Job ID = 6529983 SRX = SRX5717041 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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: 00:08:14 31574552 reads; of these: 31574552 (100.00%) were unpaired; of these: 4421966 (14.00%) aligned 0 times 17984685 (56.96%) aligned exactly 1 time 9167901 (29.04%) aligned >1 times 86.00% overall alignment rate Time searching: 00:08:14 Overall time: 00:08:14 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 8210379 / 27152586 = 0.3024 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 30 Jun 2020 03:09:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5717041/SRX5717041.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5717041/SRX5717041.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5717041/SRX5717041.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5717041/SRX5717041.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Tue, 30 Jun 2020 03:09:15: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:09:15: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:09:20: 1000000 INFO @ Tue, 30 Jun 2020 03:09:25: 2000000 INFO @ Tue, 30 Jun 2020 03:09:31: 3000000 INFO @ Tue, 30 Jun 2020 03:09:36: 4000000 INFO @ Tue, 30 Jun 2020 03:09:41: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 30 Jun 2020 03:09:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5717041/SRX5717041.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5717041/SRX5717041.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5717041/SRX5717041.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5717041/SRX5717041.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Tue, 30 Jun 2020 03:09:45: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:09:45: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:09:46: 6000000 INFO @ Tue, 30 Jun 2020 03:09:51: 1000000 INFO @ Tue, 30 Jun 2020 03:09:51: 7000000 INFO @ Tue, 30 Jun 2020 03:09:56: 8000000 INFO @ Tue, 30 Jun 2020 03:09:57: 2000000 INFO @ Tue, 30 Jun 2020 03:10:02: 9000000 INFO @ Tue, 30 Jun 2020 03:10:02: 3000000 INFO @ Tue, 30 Jun 2020 03:10:07: 10000000 INFO @ Tue, 30 Jun 2020 03:10:08: 4000000 INFO @ Tue, 30 Jun 2020 03:10:12: 11000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 30 Jun 2020 03:10:14: 5000000 INFO @ Tue, 30 Jun 2020 03:10:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5717041/SRX5717041.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5717041/SRX5717041.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5717041/SRX5717041.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5717041/SRX5717041.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Tue, 30 Jun 2020 03:10:15: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:10:15: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:10:18: 12000000 INFO @ Tue, 30 Jun 2020 03:10:20: 1000000 INFO @ Tue, 30 Jun 2020 03:10:20: 6000000 INFO @ Tue, 30 Jun 2020 03:10:23: 13000000 INFO @ Tue, 30 Jun 2020 03:10:25: 2000000 INFO @ Tue, 30 Jun 2020 03:10:27: 7000000 INFO @ Tue, 30 Jun 2020 03:10:29: 14000000 INFO @ Tue, 30 Jun 2020 03:10:30: 3000000 INFO @ Tue, 30 Jun 2020 03:10:33: 8000000 INFO @ Tue, 30 Jun 2020 03:10:34: 15000000 INFO @ Tue, 30 Jun 2020 03:10:36: 4000000 INFO @ Tue, 30 Jun 2020 03:10:39: 9000000 INFO @ Tue, 30 Jun 2020 03:10:40: 16000000 INFO @ Tue, 30 Jun 2020 03:10:41: 5000000 INFO @ Tue, 30 Jun 2020 03:10:45: 10000000 INFO @ Tue, 30 Jun 2020 03:10:45: 17000000 INFO @ Tue, 30 Jun 2020 03:10:46: 6000000 INFO @ Tue, 30 Jun 2020 03:10:51: 18000000 INFO @ Tue, 30 Jun 2020 03:10:51: 11000000 INFO @ Tue, 30 Jun 2020 03:10:52: 7000000 INFO @ Tue, 30 Jun 2020 03:10:56: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:10:56: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:10:56: #1 total tags in treatment: 18942207 INFO @ Tue, 30 Jun 2020 03:10:56: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:10:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 03:10:57: #1 tags after filtering in treatment: 18942147 INFO @ Tue, 30 Jun 2020 03:10:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:10:57: #1 finished! INFO @ Tue, 30 Jun 2020 03:10:57: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:10:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:10:57: 8000000 INFO @ Tue, 30 Jun 2020 03:10:58: #2 number of paired peaks: 152 WARNING @ Tue, 30 Jun 2020 03:10:58: Fewer paired peaks (152) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 152 pairs to build model! INFO @ Tue, 30 Jun 2020 03:10:58: start model_add_line... INFO @ Tue, 30 Jun 2020 03:10:58: start X-correlation... INFO @ Tue, 30 Jun 2020 03:10:58: end of X-cor INFO @ Tue, 30 Jun 2020 03:10:58: #2 finished! INFO @ Tue, 30 Jun 2020 03:10:58: #2 predicted fragment length is 0 bps INFO @ Tue, 30 Jun 2020 03:10:58: #2 alternative fragment length(s) may be 0,49,70,342,413,516 bps INFO @ Tue, 30 Jun 2020 03:10:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5717041/SRX5717041.05_model.r WARNING @ Tue, 30 Jun 2020 03:10:58: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:10:58: #2 You may need to consider one of the other alternative d(s): 0,49,70,342,413,516 WARNING @ Tue, 30 Jun 2020 03:10:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 03:10:58: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:10:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:10:58: 12000000 INFO @ Tue, 30 Jun 2020 03:11:02: 9000000 INFO @ Tue, 30 Jun 2020 03:11:04: 13000000 INFO @ Tue, 30 Jun 2020 03:11:07: 10000000 INFO @ Tue, 30 Jun 2020 03:11:10: 14000000 INFO @ Tue, 30 Jun 2020 03:11:12: 11000000 INFO @ Tue, 30 Jun 2020 03:11:16: 15000000 INFO @ Tue, 30 Jun 2020 03:11:18: 12000000 INFO @ Tue, 30 Jun 2020 03:11:23: 16000000 INFO @ Tue, 30 Jun 2020 03:11:23: 13000000 INFO @ Tue, 30 Jun 2020 03:11:28: 14000000 INFO @ Tue, 30 Jun 2020 03:11:29: 17000000 INFO @ Tue, 30 Jun 2020 03:11:34: 15000000 INFO @ Tue, 30 Jun 2020 03:11:35: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:11:39: 16000000 INFO @ Tue, 30 Jun 2020 03:11:41: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:11:41: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:11:41: #1 total tags in treatment: 18942207 INFO @ Tue, 30 Jun 2020 03:11:41: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:11:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 03:11:42: #1 tags after filtering in treatment: 18942147 INFO @ Tue, 30 Jun 2020 03:11:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:11:42: #1 finished! INFO @ Tue, 30 Jun 2020 03:11:42: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:11:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:11:43: #2 number of paired peaks: 152 WARNING @ Tue, 30 Jun 2020 03:11:43: Fewer paired peaks (152) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 152 pairs to build model! INFO @ Tue, 30 Jun 2020 03:11:43: start model_add_line... INFO @ Tue, 30 Jun 2020 03:11:43: start X-correlation... INFO @ Tue, 30 Jun 2020 03:11:43: end of X-cor INFO @ Tue, 30 Jun 2020 03:11:43: #2 finished! INFO @ Tue, 30 Jun 2020 03:11:43: #2 predicted fragment length is 0 bps INFO @ Tue, 30 Jun 2020 03:11:43: #2 alternative fragment length(s) may be 0,49,70,342,413,516 bps INFO @ Tue, 30 Jun 2020 03:11:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5717041/SRX5717041.10_model.r WARNING @ Tue, 30 Jun 2020 03:11:43: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:11:43: #2 You may need to consider one of the other alternative d(s): 0,49,70,342,413,516 WARNING @ Tue, 30 Jun 2020 03:11:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 03:11:43: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:11:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:11:44: 17000000 INFO @ Tue, 30 Jun 2020 03:11:50: 18000000 INFO @ Tue, 30 Jun 2020 03:11:55: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:11:55: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:11:55: #1 total tags in treatment: 18942207 INFO @ Tue, 30 Jun 2020 03:11:55: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:11:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 03:11:55: #1 tags after filtering in treatment: 18942147 INFO @ Tue, 30 Jun 2020 03:11:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:11:55: #1 finished! INFO @ Tue, 30 Jun 2020 03:11:55: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:11:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:11:56: #2 number of paired peaks: 152 WARNING @ Tue, 30 Jun 2020 03:11:56: Fewer paired peaks (152) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 152 pairs to build model! INFO @ Tue, 30 Jun 2020 03:11:56: start model_add_line... INFO @ Tue, 30 Jun 2020 03:11:56: start X-correlation... INFO @ Tue, 30 Jun 2020 03:11:56: end of X-cor INFO @ Tue, 30 Jun 2020 03:11:56: #2 finished! INFO @ Tue, 30 Jun 2020 03:11:56: #2 predicted fragment length is 0 bps INFO @ Tue, 30 Jun 2020 03:11:56: #2 alternative fragment length(s) may be 0,49,70,342,413,516 bps INFO @ Tue, 30 Jun 2020 03:11:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5717041/SRX5717041.20_model.r WARNING @ Tue, 30 Jun 2020 03:11:56: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:11:56: #2 You may need to consider one of the other alternative d(s): 0,49,70,342,413,516 WARNING @ Tue, 30 Jun 2020 03:11:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 03:11:56: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:11:56: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 /var/spool/uge/at158/job_scripts/6529983: line 293: 49539 Terminated MACS $i /var/spool/uge/at158/job_scripts/6529983: line 293: 70927 Terminated MACS $i /var/spool/uge/at158/job_scripts/6529983: line 293: 104931 Terminated MACS $i ls: cannot access SRX5717041.05.bed: No such file or directory mv: cannot stat ‘SRX5717041.05.bed’: No such file or directory mv: cannot stat ‘SRX5717041.05.bb’: No such file or directory ls: cannot access SRX5717041.10.bed: No such file or directory mv: cannot stat ‘SRX5717041.10.bed’: No such file or directory mv: cannot stat ‘SRX5717041.10.bb’: No such file or directory ls: cannot access SRX5717041.20.bed: No such file or directory mv: cannot stat ‘SRX5717041.20.bed’: No such file or directory mv: cannot stat ‘SRX5717041.20.bb’: No such file or directory