Job ID = 6529093 SRX = SRX013987 Genome = ce11 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: 00:03:13 25024500 reads; of these: 25024500 (100.00%) were unpaired; of these: 7637548 (30.52%) aligned 0 times 14714499 (58.80%) aligned exactly 1 time 2672453 (10.68%) aligned >1 times 69.48% overall alignment rate Time searching: 00:03:13 Overall time: 00:03:13 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 1631201 / 17386952 = 0.0938 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 01:26:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX013987/SRX013987.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX013987/SRX013987.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX013987/SRX013987.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX013987/SRX013987.bam'] # control file = None # effective genome size = 9.00e+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 @ Tue, 30 Jun 2020 01:26:47: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:26:47: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:26:53: 1000000 INFO @ Tue, 30 Jun 2020 01:26:59: 2000000 INFO @ Tue, 30 Jun 2020 01:27:05: 3000000 INFO @ Tue, 30 Jun 2020 01:27:11: 4000000 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 01:27:16: 5000000 INFO @ Tue, 30 Jun 2020 01:27:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX013987/SRX013987.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX013987/SRX013987.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX013987/SRX013987.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX013987/SRX013987.bam'] # control file = None # effective genome size = 9.00e+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 @ Tue, 30 Jun 2020 01:27:18: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:27:18: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:27:22: 6000000 INFO @ Tue, 30 Jun 2020 01:27:24: 1000000 INFO @ Tue, 30 Jun 2020 01:27:28: 7000000 INFO @ Tue, 30 Jun 2020 01:27:30: 2000000 INFO @ Tue, 30 Jun 2020 01:27:34: 8000000 INFO @ Tue, 30 Jun 2020 01:27:37: 3000000 INFO @ Tue, 30 Jun 2020 01:27:40: 9000000 INFO @ Tue, 30 Jun 2020 01:27:43: 4000000 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 01:27:46: 10000000 INFO @ Tue, 30 Jun 2020 01:27:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX013987/SRX013987.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX013987/SRX013987.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX013987/SRX013987.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX013987/SRX013987.bam'] # control file = None # effective genome size = 9.00e+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 @ Tue, 30 Jun 2020 01:27:47: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:27:47: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:27:49: 5000000 INFO @ Tue, 30 Jun 2020 01:27:52: 11000000 INFO @ Tue, 30 Jun 2020 01:27:53: 1000000 INFO @ Tue, 30 Jun 2020 01:27:55: 6000000 INFO @ Tue, 30 Jun 2020 01:27:59: 12000000 INFO @ Tue, 30 Jun 2020 01:27:59: 2000000 INFO @ Tue, 30 Jun 2020 01:28:01: 7000000 INFO @ Tue, 30 Jun 2020 01:28:05: 13000000 INFO @ Tue, 30 Jun 2020 01:28:05: 3000000 INFO @ Tue, 30 Jun 2020 01:28:07: 8000000 INFO @ Tue, 30 Jun 2020 01:28:11: 4000000 INFO @ Tue, 30 Jun 2020 01:28:11: 14000000 INFO @ Tue, 30 Jun 2020 01:28:14: 9000000 INFO @ Tue, 30 Jun 2020 01:28:16: 5000000 INFO @ Tue, 30 Jun 2020 01:28:17: 15000000 INFO @ Tue, 30 Jun 2020 01:28:20: 10000000 INFO @ Tue, 30 Jun 2020 01:28:22: 6000000 INFO @ Tue, 30 Jun 2020 01:28:23: #1 tag size is determined as 27 bps INFO @ Tue, 30 Jun 2020 01:28:23: #1 tag size = 27 INFO @ Tue, 30 Jun 2020 01:28:23: #1 total tags in treatment: 15755751 INFO @ Tue, 30 Jun 2020 01:28:23: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:28:23: #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 01:28:23: #1 tags after filtering in treatment: 15755751 INFO @ Tue, 30 Jun 2020 01:28:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:28:23: #1 finished! INFO @ Tue, 30 Jun 2020 01:28:23: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:28:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:28:24: #2 number of paired peaks: 214 WARNING @ Tue, 30 Jun 2020 01:28:24: Fewer paired peaks (214) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 214 pairs to build model! INFO @ Tue, 30 Jun 2020 01:28:24: start model_add_line... INFO @ Tue, 30 Jun 2020 01:28:24: start X-correlation... INFO @ Tue, 30 Jun 2020 01:28:24: end of X-cor INFO @ Tue, 30 Jun 2020 01:28:24: #2 finished! INFO @ Tue, 30 Jun 2020 01:28:24: #2 predicted fragment length is 0 bps INFO @ Tue, 30 Jun 2020 01:28:24: #2 alternative fragment length(s) may be 0,24,70,386,591 bps INFO @ Tue, 30 Jun 2020 01:28:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX013987/SRX013987.05_model.r WARNING @ Tue, 30 Jun 2020 01:28:24: #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 01:28:24: #2 You may need to consider one of the other alternative d(s): 0,24,70,386,591 WARNING @ Tue, 30 Jun 2020 01:28:24: #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 01:28:24: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:28:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:28:26: 11000000 INFO @ Tue, 30 Jun 2020 01:28:28: 7000000 INFO @ Tue, 30 Jun 2020 01:28:33: 12000000 INFO @ Tue, 30 Jun 2020 01:28:34: 8000000 INFO @ Tue, 30 Jun 2020 01:28:39: 13000000 INFO @ Tue, 30 Jun 2020 01:28:39: 9000000 INFO @ Tue, 30 Jun 2020 01:28:45: 10000000 INFO @ Tue, 30 Jun 2020 01:28:45: 14000000 INFO @ Tue, 30 Jun 2020 01:28:51: 11000000 INFO @ Tue, 30 Jun 2020 01:28:52: 15000000 INFO @ Tue, 30 Jun 2020 01:28:56: 12000000 INFO @ Tue, 30 Jun 2020 01:28:57: #1 tag size is determined as 27 bps INFO @ Tue, 30 Jun 2020 01:28:57: #1 tag size = 27 INFO @ Tue, 30 Jun 2020 01:28:57: #1 total tags in treatment: 15755751 INFO @ Tue, 30 Jun 2020 01:28:57: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:28:57: #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 01:28:57: #1 tags after filtering in treatment: 15755751 INFO @ Tue, 30 Jun 2020 01:28:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:28:57: #1 finished! INFO @ Tue, 30 Jun 2020 01:28:57: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:28:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:28:58: #2 number of paired peaks: 214 WARNING @ Tue, 30 Jun 2020 01:28:58: Fewer paired peaks (214) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 214 pairs to build model! INFO @ Tue, 30 Jun 2020 01:28:58: start model_add_line... INFO @ Tue, 30 Jun 2020 01:28:58: start X-correlation... INFO @ Tue, 30 Jun 2020 01:28:58: end of X-cor INFO @ Tue, 30 Jun 2020 01:28:58: #2 finished! INFO @ Tue, 30 Jun 2020 01:28:58: #2 predicted fragment length is 0 bps INFO @ Tue, 30 Jun 2020 01:28:58: #2 alternative fragment length(s) may be 0,24,70,386,591 bps INFO @ Tue, 30 Jun 2020 01:28:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX013987/SRX013987.10_model.r WARNING @ Tue, 30 Jun 2020 01:28:58: #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 01:28:58: #2 You may need to consider one of the other alternative d(s): 0,24,70,386,591 WARNING @ Tue, 30 Jun 2020 01:28:58: #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 01:28:58: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:28:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:29:02: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 01:29:07: 14000000 INFO @ Tue, 30 Jun 2020 01:29:12: 15000000 INFO @ Tue, 30 Jun 2020 01:29:16: #1 tag size is determined as 27 bps INFO @ Tue, 30 Jun 2020 01:29:16: #1 tag size = 27 INFO @ Tue, 30 Jun 2020 01:29:16: #1 total tags in treatment: 15755751 INFO @ Tue, 30 Jun 2020 01:29:16: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:29:16: #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 01:29:17: #1 tags after filtering in treatment: 15755751 INFO @ Tue, 30 Jun 2020 01:29:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:29:17: #1 finished! INFO @ Tue, 30 Jun 2020 01:29:17: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:29:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:29:18: #2 number of paired peaks: 214 WARNING @ Tue, 30 Jun 2020 01:29:18: Fewer paired peaks (214) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 214 pairs to build model! INFO @ Tue, 30 Jun 2020 01:29:18: start model_add_line... INFO @ Tue, 30 Jun 2020 01:29:18: start X-correlation... INFO @ Tue, 30 Jun 2020 01:29:18: end of X-cor INFO @ Tue, 30 Jun 2020 01:29:18: #2 finished! INFO @ Tue, 30 Jun 2020 01:29:18: #2 predicted fragment length is 0 bps INFO @ Tue, 30 Jun 2020 01:29:18: #2 alternative fragment length(s) may be 0,24,70,386,591 bps INFO @ Tue, 30 Jun 2020 01:29:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX013987/SRX013987.20_model.r WARNING @ Tue, 30 Jun 2020 01:29:18: #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 01:29:18: #2 You may need to consider one of the other alternative d(s): 0,24,70,386,591 WARNING @ Tue, 30 Jun 2020 01:29:18: #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 01:29:18: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:29:18: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 /var/spool/uge/at157/job_scripts/6529093: line 293: 110411 Terminated MACS $i /var/spool/uge/at157/job_scripts/6529093: line 293: 114423 Terminated MACS $i /var/spool/uge/at157/job_scripts/6529093: line 293: 4871 Terminated MACS $i ls: cannot access SRX013987.05.bed: No such file or directory mv: cannot stat ‘SRX013987.05.bed’: No such file or directory mv: cannot stat ‘SRX013987.05.bb’: No such file or directory ls: cannot access SRX013987.10.bed: No such file or directory mv: cannot stat ‘SRX013987.10.bed’: No such file or directory mv: cannot stat ‘SRX013987.10.bb’: No such file or directory ls: cannot access SRX013987.20.bed: No such file or directory mv: cannot stat ‘SRX013987.20.bed’: No such file or directory mv: cannot stat ‘SRX013987.20.bb’: No such file or directory