Job ID = 14520365 SRX = SRX11781110 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-01-15T10:00:21 prefetch.2.10.7: 1) Downloading 'SRR15481053'... 2022-01-15T10:00:21 prefetch.2.10.7: Downloading via HTTPS... 2022-01-15T10:01:56 prefetch.2.10.7: HTTPS download succeed 2022-01-15T10:01:56 prefetch.2.10.7: 1) 'SRR15481053' was downloaded successfully 2022-01-15T10:01:56 prefetch.2.10.7: 'SRR15481053' has 0 unresolved dependencies Read 16627293 spots for SRR15481053/SRR15481053.sra Written 16627293 spots for SRR15481053/SRR15481053.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: 00:32:41 16627293 reads; of these: 16627293 (100.00%) were paired; of these: 3292626 (19.80%) aligned concordantly 0 times 7132092 (42.89%) aligned concordantly exactly 1 time 6202575 (37.30%) aligned concordantly >1 times ---- 3292626 pairs aligned concordantly 0 times; of these: 108585 (3.30%) aligned discordantly 1 time ---- 3184041 pairs aligned 0 times concordantly or discordantly; of these: 6368082 mates make up the pairs; of these: 4459909 (70.04%) aligned 0 times 1037004 (16.28%) aligned exactly 1 time 871169 (13.68%) aligned >1 times 86.59% overall alignment rate Time searching: 00:32:41 Overall time: 00:32:41 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] 2926576 / 13442191 = 0.2177 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 19:46:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781110/SRX11781110.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781110/SRX11781110.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781110/SRX11781110.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781110/SRX11781110.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 19:46:53: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:46:53: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:46:59: 1000000 INFO @ Sat, 15 Jan 2022 19:47:05: 2000000 INFO @ Sat, 15 Jan 2022 19:47:10: 3000000 INFO @ Sat, 15 Jan 2022 19:47:16: 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 19:47:22: 5000000 INFO @ Sat, 15 Jan 2022 19:47:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781110/SRX11781110.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781110/SRX11781110.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781110/SRX11781110.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781110/SRX11781110.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 19:47:23: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:47:23: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:47:28: 6000000 INFO @ Sat, 15 Jan 2022 19:47:29: 1000000 INFO @ Sat, 15 Jan 2022 19:47:35: 7000000 INFO @ Sat, 15 Jan 2022 19:47:36: 2000000 INFO @ Sat, 15 Jan 2022 19:47:41: 8000000 INFO @ Sat, 15 Jan 2022 19:47:43: 3000000 INFO @ Sat, 15 Jan 2022 19:47:48: 9000000 INFO @ Sat, 15 Jan 2022 19:47:49: 4000000 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 19:47:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781110/SRX11781110.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781110/SRX11781110.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781110/SRX11781110.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781110/SRX11781110.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 19:47:53: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:47:53: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:47:55: 10000000 INFO @ Sat, 15 Jan 2022 19:47:56: 5000000 INFO @ Sat, 15 Jan 2022 19:48:01: 1000000 INFO @ Sat, 15 Jan 2022 19:48:02: 11000000 INFO @ Sat, 15 Jan 2022 19:48:04: 6000000 INFO @ Sat, 15 Jan 2022 19:48:10: 12000000 INFO @ Sat, 15 Jan 2022 19:48:10: 2000000 INFO @ Sat, 15 Jan 2022 19:48:11: 7000000 INFO @ Sat, 15 Jan 2022 19:48:17: 13000000 INFO @ Sat, 15 Jan 2022 19:48:17: 3000000 INFO @ Sat, 15 Jan 2022 19:48:19: 8000000 INFO @ Sat, 15 Jan 2022 19:48:25: 14000000 INFO @ Sat, 15 Jan 2022 19:48:25: 4000000 INFO @ Sat, 15 Jan 2022 19:48:26: 9000000 INFO @ Sat, 15 Jan 2022 19:48:32: 15000000 INFO @ Sat, 15 Jan 2022 19:48:32: 5000000 INFO @ Sat, 15 Jan 2022 19:48:34: 10000000 INFO @ Sat, 15 Jan 2022 19:48:39: 16000000 INFO @ Sat, 15 Jan 2022 19:48:39: 6000000 INFO @ Sat, 15 Jan 2022 19:48:41: 11000000 INFO @ Sat, 15 Jan 2022 19:48:46: 7000000 INFO @ Sat, 15 Jan 2022 19:48:46: 17000000 INFO @ Sat, 15 Jan 2022 19:48:48: 12000000 INFO @ Sat, 15 Jan 2022 19:48:52: 8000000 INFO @ Sat, 15 Jan 2022 19:48:53: 18000000 INFO @ Sat, 15 Jan 2022 19:48:55: 13000000 INFO @ Sat, 15 Jan 2022 19:48:59: 9000000 INFO @ Sat, 15 Jan 2022 19:49:00: 19000000 INFO @ Sat, 15 Jan 2022 19:49:02: 14000000 INFO @ Sat, 15 Jan 2022 19:49:06: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 19:49:07: 20000000 INFO @ Sat, 15 Jan 2022 19:49:09: 15000000 INFO @ Sat, 15 Jan 2022 19:49:13: 11000000 INFO @ Sat, 15 Jan 2022 19:49:14: 21000000 INFO @ Sat, 15 Jan 2022 19:49:16: 16000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 19:49:20: 12000000 INFO @ Sat, 15 Jan 2022 19:49:20: 22000000 INFO @ Sat, 15 Jan 2022 19:49:23: 17000000 INFO @ Sat, 15 Jan 2022 19:49:27: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 19:49:27: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 19:49:27: #1 total tags in treatment: 10427079 INFO @ Sat, 15 Jan 2022 19:49:27: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:49:27: #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 19:49:27: 13000000 INFO @ Sat, 15 Jan 2022 19:49:27: #1 tags after filtering in treatment: 4241697 INFO @ Sat, 15 Jan 2022 19:49:27: #1 Redundant rate of treatment: 0.59 INFO @ Sat, 15 Jan 2022 19:49:27: #1 finished! INFO @ Sat, 15 Jan 2022 19:49:27: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:49:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:49:27: #2 number of paired peaks: 158 WARNING @ Sat, 15 Jan 2022 19:49:27: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Sat, 15 Jan 2022 19:49:27: start model_add_line... INFO @ Sat, 15 Jan 2022 19:49:27: start X-correlation... INFO @ Sat, 15 Jan 2022 19:49:27: end of X-cor INFO @ Sat, 15 Jan 2022 19:49:27: #2 finished! INFO @ Sat, 15 Jan 2022 19:49:27: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 19:49:27: #2 alternative fragment length(s) may be 0,15,44,67,92,125,154,156,177,206,229,249,270,304,320,340,353,368,401,429,464,496,517,536,549,566,578 bps INFO @ Sat, 15 Jan 2022 19:49:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781110/SRX11781110.05_model.r WARNING @ Sat, 15 Jan 2022 19:49:27: #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 19:49:27: #2 You may need to consider one of the other alternative d(s): 0,15,44,67,92,125,154,156,177,206,229,249,270,304,320,340,353,368,401,429,464,496,517,536,549,566,578 WARNING @ Sat, 15 Jan 2022 19:49:27: #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 19:49:27: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:49:27: #3 Pre-compute pvalue-qvalue table... /var/spool/uge/at154/job_scripts/14520365: line 297: 52503 Terminated MACS $i /var/spool/uge/at154/job_scripts/14520365: line 297: 52669 Terminated MACS $i /var/spool/uge/at154/job_scripts/14520365: line 297: 52902 Terminated MACS $i ls: cannot access SRX11781110.05.bed: No such file or directory mv: cannot stat ‘SRX11781110.05.bed’: No such file or directory mv: cannot stat ‘SRX11781110.05.bb’: No such file or directory ls: cannot access SRX11781110.10.bed: No such file or directory mv: cannot stat ‘SRX11781110.10.bed’: No such file or directory mv: cannot stat ‘SRX11781110.10.bb’: No such file or directory ls: cannot access SRX11781110.20.bed: No such file or directory mv: cannot stat ‘SRX11781110.20.bed’: No such file or directory mv: cannot stat ‘SRX11781110.20.bb’: No such file or directory