50: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Jul 2020 12:44:55: 9000000 INFO @ Wed, 22 Jul 2020 12:44:56: 19000000 INFO @ Wed, 22 Jul 2020 12:44:58: 13000000 BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 12:45:04: 20000000 INFO @ Wed, 22 Jul 2020 12:45:04: 10000000 INFO @ Wed, 22 Jul 2020 12:45:07: 14000000 INFO @ Wed, 22 Jul 2020 12:45:12: 21000000 INFO @ Wed, 22 Jul 2020 12:45:13: 11000000 INFO @ Wed, 22 Jul 2020 12:45:16: 15000000 INFO @ Wed, 22 Jul 2020 12:45:20: 22000000 INFO @ Wed, 22 Jul 2020 12:45:22: 12000000 INFO @ Wed, 22 Jul 2020 12:45:22: #1 tag size is determined as 101 bps INFO @ Wed, 22 Jul 2020 12:45:22: #1 tag size = 101 INFO @ Wed, 22 Jul 2020 12:45:22: #1 total tags in treatment: 10188648 INFO @ Wed, 22 Jul 2020 12:45:22: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 12:45:22: #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 12:45:22: #1 tags after filtering in treatment: 3931722 INFO @ Wed, 22 Jul 2020 12:45:22: #1 Redundant rate of treatment: 0.61 INFO @ Wed, 22 Jul 2020 12:45:22: #1 finished! INFO @ Wed, 22 Jul 2020 12:45:22: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 12:45:22: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 12:45:22: #2 number of paired peaks: 728 WARNING @ Wed, 22 Jul 2020 12:45:22: Fewer paired peaks (728) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 728 pairs to build model! INFO @ Wed, 22 Jul 2020 12:45:22: start model_add_line... INFO @ Wed, 22 Jul 2020 12:45:22: start X-correlation... INFO @ Wed, 22 Jul 2020 12:45:22: end of X-cor INFO @ Wed, 22 Jul 2020 12:45:22: #2 finished! INFO @ Wed, 22 Jul 2020 12:45:22: #2 predicted fragment length is 0 bps INFO @ Wed, 22 Jul 2020 12:45:22: #2 alternative fragment length(s) may be 0,30,64,79,98,163,199,218,242,254,273,289,310,335,351,356,413,437,455,463,478,491,560,571,591 bps INFO @ Wed, 22 Jul 2020 12:45:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6911523/SRX6911523.05_model.r WARNING @ Wed, 22 Jul 2020 12:45:22: #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 12:45:22: #2 You may need to consider one of the other alternative d(s): 0,30,64,79,98,163,199,218,242,254,273,289,310,335,351,356,413,437,455,463,478,491,560,571,591 WARNING @ Wed, 22 Jul 2020 12:45:22: #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 12:45:22: #3 Call peaks... /var/spool/uge/at143/job_scripts/7103007: line 297: 112254 Terminated MACS $i /var/spool/uge/at143/job_scripts/7103007: line 297: 114145 Terminated MACS $i /var/spool/uge/at143/job_scripts/7103007: line 297: 115918 Terminated MACS $i INFO @ Wed, 22 Jul 2020 12:45:22: #3 Pre-compute pvalue-qvalue table... ls: cannot access SRX6911523.05.bed: No such file or directory mv: cannot stat ‘SRX6911523.05.bed’: No such file or directory mv: cannot stat ‘SRX6911523.05.bb’: No such file or directory ls: cannot access SRX6911523.10.bed: No such file or directory mv: cannot stat ‘SRX6911523.10.bed’: No such file or directory mv: cannot stat ‘SRX6911523.10.bb’: No such file or directory ls: cannot access SRX6911523.20.bed: No such file or directory mv: cannot stat ‘SRX6911523.20.bed’: No such file or directory mv: cannot stat ‘SRX6911523.20.bb’: No such file or directory