Job ID = 14521090 SRX = SRX8245352 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 10441278 spots for SRR11684563/SRR11684563.sra Written 10441278 spots for SRR11684563/SRR11684563.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: 00:05:27 10441278 reads; of these: 10441278 (100.00%) were paired; of these: 5152642 (49.35%) aligned concordantly 0 times 4764467 (45.63%) aligned concordantly exactly 1 time 524169 (5.02%) aligned concordantly >1 times ---- 5152642 pairs aligned concordantly 0 times; of these: 114021 (2.21%) aligned discordantly 1 time ---- 5038621 pairs aligned 0 times concordantly or discordantly; of these: 10077242 mates make up the pairs; of these: 6292948 (62.45%) aligned 0 times 3306064 (32.81%) aligned exactly 1 time 478230 (4.75%) aligned >1 times 69.87% overall alignment rate Time searching: 00:05:27 Overall time: 00:05:27 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] 423155 / 5402078 = 0.0783 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 20:35:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245352/SRX8245352.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245352/SRX8245352.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245352/SRX8245352.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245352/SRX8245352.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 20:35:50: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:35:50: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:35:56: 1000000 INFO @ Sat, 15 Jan 2022 20:36:03: 2000000 INFO @ Sat, 15 Jan 2022 20:36:09: 3000000 INFO @ Sat, 15 Jan 2022 20:36:16: 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 20:36:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245352/SRX8245352.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245352/SRX8245352.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245352/SRX8245352.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245352/SRX8245352.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 20:36:21: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:36:21: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:36:21: 5000000 INFO @ Sat, 15 Jan 2022 20:36:27: 1000000 INFO @ Sat, 15 Jan 2022 20:36:27: 6000000 INFO @ Sat, 15 Jan 2022 20:36:34: 2000000 INFO @ Sat, 15 Jan 2022 20:36:36: 7000000 INFO @ Sat, 15 Jan 2022 20:36:41: 3000000 INFO @ Sat, 15 Jan 2022 20:36:43: 8000000 INFO @ Sat, 15 Jan 2022 20:36:48: 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 BedGraph に変換中... INFO @ Sat, 15 Jan 2022 20:36:49: 9000000 INFO @ Sat, 15 Jan 2022 20:36:53: 5000000 INFO @ Sat, 15 Jan 2022 20:37:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245352/SRX8245352.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245352/SRX8245352.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245352/SRX8245352.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245352/SRX8245352.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 20:37:03: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:37:03: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:37:08: 10000000 INFO @ Sat, 15 Jan 2022 20:37:10: 6000000 INFO @ Sat, 15 Jan 2022 20:37:10: 1000000 INFO @ Sat, 15 Jan 2022 20:37:15: 11000000 INFO @ Sat, 15 Jan 2022 20:37:22: 7000000 INFO @ Sat, 15 Jan 2022 20:37:24: 2000000 INFO @ Sat, 15 Jan 2022 20:37:25: 12000000 INFO @ Sat, 15 Jan 2022 20:37:29: 8000000 INFO @ Sat, 15 Jan 2022 20:37:32: 3000000 INFO @ Sat, 15 Jan 2022 20:37:33: 13000000 INFO @ Sat, 15 Jan 2022 20:37:36: 9000000 INFO @ Sat, 15 Jan 2022 20:37:39: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:37:39: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:37:39: #1 total tags in treatment: 4868689 INFO @ Sat, 15 Jan 2022 20:37:39: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:37:39: #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 20:37:39: #1 tags after filtering in treatment: 2786500 INFO @ Sat, 15 Jan 2022 20:37:39: 4000000 INFO @ Sat, 15 Jan 2022 20:37:42: #1 Redundant rate of treatment: 0.43 INFO @ Sat, 15 Jan 2022 20:37:43: 10000000 INFO @ Sat, 15 Jan 2022 20:37:46: #1 finished! INFO @ Sat, 15 Jan 2022 20:37:46: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:37:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:37:46: #2 number of paired peaks: 173 WARNING @ Sat, 15 Jan 2022 20:37:46: Fewer paired peaks (173) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 173 pairs to build model! INFO @ Sat, 15 Jan 2022 20:37:46: start model_add_line... INFO @ Sat, 15 Jan 2022 20:37:46: start X-correlation... INFO @ Sat, 15 Jan 2022 20:37:46: end of X-cor INFO @ Sat, 15 Jan 2022 20:37:46: #2 finished! INFO @ Sat, 15 Jan 2022 20:37:46: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 20:37:46: #2 alternative fragment length(s) may be 0,49,67,126,139,212,225,267,307,328,342,377,395,425,479,518,551,565,578 bps INFO @ Sat, 15 Jan 2022 20:37:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245352/SRX8245352.05_model.r WARNING @ Sat, 15 Jan 2022 20:37:47: #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 20:37:47: #2 You may need to consider one of the other alternative d(s): 0,49,67,126,139,212,225,267,307,328,342,377,395,425,479,518,551,565,578 WARNING @ Sat, 15 Jan 2022 20:37:47: #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 20:37:47: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:37:47: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:37:53: 5000000 INFO @ Sat, 15 Jan 2022 20:37:53: 11000000 BigWig に変換しました。 /var/spool/uge/at147/job_scripts/14521090: line 297: 121719 Terminated MACS $i /var/spool/uge/at147/job_scripts/14521090: line 297: 7760 Terminated MACS $i /var/spool/uge/at147/job_scripts/14521090: line 297: 23728 Terminated MACS $i ls: cannot access SRX8245352.05.bed: No such file or directory mv: cannot stat ‘SRX8245352.05.bed’: No such file or directory mv: cannot stat ‘SRX8245352.05.bb’: No such file or directory ls: cannot access SRX8245352.10.bed: No such file or directory mv: cannot stat ‘SRX8245352.10.bed’: No such file or directory mv: cannot stat ‘SRX8245352.10.bb’: No such file or directory ls: cannot access SRX8245352.20.bed: No such file or directory mv: cannot stat ‘SRX8245352.20.bed’: No such file or directory mv: cannot stat ‘SRX8245352.20.bb’: No such file or directory