Job ID = 14519835 SRX = SRX9786280 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 10601267 spots for SRR13362144/SRR13362144.sra Written 10601267 spots for SRR13362144/SRR13362144.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: 00:05:19 10601267 reads; of these: 10601267 (100.00%) were paired; of these: 5873205 (55.40%) aligned concordantly 0 times 4297505 (40.54%) aligned concordantly exactly 1 time 430557 (4.06%) aligned concordantly >1 times ---- 5873205 pairs aligned concordantly 0 times; of these: 66010 (1.12%) aligned discordantly 1 time ---- 5807195 pairs aligned 0 times concordantly or discordantly; of these: 11614390 mates make up the pairs; of these: 7638971 (65.77%) aligned 0 times 3536687 (30.45%) aligned exactly 1 time 438732 (3.78%) aligned >1 times 63.97% overall alignment rate Time searching: 00:05:19 Overall time: 00:05:19 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] 339297 / 4793170 = 0.0708 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 18:00:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9786280/SRX9786280.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9786280/SRX9786280.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9786280/SRX9786280.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9786280/SRX9786280.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 18:00:33: #1 read tag files... INFO @ Sat, 15 Jan 2022 18:00:33: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 18:00:38: 1000000 INFO @ Sat, 15 Jan 2022 18:00:43: 2000000 INFO @ Sat, 15 Jan 2022 18:00:48: 3000000 INFO @ Sat, 15 Jan 2022 18:00:53: 4000000 INFO @ Sat, 15 Jan 2022 18:00:58: 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 18:01:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9786280/SRX9786280.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9786280/SRX9786280.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9786280/SRX9786280.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9786280/SRX9786280.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 18:01:03: #1 read tag files... INFO @ Sat, 15 Jan 2022 18:01:03: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 18:01:04: 6000000 INFO @ Sat, 15 Jan 2022 18:01:08: 1000000 INFO @ Sat, 15 Jan 2022 18:01:09: 7000000 INFO @ Sat, 15 Jan 2022 18:01:14: 2000000 INFO @ Sat, 15 Jan 2022 18:01:14: 8000000 INFO @ Sat, 15 Jan 2022 18:01:19: 3000000 INFO @ Sat, 15 Jan 2022 18:01:20: 9000000 INFO @ Sat, 15 Jan 2022 18:01:24: 4000000 INFO @ Sat, 15 Jan 2022 18:01:25: 10000000 INFO @ Sat, 15 Jan 2022 18:01:30: 5000000 INFO @ Sat, 15 Jan 2022 18:01:31: 11000000 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 18:01:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9786280/SRX9786280.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9786280/SRX9786280.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9786280/SRX9786280.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9786280/SRX9786280.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 18:01:33: #1 read tag files... INFO @ Sat, 15 Jan 2022 18:01:33: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 18:01:35: 6000000 INFO @ Sat, 15 Jan 2022 18:01:36: 12000000 INFO @ Sat, 15 Jan 2022 18:01:38: 1000000 INFO @ Sat, 15 Jan 2022 18:01:40: 7000000 INFO @ Sat, 15 Jan 2022 18:01:41: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 18:01:41: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 18:01:41: #1 total tags in treatment: 4389997 INFO @ Sat, 15 Jan 2022 18:01:41: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 18:01:41: #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 18:01:41: #1 tags after filtering in treatment: 3246660 INFO @ Sat, 15 Jan 2022 18:01:41: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 15 Jan 2022 18:01:41: #1 finished! INFO @ Sat, 15 Jan 2022 18:01:41: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 18:01:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 18:01:41: #2 number of paired peaks: 170 WARNING @ Sat, 15 Jan 2022 18:01:41: 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 18:01:41: start model_add_line... INFO @ Sat, 15 Jan 2022 18:01:41: start X-correlation... INFO @ Sat, 15 Jan 2022 18:01:41: end of X-cor INFO @ Sat, 15 Jan 2022 18:01:41: #2 finished! INFO @ Sat, 15 Jan 2022 18:01:41: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 18:01:41: #2 alternative fragment length(s) may be 0,14,35,46,71,95,105,146,152,190,210,239,258,273,287,312,357,380,412,428,470,487,509,532,582 bps INFO @ Sat, 15 Jan 2022 18:01:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX9786280/SRX9786280.05_model.r WARNING @ Sat, 15 Jan 2022 18:01:42: #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 18:01:42: #2 You may need to consider one of the other alternative d(s): 0,14,35,46,71,95,105,146,152,190,210,239,258,273,287,312,357,380,412,428,470,487,509,532,582 WARNING @ Sat, 15 Jan 2022 18:01:42: #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 18:01:42: #3 Call peaks... INFO @ Sat, 15 Jan 2022 18:01:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 18:01:44: 2000000 INFO @ Sat, 15 Jan 2022 18:01:46: 8000000 INFO @ Sat, 15 Jan 2022 18:01:49: 3000000 INFO @ Sat, 15 Jan 2022 18:01:51: 9000000 INFO @ Sat, 15 Jan 2022 18:01:54: 4000000 INFO @ Sat, 15 Jan 2022 18:01:56: 10000000 INFO @ Sat, 15 Jan 2022 18:02:00: 5000000 INFO @ Sat, 15 Jan 2022 18:02:02: 11000000 INFO @ Sat, 15 Jan 2022 18:02:05: 6000000 INFO @ Sat, 15 Jan 2022 18:02:07: 12000000 INFO @ Sat, 15 Jan 2022 18:02:11: 7000000 INFO @ Sat, 15 Jan 2022 18:02:12: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 18:02:12: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 18:02:12: #1 total tags in treatment: 4389997 INFO @ Sat, 15 Jan 2022 18:02:12: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 18:02:12: #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 18:02:12: #1 tags after filtering in treatment: 3246660 INFO @ Sat, 15 Jan 2022 18:02:12: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 15 Jan 2022 18:02:12: #1 finished! INFO @ Sat, 15 Jan 2022 18:02:12: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 18:02:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 18:02:12: #2 number of paired peaks: 170 WARNING @ Sat, 15 Jan 2022 18:02:12: 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 18:02:12: start model_add_line... INFO @ Sat, 15 Jan 2022 18:02:12: start X-correlation... INFO @ Sat, 15 Jan 2022 18:02:12: end of X-cor INFO @ Sat, 15 Jan 2022 18:02:12: #2 finished! INFO @ Sat, 15 Jan 2022 18:02:12: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 18:02:12: #2 alternative fragment length(s) may be 0,14,35,46,71,95,105,146,152,190,210,239,258,273,287,312,357,380,412,428,470,487,509,532,582 bps INFO @ Sat, 15 Jan 2022 18:02:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX9786280/SRX9786280.10_model.r WARNING @ Sat, 15 Jan 2022 18:02:12: #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 18:02:12: #2 You may need to consider one of the other alternative d(s): 0,14,35,46,71,95,105,146,152,190,210,239,258,273,287,312,357,380,412,428,470,487,509,532,582 WARNING @ Sat, 15 Jan 2022 18:02:12: #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 18:02:12: #3 Call peaks... INFO @ Sat, 15 Jan 2022 18:02:12: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 18:02:16: 8000000 INFO @ Sat, 15 Jan 2022 18:02:22: 9000000 BigWig に変換しました。 /var/spool/uge/at157/job_scripts/14519835: line 297: 88095 Terminated MACS $i /var/spool/uge/at157/job_scripts/14519835: line 297: 88200 Terminated MACS $i /var/spool/uge/at157/job_scripts/14519835: line 297: 88336 Terminated MACS $i ls: cannot access SRX9786280.05.bed: No such file or directory mv: cannot stat ‘SRX9786280.05.bed’: No such file or directory mv: cannot stat ‘SRX9786280.05.bb’: No such file or directory ls: cannot access SRX9786280.10.bed: No such file or directory mv: cannot stat ‘SRX9786280.10.bed’: No such file or directory mv: cannot stat ‘SRX9786280.10.bb’: No such file or directory ls: cannot access SRX9786280.20.bed: No such file or directory mv: cannot stat ‘SRX9786280.20.bed’: No such file or directory mv: cannot stat ‘SRX9786280.20.bb’: No such file or directory