Job ID = 14519836 SRX = SRX9786281 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 14185743 spots for SRR13362145/SRR13362145.sra Written 14185743 spots for SRR13362145/SRR13362145.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:43 14185743 reads; of these: 14185743 (100.00%) were paired; of these: 7581166 (53.44%) aligned concordantly 0 times 5903568 (41.62%) aligned concordantly exactly 1 time 701009 (4.94%) aligned concordantly >1 times ---- 7581166 pairs aligned concordantly 0 times; of these: 122703 (1.62%) aligned discordantly 1 time ---- 7458463 pairs aligned 0 times concordantly or discordantly; of these: 14916926 mates make up the pairs; of these: 9524113 (63.85%) aligned 0 times 4715784 (31.61%) aligned exactly 1 time 677029 (4.54%) aligned >1 times 66.43% overall alignment rate Time searching: 00:06:44 Overall time: 00:06:44 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] 560515 / 6726012 = 0.0833 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 18:03:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9786281/SRX9786281.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9786281/SRX9786281.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9786281/SRX9786281.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9786281/SRX9786281.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 @ Sat, 15 Jan 2022 18:03:51: #1 read tag files... INFO @ Sat, 15 Jan 2022 18:03:51: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 18:03:57: 1000000 INFO @ Sat, 15 Jan 2022 18:04:01: 2000000 INFO @ Sat, 15 Jan 2022 18:04:06: 3000000 INFO @ Sat, 15 Jan 2022 18:04:10: 4000000 INFO @ Sat, 15 Jan 2022 18:04:15: 5000000 INFO @ Sat, 15 Jan 2022 18:04:19: 6000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 18:04:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9786281/SRX9786281.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9786281/SRX9786281.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9786281/SRX9786281.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9786281/SRX9786281.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 @ Sat, 15 Jan 2022 18:04:21: #1 read tag files... INFO @ Sat, 15 Jan 2022 18:04:21: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 18:04:24: 7000000 INFO @ Sat, 15 Jan 2022 18:04:27: 1000000 INFO @ Sat, 15 Jan 2022 18:04:29: 8000000 INFO @ Sat, 15 Jan 2022 18:04:33: 2000000 INFO @ Sat, 15 Jan 2022 18:04:34: 9000000 INFO @ Sat, 15 Jan 2022 18:04:39: 3000000 INFO @ Sat, 15 Jan 2022 18:04:39: 10000000 INFO @ Sat, 15 Jan 2022 18:04:44: 4000000 INFO @ Sat, 15 Jan 2022 18:04:45: 11000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 18:04:50: 12000000 INFO @ Sat, 15 Jan 2022 18:04:50: 5000000 INFO @ Sat, 15 Jan 2022 18:04:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9786281/SRX9786281.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9786281/SRX9786281.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9786281/SRX9786281.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9786281/SRX9786281.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 @ Sat, 15 Jan 2022 18:04:51: #1 read tag files... INFO @ Sat, 15 Jan 2022 18:04:51: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 18:04:55: 13000000 INFO @ Sat, 15 Jan 2022 18:04:56: 6000000 INFO @ Sat, 15 Jan 2022 18:04:57: 1000000 INFO @ Sat, 15 Jan 2022 18:05:01: 14000000 INFO @ Sat, 15 Jan 2022 18:05:01: 7000000 INFO @ Sat, 15 Jan 2022 18:05:03: 2000000 INFO @ Sat, 15 Jan 2022 18:05:06: 15000000 INFO @ Sat, 15 Jan 2022 18:05:07: 8000000 INFO @ Sat, 15 Jan 2022 18:05:09: 3000000 INFO @ Sat, 15 Jan 2022 18:05:11: 16000000 INFO @ Sat, 15 Jan 2022 18:05:13: 9000000 INFO @ Sat, 15 Jan 2022 18:05:15: 4000000 INFO @ Sat, 15 Jan 2022 18:05:17: 17000000 INFO @ Sat, 15 Jan 2022 18:05:19: 10000000 INFO @ Sat, 15 Jan 2022 18:05:20: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 18:05:20: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 18:05:20: #1 total tags in treatment: 6047667 INFO @ Sat, 15 Jan 2022 18:05:20: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 18:05:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 18:05:21: #1 tags after filtering in treatment: 4372374 INFO @ Sat, 15 Jan 2022 18:05:21: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 15 Jan 2022 18:05:21: #1 finished! INFO @ Sat, 15 Jan 2022 18:05:21: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 18:05:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 18:05:21: 5000000 INFO @ Sat, 15 Jan 2022 18:05:21: #2 number of paired peaks: 141 WARNING @ Sat, 15 Jan 2022 18:05:21: Fewer paired peaks (141) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 141 pairs to build model! INFO @ Sat, 15 Jan 2022 18:05:21: start model_add_line... INFO @ Sat, 15 Jan 2022 18:05:21: start X-correlation... INFO @ Sat, 15 Jan 2022 18:05:21: end of X-cor INFO @ Sat, 15 Jan 2022 18:05:21: #2 finished! INFO @ Sat, 15 Jan 2022 18:05:21: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 18:05:21: #2 alternative fragment length(s) may be 0,11,21,48,73,87,100,136,169,199,205,211,227,253,292,312,336,356,378,409,419,422,451,458,464,480,499,513,516,563,592 bps INFO @ Sat, 15 Jan 2022 18:05:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX9786281/SRX9786281.05_model.r WARNING @ Sat, 15 Jan 2022 18:05:21: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 18:05:21: #2 You may need to consider one of the other alternative d(s): 0,11,21,48,73,87,100,136,169,199,205,211,227,253,292,312,336,356,378,409,419,422,451,458,464,480,499,513,516,563,592 WARNING @ Sat, 15 Jan 2022 18:05:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Jan 2022 18:05:21: #3 Call peaks... INFO @ Sat, 15 Jan 2022 18:05:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 18:05:25: 11000000 INFO @ Sat, 15 Jan 2022 18:05:26: 6000000 INFO @ Sat, 15 Jan 2022 18:05:30: 12000000 INFO @ Sat, 15 Jan 2022 18:05:32: 7000000 INFO @ Sat, 15 Jan 2022 18:05:36: 13000000 INFO @ Sat, 15 Jan 2022 18:05:38: 8000000 INFO @ Sat, 15 Jan 2022 18:05:42: 14000000 INFO @ Sat, 15 Jan 2022 18:05:44: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 18:05:48: 15000000 INFO @ Sat, 15 Jan 2022 18:05:49: 10000000 INFO @ Sat, 15 Jan 2022 18:05:53: 16000000 INFO @ Sat, 15 Jan 2022 18:05:55: 11000000 BigWig に変換しました。 /var/spool/uge/at141/job_scripts/14519836: line 297: 88405 Terminated MACS $i /var/spool/uge/at141/job_scripts/14519836: line 297: 90466 Terminated MACS $i /var/spool/uge/at141/job_scripts/14519836: line 297: 90562 Terminated MACS $i ls: cannot access SRX9786281.05.bed: No such file or directory mv: cannot stat ‘SRX9786281.05.bed’: No such file or directory mv: cannot stat ‘SRX9786281.05.bb’: No such file or directory ls: cannot access SRX9786281.10.bed: No such file or directory mv: cannot stat ‘SRX9786281.10.bed’: No such file or directory mv: cannot stat ‘SRX9786281.10.bb’: No such file or directory ls: cannot access SRX9786281.20.bed: No such file or directory mv: cannot stat ‘SRX9786281.20.bed’: No such file or directory mv: cannot stat ‘SRX9786281.20.bb’: No such file or directory