Job ID = 14520358 SRX = SRX11781105 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 17387379 spots for SRR15481048/SRR15481048.sra Written 17387379 spots for SRR15481048/SRR15481048.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: 00:19:00 17387379 reads; of these: 17387379 (100.00%) were paired; of these: 5604164 (32.23%) aligned concordantly 0 times 10633652 (61.16%) aligned concordantly exactly 1 time 1149563 (6.61%) aligned concordantly >1 times ---- 5604164 pairs aligned concordantly 0 times; of these: 209782 (3.74%) aligned discordantly 1 time ---- 5394382 pairs aligned 0 times concordantly or discordantly; of these: 10788764 mates make up the pairs; of these: 6339786 (58.76%) aligned 0 times 3907871 (36.22%) aligned exactly 1 time 541107 (5.02%) aligned >1 times 81.77% overall alignment rate Time searching: 00:19:00 Overall time: 00:19:00 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] 4066645 / 11992036 = 0.3391 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 19:35:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781105/SRX11781105.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781105/SRX11781105.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781105/SRX11781105.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781105/SRX11781105.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 19:35:48: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:35:48: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:35:56: 1000000 INFO @ Sat, 15 Jan 2022 19:36:04: 2000000 INFO @ Sat, 15 Jan 2022 19:36:13: 3000000 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 19:36:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781105/SRX11781105.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781105/SRX11781105.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781105/SRX11781105.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781105/SRX11781105.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 19:36:17: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:36:17: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:36:22: 4000000 INFO @ Sat, 15 Jan 2022 19:36:27: 1000000 INFO @ Sat, 15 Jan 2022 19:36:32: 5000000 INFO @ Sat, 15 Jan 2022 19:36:36: 2000000 INFO @ Sat, 15 Jan 2022 19:36:42: 6000000 INFO @ Sat, 15 Jan 2022 19:36:44: 3000000 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 19:36:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781105/SRX11781105.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781105/SRX11781105.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781105/SRX11781105.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781105/SRX11781105.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 19:36:47: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:36:47: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:36:51: 7000000 INFO @ Sat, 15 Jan 2022 19:36:53: 4000000 INFO @ Sat, 15 Jan 2022 19:36:57: 1000000 INFO @ Sat, 15 Jan 2022 19:37:01: 8000000 INFO @ Sat, 15 Jan 2022 19:37:02: 5000000 INFO @ Sat, 15 Jan 2022 19:37:08: 2000000 INFO @ Sat, 15 Jan 2022 19:37:11: 6000000 INFO @ Sat, 15 Jan 2022 19:37:11: 9000000 INFO @ Sat, 15 Jan 2022 19:37:19: 3000000 INFO @ Sat, 15 Jan 2022 19:37:19: 7000000 INFO @ Sat, 15 Jan 2022 19:37:21: 10000000 INFO @ Sat, 15 Jan 2022 19:37:28: 8000000 INFO @ Sat, 15 Jan 2022 19:37:29: 4000000 INFO @ Sat, 15 Jan 2022 19:37:31: 11000000 INFO @ Sat, 15 Jan 2022 19:37:37: 9000000 INFO @ Sat, 15 Jan 2022 19:37:38: 5000000 INFO @ Sat, 15 Jan 2022 19:37:42: 12000000 INFO @ Sat, 15 Jan 2022 19:37:46: 10000000 INFO @ Sat, 15 Jan 2022 19:37:47: 6000000 INFO @ Sat, 15 Jan 2022 19:37:52: 13000000 INFO @ Sat, 15 Jan 2022 19:37:55: 7000000 INFO @ Sat, 15 Jan 2022 19:37:56: 11000000 INFO @ Sat, 15 Jan 2022 19:38:02: 14000000 INFO @ Sat, 15 Jan 2022 19:38:04: 8000000 INFO @ Sat, 15 Jan 2022 19:38:07: 12000000 INFO @ Sat, 15 Jan 2022 19:38:12: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 19:38:13: 9000000 INFO @ Sat, 15 Jan 2022 19:38:17: 13000000 INFO @ Sat, 15 Jan 2022 19:38:22: 16000000 INFO @ Sat, 15 Jan 2022 19:38:23: 10000000 INFO @ Sat, 15 Jan 2022 19:38:27: 14000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 19:38:32: 17000000 INFO @ Sat, 15 Jan 2022 19:38:32: 11000000 INFO @ Sat, 15 Jan 2022 19:38:36: 15000000 INFO @ Sat, 15 Jan 2022 19:38:41: 12000000 INFO @ Sat, 15 Jan 2022 19:38:42: 18000000 INFO @ Sat, 15 Jan 2022 19:38:45: 16000000 INFO @ Sat, 15 Jan 2022 19:38:51: 13000000 INFO @ Sat, 15 Jan 2022 19:38:52: 19000000 INFO @ Sat, 15 Jan 2022 19:38:55: 17000000 INFO @ Sat, 15 Jan 2022 19:39:00: 14000000 INFO @ Sat, 15 Jan 2022 19:39:02: 20000000 INFO @ Sat, 15 Jan 2022 19:39:04: 18000000 INFO @ Sat, 15 Jan 2022 19:39:05: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 19:39:05: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 19:39:05: #1 total tags in treatment: 7758964 INFO @ Sat, 15 Jan 2022 19:39:05: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:39:05: #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 19:39:05: #1 tags after filtering in treatment: 4182655 INFO @ Sat, 15 Jan 2022 19:39:05: #1 Redundant rate of treatment: 0.46 INFO @ Sat, 15 Jan 2022 19:39:05: #1 finished! INFO @ Sat, 15 Jan 2022 19:39:05: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:39:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:39:06: #2 number of paired peaks: 161 WARNING @ Sat, 15 Jan 2022 19:39:06: Fewer paired peaks (161) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 161 pairs to build model! INFO @ Sat, 15 Jan 2022 19:39:06: start model_add_line... INFO @ Sat, 15 Jan 2022 19:39:06: start X-correlation... INFO @ Sat, 15 Jan 2022 19:39:06: end of X-cor INFO @ Sat, 15 Jan 2022 19:39:06: #2 finished! INFO @ Sat, 15 Jan 2022 19:39:06: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 19:39:06: #2 alternative fragment length(s) may be 0,18,62,126,143,155,187,209,233,249,280,320,350,373,375,416,434,506,518,574 bps INFO @ Sat, 15 Jan 2022 19:39:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781105/SRX11781105.05_model.r WARNING @ Sat, 15 Jan 2022 19:39:06: #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 19:39:06: #2 You may need to consider one of the other alternative d(s): 0,18,62,126,143,155,187,209,233,249,280,320,350,373,375,416,434,506,518,574 WARNING @ Sat, 15 Jan 2022 19:39:06: #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 19:39:06: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:39:06: #3 Pre-compute pvalue-qvalue table... /var/spool/uge/it007/job_scripts/14520358: line 297: 18335 Terminated MACS $i /var/spool/uge/it007/job_scripts/14520358: line 297: 19581 Terminated MACS $i /var/spool/uge/it007/job_scripts/14520358: line 297: 21662 Terminated MACS $i ls: cannot access SRX11781105.05.bed: No such file or directory mv: cannot stat ‘SRX11781105.05.bed’: No such file or directory mv: cannot stat ‘SRX11781105.05.bb’: No such file or directory ls: cannot access SRX11781105.10.bed: No such file or directory mv: cannot stat ‘SRX11781105.10.bed’: No such file or directory mv: cannot stat ‘SRX11781105.10.bb’: No such file or directory ls: cannot access SRX11781105.20.bed: No such file or directory mv: cannot stat ‘SRX11781105.20.bed’: No such file or directory mv: cannot stat ‘SRX11781105.20.bb’: No such file or directory