Job ID = 14521193 SRX = SRX8245371 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 11118139 spots for SRR11684582/SRR11684582.sra Written 11118139 spots for SRR11684582/SRR11684582.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: 00:06:48 11118139 reads; of these: 11118139 (100.00%) were paired; of these: 5654183 (50.86%) aligned concordantly 0 times 4579934 (41.19%) aligned concordantly exactly 1 time 884022 (7.95%) aligned concordantly >1 times ---- 5654183 pairs aligned concordantly 0 times; of these: 87136 (1.54%) aligned discordantly 1 time ---- 5567047 pairs aligned 0 times concordantly or discordantly; of these: 11134094 mates make up the pairs; of these: 6582521 (59.12%) aligned 0 times 3751342 (33.69%) aligned exactly 1 time 800231 (7.19%) aligned >1 times 70.40% overall alignment rate Time searching: 00:06:48 Overall time: 00:06:48 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] 364369 / 5550427 = 0.0656 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 20:48:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245371/SRX8245371.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245371/SRX8245371.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245371/SRX8245371.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245371/SRX8245371.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 20:48:13: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:48:13: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:48:20: 1000000 INFO @ Sat, 15 Jan 2022 20:48:26: 2000000 INFO @ Sat, 15 Jan 2022 20:48:32: 3000000 INFO @ Sat, 15 Jan 2022 20:48:39: 4000000 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 20:48:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245371/SRX8245371.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245371/SRX8245371.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245371/SRX8245371.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245371/SRX8245371.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 20:48:41: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:48:41: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:48:46: 5000000 INFO @ Sat, 15 Jan 2022 20:48:48: 1000000 INFO @ Sat, 15 Jan 2022 20:48:54: 6000000 INFO @ Sat, 15 Jan 2022 20:48:55: 2000000 INFO @ Sat, 15 Jan 2022 20:49:01: 7000000 INFO @ Sat, 15 Jan 2022 20:49:02: 3000000 INFO @ Sat, 15 Jan 2022 20:49:09: 4000000 INFO @ Sat, 15 Jan 2022 20:49:09: 8000000 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 BedGraph に変換中... INFO @ Sat, 15 Jan 2022 20:49:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245371/SRX8245371.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245371/SRX8245371.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245371/SRX8245371.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245371/SRX8245371.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 20:49:12: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:49:12: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:49:15: 5000000 INFO @ Sat, 15 Jan 2022 20:49:16: 9000000 INFO @ Sat, 15 Jan 2022 20:49:19: 1000000 INFO @ Sat, 15 Jan 2022 20:49:22: 6000000 INFO @ Sat, 15 Jan 2022 20:49:24: 10000000 INFO @ Sat, 15 Jan 2022 20:49:25: 2000000 INFO @ Sat, 15 Jan 2022 20:49:29: 7000000 INFO @ Sat, 15 Jan 2022 20:49:31: 11000000 INFO @ Sat, 15 Jan 2022 20:49:32: 3000000 INFO @ Sat, 15 Jan 2022 20:49:35: 8000000 INFO @ Sat, 15 Jan 2022 20:49:39: 12000000 INFO @ Sat, 15 Jan 2022 20:49:39: 4000000 INFO @ Sat, 15 Jan 2022 20:49:42: 9000000 INFO @ Sat, 15 Jan 2022 20:49:46: 5000000 INFO @ Sat, 15 Jan 2022 20:49:46: 13000000 INFO @ Sat, 15 Jan 2022 20:49:49: 10000000 INFO @ Sat, 15 Jan 2022 20:49:53: 6000000 INFO @ Sat, 15 Jan 2022 20:49:54: 14000000 INFO @ Sat, 15 Jan 2022 20:49:56: 11000000 INFO @ Sat, 15 Jan 2022 20:50:00: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:50:01: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:50:01: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:50:01: #1 total tags in treatment: 5101450 INFO @ Sat, 15 Jan 2022 20:50:01: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:50:01: #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 20:50:01: #1 tags after filtering in treatment: 3393236 INFO @ Sat, 15 Jan 2022 20:50:01: #1 Redundant rate of treatment: 0.33 INFO @ Sat, 15 Jan 2022 20:50:01: #1 finished! INFO @ Sat, 15 Jan 2022 20:50:01: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:50:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:50:02: #2 number of paired peaks: 168 WARNING @ Sat, 15 Jan 2022 20:50:02: Fewer paired peaks (168) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 168 pairs to build model! INFO @ Sat, 15 Jan 2022 20:50:02: start model_add_line... INFO @ Sat, 15 Jan 2022 20:50:02: start X-correlation... INFO @ Sat, 15 Jan 2022 20:50:02: end of X-cor INFO @ Sat, 15 Jan 2022 20:50:02: #2 finished! INFO @ Sat, 15 Jan 2022 20:50:02: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 20:50:02: #2 alternative fragment length(s) may be 0,43,87,134,167,214,240,265,289,296,320,344,361,394,417,447,465,485,496,516,561,578 bps INFO @ Sat, 15 Jan 2022 20:50:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245371/SRX8245371.05_model.r WARNING @ Sat, 15 Jan 2022 20:50:02: #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 20:50:02: #2 You may need to consider one of the other alternative d(s): 0,43,87,134,167,214,240,265,289,296,320,344,361,394,417,447,465,485,496,516,561,578 WARNING @ Sat, 15 Jan 2022 20:50:02: #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 20:50:02: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:50:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:50:03: 12000000 INFO @ Sat, 15 Jan 2022 20:50:06: 8000000 INFO @ Sat, 15 Jan 2022 20:50:10: 13000000 BigWig に変換しました。 /var/spool/uge/at147/job_scripts/14521193: line 297: 85407 Terminated MACS $i /var/spool/uge/at147/job_scripts/14521193: line 297: 92662 Terminated MACS $i /var/spool/uge/at147/job_scripts/14521193: line 297: 98676 Terminated MACS $i ls: cannot access SRX8245371.05.bed: No such file or directory mv: cannot stat ‘SRX8245371.05.bed’: No such file or directory mv: cannot stat ‘SRX8245371.05.bb’: No such file or directory ls: cannot access SRX8245371.10.bed: No such file or directory mv: cannot stat ‘SRX8245371.10.bed’: No such file or directory mv: cannot stat ‘SRX8245371.10.bb’: No such file or directory ls: cannot access SRX8245371.20.bed: No such file or directory mv: cannot stat ‘SRX8245371.20.bed’: No such file or directory mv: cannot stat ‘SRX8245371.20.bb’: No such file or directory