Job ID = 14521266 SRX = SRX8245395 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 9699774 spots for SRR11684606/SRR11684606.sra Written 9699774 spots for SRR11684606/SRR11684606.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: 00:04:30 9699774 reads; of these: 9699774 (100.00%) were paired; of these: 5212565 (53.74%) aligned concordantly 0 times 3986655 (41.10%) aligned concordantly exactly 1 time 500554 (5.16%) aligned concordantly >1 times ---- 5212565 pairs aligned concordantly 0 times; of these: 12864 (0.25%) aligned discordantly 1 time ---- 5199701 pairs aligned 0 times concordantly or discordantly; of these: 10399402 mates make up the pairs; of these: 6601673 (63.48%) aligned 0 times 3329765 (32.02%) aligned exactly 1 time 467964 (4.50%) aligned >1 times 65.97% overall alignment rate Time searching: 00:04:31 Overall time: 00:04:31 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] 290990 / 4499309 = 0.0647 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 20:53:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245395/SRX8245395.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245395/SRX8245395.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245395/SRX8245395.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245395/SRX8245395.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 20:53:39: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:53:39: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:53:44: 1000000 INFO @ Sat, 15 Jan 2022 20:53:49: 2000000 INFO @ Sat, 15 Jan 2022 20:53:54: 3000000 INFO @ Sat, 15 Jan 2022 20:53:59: 4000000 INFO @ Sat, 15 Jan 2022 20:54:04: 5000000 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 20:54:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245395/SRX8245395.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245395/SRX8245395.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245395/SRX8245395.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245395/SRX8245395.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 20:54:09: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:54:09: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:54:10: 6000000 INFO @ Sat, 15 Jan 2022 20:54:15: 1000000 INFO @ Sat, 15 Jan 2022 20:54:16: 7000000 INFO @ Sat, 15 Jan 2022 20:54:21: 2000000 INFO @ Sat, 15 Jan 2022 20:54:23: 8000000 INFO @ Sat, 15 Jan 2022 20:54:27: 3000000 INFO @ Sat, 15 Jan 2022 20:54:29: 9000000 INFO @ Sat, 15 Jan 2022 20:54:34: 4000000 INFO @ Sat, 15 Jan 2022 20:54:36: 10000000 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 20:54:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245395/SRX8245395.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245395/SRX8245395.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245395/SRX8245395.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245395/SRX8245395.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 20:54:39: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:54:39: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:54:40: 5000000 INFO @ Sat, 15 Jan 2022 20:54:42: 11000000 INFO @ Sat, 15 Jan 2022 20:54:47: 1000000 INFO @ Sat, 15 Jan 2022 20:54:47: 6000000 INFO @ Sat, 15 Jan 2022 20:54:49: 12000000 INFO @ Sat, 15 Jan 2022 20:54:51: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:54:51: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:54:51: #1 total tags in treatment: 4196836 INFO @ Sat, 15 Jan 2022 20:54:51: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:54:51: #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 20:54:51: #1 tags after filtering in treatment: 2563412 INFO @ Sat, 15 Jan 2022 20:54:51: #1 Redundant rate of treatment: 0.39 INFO @ Sat, 15 Jan 2022 20:54:51: #1 finished! INFO @ Sat, 15 Jan 2022 20:54:51: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:54:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:54:51: #2 number of paired peaks: 170 WARNING @ Sat, 15 Jan 2022 20:54:51: Fewer paired peaks (170) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 170 pairs to build model! INFO @ Sat, 15 Jan 2022 20:54:51: start model_add_line... INFO @ Sat, 15 Jan 2022 20:54:51: start X-correlation... INFO @ Sat, 15 Jan 2022 20:54:51: end of X-cor INFO @ Sat, 15 Jan 2022 20:54:51: #2 finished! INFO @ Sat, 15 Jan 2022 20:54:51: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 20:54:51: #2 alternative fragment length(s) may be 0,48,66,86,99,129,195,222,225,241,247,294,335,356,395,417,421,429,449,468,486,512,549,570 bps INFO @ Sat, 15 Jan 2022 20:54:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245395/SRX8245395.05_model.r WARNING @ Sat, 15 Jan 2022 20:54:51: #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 20:54:51: #2 You may need to consider one of the other alternative d(s): 0,48,66,86,99,129,195,222,225,241,247,294,335,356,395,417,421,429,449,468,486,512,549,570 WARNING @ Sat, 15 Jan 2022 20:54:51: #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 20:54:51: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:54:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:54:54: 7000000 INFO @ Sat, 15 Jan 2022 20:54:55: 2000000 INFO @ Sat, 15 Jan 2022 20:55:01: 8000000 INFO @ Sat, 15 Jan 2022 20:55:03: 3000000 INFO @ Sat, 15 Jan 2022 20:55:08: 9000000 INFO @ Sat, 15 Jan 2022 20:55:11: 4000000 INFO @ Sat, 15 Jan 2022 20:55:15: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:55:19: 5000000 INFO @ Sat, 15 Jan 2022 20:55:23: 11000000 BigWig に変換しました。 /var/spool/uge/at149/job_scripts/14521266: line 297: 52916 Terminated MACS $i /var/spool/uge/at149/job_scripts/14521266: line 297: 55056 Terminated MACS $i /var/spool/uge/at149/job_scripts/14521266: line 297: 55355 Terminated MACS $i ls: cannot access SRX8245395.05.bed: No such file or directory mv: cannot stat ‘SRX8245395.05.bed’: No such file or directory mv: cannot stat ‘SRX8245395.05.bb’: No such file or directory ls: cannot access SRX8245395.10.bed: No such file or directory mv: cannot stat ‘SRX8245395.10.bed’: No such file or directory mv: cannot stat ‘SRX8245395.10.bb’: No such file or directory ls: cannot access SRX8245395.20.bed: No such file or directory mv: cannot stat ‘SRX8245395.20.bed’: No such file or directory mv: cannot stat ‘SRX8245395.20.bb’: No such file or directory