Job ID = 14521263 SRX = SRX8245392 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 9869974 spots for SRR11684603/SRR11684603.sra Written 9869974 spots for SRR11684603/SRR11684603.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: 00:08:42 9869974 reads; of these: 9869974 (100.00%) were paired; of these: 5457898 (55.30%) aligned concordantly 0 times 3916271 (39.68%) aligned concordantly exactly 1 time 495805 (5.02%) aligned concordantly >1 times ---- 5457898 pairs aligned concordantly 0 times; of these: 30065 (0.55%) aligned discordantly 1 time ---- 5427833 pairs aligned 0 times concordantly or discordantly; of these: 10855666 mates make up the pairs; of these: 7104382 (65.44%) aligned 0 times 3282024 (30.23%) aligned exactly 1 time 469260 (4.32%) aligned >1 times 64.01% overall alignment rate Time searching: 00:08:43 Overall time: 00:08:43 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] 375507 / 4441341 = 0.0845 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 21:02:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245392/SRX8245392.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245392/SRX8245392.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245392/SRX8245392.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245392/SRX8245392.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 21:02:18: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:02:18: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:02:27: 1000000 INFO @ Sat, 15 Jan 2022 21:02:39: 2000000 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 21:02:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245392/SRX8245392.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245392/SRX8245392.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245392/SRX8245392.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245392/SRX8245392.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 21:02:48: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:02:48: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:02:48: 3000000 INFO @ Sat, 15 Jan 2022 21:02:56: 1000000 INFO @ Sat, 15 Jan 2022 21:02:58: 4000000 INFO @ Sat, 15 Jan 2022 21:03:04: 2000000 INFO @ Sat, 15 Jan 2022 21:03:08: 5000000 INFO @ Sat, 15 Jan 2022 21:03:12: 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 21:03:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245392/SRX8245392.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245392/SRX8245392.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245392/SRX8245392.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245392/SRX8245392.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 21:03:18: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:03:18: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:03:18: 6000000 INFO @ Sat, 15 Jan 2022 21:03:20: 4000000 INFO @ Sat, 15 Jan 2022 21:03:28: 5000000 INFO @ Sat, 15 Jan 2022 21:03:28: 1000000 INFO @ Sat, 15 Jan 2022 21:03:29: 7000000 INFO @ Sat, 15 Jan 2022 21:03:35: 6000000 INFO @ Sat, 15 Jan 2022 21:03:38: 2000000 INFO @ Sat, 15 Jan 2022 21:03:39: 8000000 INFO @ Sat, 15 Jan 2022 21:03:43: 7000000 INFO @ Sat, 15 Jan 2022 21:03:48: 3000000 INFO @ Sat, 15 Jan 2022 21:03:50: 9000000 INFO @ Sat, 15 Jan 2022 21:03:51: 8000000 INFO @ Sat, 15 Jan 2022 21:03:59: 4000000 INFO @ Sat, 15 Jan 2022 21:03:59: 9000000 INFO @ Sat, 15 Jan 2022 21:04:01: 10000000 INFO @ Sat, 15 Jan 2022 21:04:07: 10000000 INFO @ Sat, 15 Jan 2022 21:04:09: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 21:04:11: 11000000 INFO @ Sat, 15 Jan 2022 21:04:14: 11000000 INFO @ Sat, 15 Jan 2022 21:04:19: 6000000 INFO @ Sat, 15 Jan 2022 21:04:20: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 21:04:20: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 21:04:20: #1 total tags in treatment: 4037919 INFO @ Sat, 15 Jan 2022 21:04:20: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:04:20: #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 21:04:20: #1 tags after filtering in treatment: 2452497 INFO @ Sat, 15 Jan 2022 21:04:20: #1 Redundant rate of treatment: 0.39 INFO @ Sat, 15 Jan 2022 21:04:20: #1 finished! INFO @ Sat, 15 Jan 2022 21:04:20: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:04:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:04:21: #2 number of paired peaks: 171 WARNING @ Sat, 15 Jan 2022 21:04:21: Fewer paired peaks (171) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 171 pairs to build model! INFO @ Sat, 15 Jan 2022 21:04:21: start model_add_line... INFO @ Sat, 15 Jan 2022 21:04:21: start X-correlation... INFO @ Sat, 15 Jan 2022 21:04:21: end of X-cor INFO @ Sat, 15 Jan 2022 21:04:21: #2 finished! INFO @ Sat, 15 Jan 2022 21:04:21: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 21:04:21: #2 alternative fragment length(s) may be 0,12,48,95,118,193,219,255,280,307,321,342,383,403,429,490,521,542,582 bps INFO @ Sat, 15 Jan 2022 21:04:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245392/SRX8245392.05_model.r WARNING @ Sat, 15 Jan 2022 21:04:21: #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 21:04:21: #2 You may need to consider one of the other alternative d(s): 0,12,48,95,118,193,219,255,280,307,321,342,383,403,429,490,521,542,582 WARNING @ Sat, 15 Jan 2022 21:04:21: #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 21:04:21: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:04:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:04:21: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 21:04:21: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 21:04:21: #1 total tags in treatment: 4037919 INFO @ Sat, 15 Jan 2022 21:04:21: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:04:21: #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 21:04:21: #1 tags after filtering in treatment: 2452497 INFO @ Sat, 15 Jan 2022 21:04:21: #1 Redundant rate of treatment: 0.39 INFO @ Sat, 15 Jan 2022 21:04:21: #1 finished! INFO @ Sat, 15 Jan 2022 21:04:21: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:04:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:04:22: #2 number of paired peaks: 171 WARNING @ Sat, 15 Jan 2022 21:04:22: Fewer paired peaks (171) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 171 pairs to build model! INFO @ Sat, 15 Jan 2022 21:04:22: start model_add_line... INFO @ Sat, 15 Jan 2022 21:04:22: start X-correlation... INFO @ Sat, 15 Jan 2022 21:04:22: end of X-cor INFO @ Sat, 15 Jan 2022 21:04:22: #2 finished! INFO @ Sat, 15 Jan 2022 21:04:22: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 21:04:22: #2 alternative fragment length(s) may be 0,12,48,95,118,193,219,255,280,307,321,342,383,403,429,490,521,542,582 bps INFO @ Sat, 15 Jan 2022 21:04:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245392/SRX8245392.10_model.r WARNING @ Sat, 15 Jan 2022 21:04:22: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 21:04:22: #2 You may need to consider one of the other alternative d(s): 0,12,48,95,118,193,219,255,280,307,321,342,383,403,429,490,521,542,582 WARNING @ Sat, 15 Jan 2022 21:04:22: #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 21:04:22: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:04:22: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 /var/spool/uge/at085/job_scripts/14521263: line 297: 29249 Terminated MACS $i /var/spool/uge/at085/job_scripts/14521263: line 297: 29416 Terminated MACS $i /var/spool/uge/at085/job_scripts/14521263: line 297: 31452 Terminated MACS $i ls: cannot access SRX8245392.05.bed: No such file or directory mv: cannot stat ‘SRX8245392.05.bed’: No such file or directory mv: cannot stat ‘SRX8245392.05.bb’: No such file or directory ls: cannot access SRX8245392.10.bed: No such file or directory mv: cannot stat ‘SRX8245392.10.bed’: No such file or directory mv: cannot stat ‘SRX8245392.10.bb’: No such file or directory ls: cannot access SRX8245392.20.bed: No such file or directory mv: cannot stat ‘SRX8245392.20.bed’: No such file or directory mv: cannot stat ‘SRX8245392.20.bb’: No such file or directory