Job ID = 14522130 SRX = SRX9786305 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 7622277 spots for SRR13362169/SRR13362169.sra Written 7622277 spots for SRR13362169/SRR13362169.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: 00:06:07 7622277 reads; of these: 7622277 (100.00%) were paired; of these: 1387590 (18.20%) aligned concordantly 0 times 5754448 (75.50%) aligned concordantly exactly 1 time 480239 (6.30%) aligned concordantly >1 times ---- 1387590 pairs aligned concordantly 0 times; of these: 149790 (10.79%) aligned discordantly 1 time ---- 1237800 pairs aligned 0 times concordantly or discordantly; of these: 2475600 mates make up the pairs; of these: 1607488 (64.93%) aligned 0 times 761262 (30.75%) aligned exactly 1 time 106850 (4.32%) aligned >1 times 89.46% overall alignment rate Time searching: 00:06:07 Overall time: 00:06:07 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] 497323 / 6383996 = 0.0779 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 22:26:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9786305/SRX9786305.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9786305/SRX9786305.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9786305/SRX9786305.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9786305/SRX9786305.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 22:26:33: #1 read tag files... INFO @ Sat, 15 Jan 2022 22:26:33: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 22:26:38: 1000000 INFO @ Sat, 15 Jan 2022 22:26:44: 2000000 INFO @ Sat, 15 Jan 2022 22:26:49: 3000000 INFO @ Sat, 15 Jan 2022 22:26:54: 4000000 INFO @ Sat, 15 Jan 2022 22:26:59: 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 22:27:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9786305/SRX9786305.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9786305/SRX9786305.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9786305/SRX9786305.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9786305/SRX9786305.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 22:27:03: #1 read tag files... INFO @ Sat, 15 Jan 2022 22:27:03: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 22:27:04: 6000000 INFO @ Sat, 15 Jan 2022 22:27:09: 1000000 INFO @ Sat, 15 Jan 2022 22:27:10: 7000000 INFO @ Sat, 15 Jan 2022 22:27:16: 2000000 INFO @ Sat, 15 Jan 2022 22:27:17: 8000000 INFO @ Sat, 15 Jan 2022 22:27:22: 3000000 INFO @ Sat, 15 Jan 2022 22:27:23: 9000000 INFO @ Sat, 15 Jan 2022 22:27:28: 4000000 INFO @ Sat, 15 Jan 2022 22:27:29: 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 22:27:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9786305/SRX9786305.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9786305/SRX9786305.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9786305/SRX9786305.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9786305/SRX9786305.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 22:27:33: #1 read tag files... INFO @ Sat, 15 Jan 2022 22:27:33: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 22:27:34: 5000000 INFO @ Sat, 15 Jan 2022 22:27:35: 11000000 INFO @ Sat, 15 Jan 2022 22:27:39: 1000000 INFO @ Sat, 15 Jan 2022 22:27:40: 6000000 INFO @ Sat, 15 Jan 2022 22:27:41: 12000000 INFO @ Sat, 15 Jan 2022 22:27:45: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 22:27:45: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 22:27:45: #1 total tags in treatment: 5742359 INFO @ Sat, 15 Jan 2022 22:27:45: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 22:27:45: #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 22:27:45: #1 tags after filtering in treatment: 3311637 INFO @ Sat, 15 Jan 2022 22:27:45: #1 Redundant rate of treatment: 0.42 INFO @ Sat, 15 Jan 2022 22:27:45: #1 finished! INFO @ Sat, 15 Jan 2022 22:27:45: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 22:27:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 22:27:45: #2 number of paired peaks: 171 WARNING @ Sat, 15 Jan 2022 22:27:45: 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 22:27:45: start model_add_line... INFO @ Sat, 15 Jan 2022 22:27:45: start X-correlation... INFO @ Sat, 15 Jan 2022 22:27:45: end of X-cor INFO @ Sat, 15 Jan 2022 22:27:45: #2 finished! INFO @ Sat, 15 Jan 2022 22:27:45: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 22:27:45: #2 alternative fragment length(s) may be 0,36,51,66,71,120,140,155,182,248,285,321,352,378,414,503,548,565 bps INFO @ Sat, 15 Jan 2022 22:27:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX9786305/SRX9786305.05_model.r WARNING @ Sat, 15 Jan 2022 22:27:45: #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 22:27:45: #2 You may need to consider one of the other alternative d(s): 0,36,51,66,71,120,140,155,182,248,285,321,352,378,414,503,548,565 WARNING @ Sat, 15 Jan 2022 22:27:45: #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 22:27:45: #3 Call peaks... INFO @ Sat, 15 Jan 2022 22:27:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 22:27:46: 2000000 INFO @ Sat, 15 Jan 2022 22:27:46: 7000000 INFO @ Sat, 15 Jan 2022 22:27:53: 3000000 INFO @ Sat, 15 Jan 2022 22:27:53: 8000000 INFO @ Sat, 15 Jan 2022 22:27:59: 9000000 INFO @ Sat, 15 Jan 2022 22:27:59: 4000000 INFO @ Sat, 15 Jan 2022 22:28:05: 10000000 INFO @ Sat, 15 Jan 2022 22:28:06: 5000000 INFO @ Sat, 15 Jan 2022 22:28:11: 11000000 INFO @ Sat, 15 Jan 2022 22:28:12: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 22:28:17: 12000000 INFO @ Sat, 15 Jan 2022 22:28:19: 7000000 INFO @ Sat, 15 Jan 2022 22:28:21: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 22:28:21: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 22:28:21: #1 total tags in treatment: 5742359 INFO @ Sat, 15 Jan 2022 22:28:21: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 22:28:21: #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 22:28:21: #1 tags after filtering in treatment: 3311637 INFO @ Sat, 15 Jan 2022 22:28:21: #1 Redundant rate of treatment: 0.42 INFO @ Sat, 15 Jan 2022 22:28:21: #1 finished! INFO @ Sat, 15 Jan 2022 22:28:21: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 22:28:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 22:28:21: #2 number of paired peaks: 171 WARNING @ Sat, 15 Jan 2022 22:28:21: 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 22:28:21: start model_add_line... INFO @ Sat, 15 Jan 2022 22:28:21: start X-correlation... INFO @ Sat, 15 Jan 2022 22:28:22: end of X-cor INFO @ Sat, 15 Jan 2022 22:28:22: #2 finished! INFO @ Sat, 15 Jan 2022 22:28:22: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 22:28:22: #2 alternative fragment length(s) may be 0,36,51,66,71,120,140,155,182,248,285,321,352,378,414,503,548,565 bps INFO @ Sat, 15 Jan 2022 22:28:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX9786305/SRX9786305.10_model.r WARNING @ Sat, 15 Jan 2022 22:28:22: #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 22:28:22: #2 You may need to consider one of the other alternative d(s): 0,36,51,66,71,120,140,155,182,248,285,321,352,378,414,503,548,565 WARNING @ Sat, 15 Jan 2022 22:28:22: #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 22:28:22: #3 Call peaks... INFO @ Sat, 15 Jan 2022 22:28:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 22:28:25: 8000000 BigWig に変換しました。 /var/spool/uge/at150/job_scripts/14522130: line 297: 118036 Terminated MACS $i /var/spool/uge/at150/job_scripts/14522130: line 297: 120072 Terminated MACS $i /var/spool/uge/at150/job_scripts/14522130: line 297: 130909 Terminated MACS $i ls: cannot access SRX9786305.05.bed: No such file or directory mv: cannot stat ‘SRX9786305.05.bed’: No such file or directory mv: cannot stat ‘SRX9786305.05.bb’: No such file or directory ls: cannot access SRX9786305.10.bed: No such file or directory mv: cannot stat ‘SRX9786305.10.bed’: No such file or directory mv: cannot stat ‘SRX9786305.10.bb’: No such file or directory ls: cannot access SRX9786305.20.bed: No such file or directory mv: cannot stat ‘SRX9786305.20.bed’: No such file or directory mv: cannot stat ‘SRX9786305.20.bb’: No such file or directory