Job ID = 7104900 SRX = SRX6911528 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 13984584 spots for SRR10191139/SRR10191139.sra Written 13984584 spots for SRR10191139/SRR10191139.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: 00:18:27 13984584 reads; of these: 13984584 (100.00%) were paired; of these: 3988616 (28.52%) aligned concordantly 0 times 7786105 (55.68%) aligned concordantly exactly 1 time 2209863 (15.80%) aligned concordantly >1 times ---- 3988616 pairs aligned concordantly 0 times; of these: 1219683 (30.58%) aligned discordantly 1 time ---- 2768933 pairs aligned 0 times concordantly or discordantly; of these: 5537866 mates make up the pairs; of these: 3475543 (62.76%) aligned 0 times 1018809 (18.40%) aligned exactly 1 time 1043514 (18.84%) aligned >1 times 87.57% overall alignment rate Time searching: 00:18:27 Overall time: 00:18:27 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] 2215165 / 11213954 = 0.1975 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 13:02:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6911528/SRX6911528.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6911528/SRX6911528.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6911528/SRX6911528.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6911528/SRX6911528.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 13:02:36: #1 read tag files... INFO @ Wed, 22 Jul 2020 13:02:36: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 13:02:43: 1000000 INFO @ Wed, 22 Jul 2020 13:02:50: 2000000 INFO @ Wed, 22 Jul 2020 13:02:58: 3000000 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 13:03:05: 4000000 INFO @ Wed, 22 Jul 2020 13:03:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6911528/SRX6911528.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6911528/SRX6911528.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6911528/SRX6911528.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6911528/SRX6911528.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 13:03:06: #1 read tag files... INFO @ Wed, 22 Jul 2020 13:03:06: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 13:03:13: 5000000 INFO @ Wed, 22 Jul 2020 13:03:14: 1000000 INFO @ Wed, 22 Jul 2020 13:03:22: 6000000 INFO @ Wed, 22 Jul 2020 13:03:22: 2000000 INFO @ Wed, 22 Jul 2020 13:03:30: 7000000 INFO @ Wed, 22 Jul 2020 13:03:31: 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 13:03:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6911528/SRX6911528.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6911528/SRX6911528.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6911528/SRX6911528.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6911528/SRX6911528.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 13:03:36: #1 read tag files... INFO @ Wed, 22 Jul 2020 13:03:36: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 13:03:38: 8000000 INFO @ Wed, 22 Jul 2020 13:03:39: 4000000 INFO @ Wed, 22 Jul 2020 13:03:44: 1000000 INFO @ Wed, 22 Jul 2020 13:03:46: 9000000 INFO @ Wed, 22 Jul 2020 13:03:47: 5000000 INFO @ Wed, 22 Jul 2020 13:03:53: 2000000 INFO @ Wed, 22 Jul 2020 13:03:55: 10000000 INFO @ Wed, 22 Jul 2020 13:03:56: 6000000 INFO @ Wed, 22 Jul 2020 13:04:01: 3000000 INFO @ Wed, 22 Jul 2020 13:04:03: 11000000 INFO @ Wed, 22 Jul 2020 13:04:04: 7000000 INFO @ Wed, 22 Jul 2020 13:04:09: 4000000 INFO @ Wed, 22 Jul 2020 13:04:12: 12000000 INFO @ Wed, 22 Jul 2020 13:04:13: 8000000 INFO @ Wed, 22 Jul 2020 13:04:18: 5000000 INFO @ Wed, 22 Jul 2020 13:04:21: 13000000 INFO @ Wed, 22 Jul 2020 13:04:21: 9000000 INFO @ Wed, 22 Jul 2020 13:04:26: 6000000 INFO @ Wed, 22 Jul 2020 13:04:29: 14000000 INFO @ Wed, 22 Jul 2020 13:04:29: 10000000 INFO @ Wed, 22 Jul 2020 13:04:35: 7000000 INFO @ Wed, 22 Jul 2020 13:04:38: 15000000 INFO @ Wed, 22 Jul 2020 13:04:38: 11000000 INFO @ Wed, 22 Jul 2020 13:04:43: 8000000 INFO @ Wed, 22 Jul 2020 13:04:46: 16000000 INFO @ Wed, 22 Jul 2020 13:04:47: 12000000 INFO @ Wed, 22 Jul 2020 13:04:51: 9000000 INFO @ Wed, 22 Jul 2020 13:04:55: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Jul 2020 13:04:55: 13000000 INFO @ Wed, 22 Jul 2020 13:05:00: 10000000 INFO @ Wed, 22 Jul 2020 13:05:03: 18000000 INFO @ Wed, 22 Jul 2020 13:05:04: 14000000 BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 13:05:09: 11000000 INFO @ Wed, 22 Jul 2020 13:05:12: 19000000 INFO @ Wed, 22 Jul 2020 13:05:12: 15000000 INFO @ Wed, 22 Jul 2020 13:05:17: 12000000 INFO @ Wed, 22 Jul 2020 13:05:21: 20000000 INFO @ Wed, 22 Jul 2020 13:05:21: 16000000 INFO @ Wed, 22 Jul 2020 13:05:21: #1 tag size is determined as 101 bps INFO @ Wed, 22 Jul 2020 13:05:21: #1 tag size = 101 INFO @ Wed, 22 Jul 2020 13:05:21: #1 total tags in treatment: 7918210 INFO @ Wed, 22 Jul 2020 13:05:21: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 13:05:21: #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 13:05:22: #1 tags after filtering in treatment: 3200268 INFO @ Wed, 22 Jul 2020 13:05:22: #1 Redundant rate of treatment: 0.60 INFO @ Wed, 22 Jul 2020 13:05:22: #1 finished! INFO @ Wed, 22 Jul 2020 13:05:22: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 13:05:22: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 13:05:22: #2 number of paired peaks: 235 WARNING @ Wed, 22 Jul 2020 13:05:22: Fewer paired peaks (235) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 235 pairs to build model! INFO @ Wed, 22 Jul 2020 13:05:22: start model_add_line... INFO @ Wed, 22 Jul 2020 13:05:22: start X-correlation... INFO @ Wed, 22 Jul 2020 13:05:22: end of X-cor INFO @ Wed, 22 Jul 2020 13:05:22: #2 finished! INFO @ Wed, 22 Jul 2020 13:05:22: #2 predicted fragment length is 0 bps INFO @ Wed, 22 Jul 2020 13:05:22: #2 alternative fragment length(s) may be 0,48,72,91,110,124,137,174,187,228,264,332,335,361,367,394,444,536,557,565,581,597 bps INFO @ Wed, 22 Jul 2020 13:05:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6911528/SRX6911528.05_model.r WARNING @ Wed, 22 Jul 2020 13:05:22: #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 13:05:22: #2 You may need to consider one of the other alternative d(s): 0,48,72,91,110,124,137,174,187,228,264,332,335,361,367,394,444,536,557,565,581,597 WARNING @ Wed, 22 Jul 2020 13:05:22: #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 13:05:22: #3 Call peaks... INFO @ Wed, 22 Jul 2020 13:05:22: #3 Pre-compute pvalue-qvalue table... /var/spool/uge/at141/job_scripts/7104900: line 297: 68552 Terminated MACS $i /var/spool/uge/at141/job_scripts/7104900: line 297: 68676 Terminated MACS $i /var/spool/uge/at141/job_scripts/7104900: line 297: 68820 Terminated MACS $i ls: cannot access SRX6911528.05.bed: No such file or directory mv: cannot stat ‘SRX6911528.05.bed’: No such file or directory mv: cannot stat ‘SRX6911528.05.bb’: No such file or directory ls: cannot access SRX6911528.10.bed: No such file or directory mv: cannot stat ‘SRX6911528.10.bed’: No such file or directory mv: cannot stat ‘SRX6911528.10.bb’: No such file or directory ls: cannot access SRX6911528.20.bed: No such file or directory mv: cannot stat ‘SRX6911528.20.bed’: No such file or directory mv: cannot stat ‘SRX6911528.20.bb’: No such file or directory