Job ID = 6367027 SRX = SRX2737086 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:12:31 prefetch.2.10.7: 1) Downloading 'SRR5448124'... 2020-06-15T23:12:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:14:19 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:14:19 prefetch.2.10.7: 1) 'SRR5448124' was downloaded successfully 2020-06-15T23:14:19 prefetch.2.10.7: 'SRR5448124' has 0 unresolved dependencies Read 35613013 spots for SRR5448124/SRR5448124.sra Written 35613013 spots for SRR5448124/SRR5448124.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: 00:07:44 35613013 reads; of these: 35613013 (100.00%) were unpaired; of these: 1393770 (3.91%) aligned 0 times 29140730 (81.83%) aligned exactly 1 time 5078513 (14.26%) aligned >1 times 96.09% overall alignment rate Time searching: 00:07:44 Overall time: 00:07:44 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 16 files... [bam_rmdupse_core] 6820780 / 34219243 = 0.1993 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, 16 Jun 2020 08:29:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2737086/SRX2737086.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2737086/SRX2737086.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2737086/SRX2737086.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2737086/SRX2737086.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, 16 Jun 2020 08:29:56: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:29:56: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:30:00: 1000000 INFO @ Tue, 16 Jun 2020 08:30:05: 2000000 INFO @ Tue, 16 Jun 2020 08:30:10: 3000000 INFO @ Tue, 16 Jun 2020 08:30:15: 4000000 INFO @ Tue, 16 Jun 2020 08:30:20: 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, 16 Jun 2020 08:30:25: 6000000 INFO @ Tue, 16 Jun 2020 08:30:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2737086/SRX2737086.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2737086/SRX2737086.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2737086/SRX2737086.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2737086/SRX2737086.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, 16 Jun 2020 08:30:26: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:30:26: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:30:30: 7000000 INFO @ Tue, 16 Jun 2020 08:30:31: 1000000 INFO @ Tue, 16 Jun 2020 08:30:35: 8000000 INFO @ Tue, 16 Jun 2020 08:30:36: 2000000 INFO @ Tue, 16 Jun 2020 08:30:40: 9000000 INFO @ Tue, 16 Jun 2020 08:30:41: 3000000 INFO @ Tue, 16 Jun 2020 08:30:45: 10000000 INFO @ Tue, 16 Jun 2020 08:30:46: 4000000 INFO @ Tue, 16 Jun 2020 08:30:49: 11000000 INFO @ Tue, 16 Jun 2020 08:30:51: 5000000 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, 16 Jun 2020 08:30:54: 12000000 INFO @ Tue, 16 Jun 2020 08:30:56: 6000000 INFO @ Tue, 16 Jun 2020 08:30:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2737086/SRX2737086.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2737086/SRX2737086.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2737086/SRX2737086.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2737086/SRX2737086.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, 16 Jun 2020 08:30:56: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:30:56: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:30:59: 13000000 INFO @ Tue, 16 Jun 2020 08:31:01: 7000000 INFO @ Tue, 16 Jun 2020 08:31:01: 1000000 INFO @ Tue, 16 Jun 2020 08:31:04: 14000000 INFO @ Tue, 16 Jun 2020 08:31:06: 8000000 INFO @ Tue, 16 Jun 2020 08:31:06: 2000000 INFO @ Tue, 16 Jun 2020 08:31:09: 15000000 INFO @ Tue, 16 Jun 2020 08:31:11: 9000000 INFO @ Tue, 16 Jun 2020 08:31:11: 3000000 INFO @ Tue, 16 Jun 2020 08:31:14: 16000000 INFO @ Tue, 16 Jun 2020 08:31:16: 10000000 INFO @ Tue, 16 Jun 2020 08:31:16: 4000000 INFO @ Tue, 16 Jun 2020 08:31:19: 17000000 INFO @ Tue, 16 Jun 2020 08:31:21: 11000000 INFO @ Tue, 16 Jun 2020 08:31:22: 5000000 INFO @ Tue, 16 Jun 2020 08:31:25: 18000000 INFO @ Tue, 16 Jun 2020 08:31:26: 12000000 INFO @ Tue, 16 Jun 2020 08:31:27: 6000000 INFO @ Tue, 16 Jun 2020 08:31:29: 19000000 INFO @ Tue, 16 Jun 2020 08:31:31: 13000000 INFO @ Tue, 16 Jun 2020 08:31:32: 7000000 INFO @ Tue, 16 Jun 2020 08:31:34: 20000000 INFO @ Tue, 16 Jun 2020 08:31:36: 14000000 INFO @ Tue, 16 Jun 2020 08:31:37: 8000000 INFO @ Tue, 16 Jun 2020 08:31:39: 21000000 INFO @ Tue, 16 Jun 2020 08:31:41: 15000000 INFO @ Tue, 16 Jun 2020 08:31:42: 9000000 INFO @ Tue, 16 Jun 2020 08:31:44: 22000000 INFO @ Tue, 16 Jun 2020 08:31:46: 16000000 INFO @ Tue, 16 Jun 2020 08:31:47: 10000000 INFO @ Tue, 16 Jun 2020 08:31:49: 23000000 INFO @ Tue, 16 Jun 2020 08:31:51: 17000000 INFO @ Tue, 16 Jun 2020 08:31:52: 11000000 INFO @ Tue, 16 Jun 2020 08:31:54: 24000000 INFO @ Tue, 16 Jun 2020 08:31:56: 18000000 INFO @ Tue, 16 Jun 2020 08:31:57: 12000000 INFO @ Tue, 16 Jun 2020 08:31:59: 25000000 INFO @ Tue, 16 Jun 2020 08:32:01: 19000000 INFO @ Tue, 16 Jun 2020 08:32:02: 13000000 INFO @ Tue, 16 Jun 2020 08:32:04: 26000000 INFO @ Tue, 16 Jun 2020 08:32:06: 20000000 INFO @ Tue, 16 Jun 2020 08:32:07: 14000000 INFO @ Tue, 16 Jun 2020 08:32:09: 27000000 INFO @ Tue, 16 Jun 2020 08:32:10: 21000000 INFO @ Tue, 16 Jun 2020 08:32:11: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:32:11: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:32:11: #1 total tags in treatment: 27398463 INFO @ Tue, 16 Jun 2020 08:32:11: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:32:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:32:12: #1 tags after filtering in treatment: 27398463 INFO @ Tue, 16 Jun 2020 08:32:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:32:12: #1 finished! INFO @ Tue, 16 Jun 2020 08:32:12: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:32:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:32:12: 15000000 INFO @ Tue, 16 Jun 2020 08:32:13: #2 number of paired peaks: 105 WARNING @ Tue, 16 Jun 2020 08:32:13: Fewer paired peaks (105) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 105 pairs to build model! INFO @ Tue, 16 Jun 2020 08:32:13: start model_add_line... INFO @ Tue, 16 Jun 2020 08:32:13: start X-correlation... INFO @ Tue, 16 Jun 2020 08:32:13: end of X-cor INFO @ Tue, 16 Jun 2020 08:32:13: #2 finished! INFO @ Tue, 16 Jun 2020 08:32:13: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 08:32:13: #2 alternative fragment length(s) may be 0,46,464,491,541 bps INFO @ Tue, 16 Jun 2020 08:32:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2737086/SRX2737086.05_model.r WARNING @ Tue, 16 Jun 2020 08:32:13: #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, 16 Jun 2020 08:32:13: #2 You may need to consider one of the other alternative d(s): 0,46,464,491,541 WARNING @ Tue, 16 Jun 2020 08:32:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:32:13: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:32:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:32:15: 22000000 INFO @ Tue, 16 Jun 2020 08:32:17: 16000000 INFO @ Tue, 16 Jun 2020 08:32:20: 23000000 INFO @ Tue, 16 Jun 2020 08:32:22: 17000000 INFO @ Tue, 16 Jun 2020 08:32:25: 24000000 INFO @ Tue, 16 Jun 2020 08:32:27: 18000000 INFO @ Tue, 16 Jun 2020 08:32:30: 25000000 INFO @ Tue, 16 Jun 2020 08:32:32: 19000000 INFO @ Tue, 16 Jun 2020 08:32:35: 26000000 INFO @ Tue, 16 Jun 2020 08:32:36: 20000000 INFO @ Tue, 16 Jun 2020 08:32:40: 27000000 INFO @ Tue, 16 Jun 2020 08:32:42: 21000000 INFO @ Tue, 16 Jun 2020 08:32:42: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:32:42: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:32:42: #1 total tags in treatment: 27398463 INFO @ Tue, 16 Jun 2020 08:32:42: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:32:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:32:43: #1 tags after filtering in treatment: 27398463 INFO @ Tue, 16 Jun 2020 08:32:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:32:43: #1 finished! INFO @ Tue, 16 Jun 2020 08:32:43: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:32:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:32:44: #2 number of paired peaks: 105 WARNING @ Tue, 16 Jun 2020 08:32:44: Fewer paired peaks (105) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 105 pairs to build model! INFO @ Tue, 16 Jun 2020 08:32:44: start model_add_line... INFO @ Tue, 16 Jun 2020 08:32:45: start X-correlation... INFO @ Tue, 16 Jun 2020 08:32:45: end of X-cor INFO @ Tue, 16 Jun 2020 08:32:45: #2 finished! INFO @ Tue, 16 Jun 2020 08:32:45: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 08:32:45: #2 alternative fragment length(s) may be 0,46,464,491,541 bps INFO @ Tue, 16 Jun 2020 08:32:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2737086/SRX2737086.10_model.r WARNING @ Tue, 16 Jun 2020 08:32:45: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:32:45: #2 You may need to consider one of the other alternative d(s): 0,46,464,491,541 WARNING @ Tue, 16 Jun 2020 08:32:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:32:45: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:32:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:32:46: 22000000 INFO @ Tue, 16 Jun 2020 08:32:51: 23000000 INFO @ Tue, 16 Jun 2020 08:32:56: 24000000 INFO @ Tue, 16 Jun 2020 08:33:00: 25000000 INFO @ Tue, 16 Jun 2020 08:33:05: 26000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:33:10: 27000000 INFO @ Tue, 16 Jun 2020 08:33:12: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:33:12: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:33:12: #1 total tags in treatment: 27398463 INFO @ Tue, 16 Jun 2020 08:33:12: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:33:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:33:12: #1 tags after filtering in treatment: 27398463 INFO @ Tue, 16 Jun 2020 08:33:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:33:12: #1 finished! INFO @ Tue, 16 Jun 2020 08:33:12: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:33:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:33:14: #2 number of paired peaks: 105 WARNING @ Tue, 16 Jun 2020 08:33:14: Fewer paired peaks (105) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 105 pairs to build model! INFO @ Tue, 16 Jun 2020 08:33:14: start model_add_line... INFO @ Tue, 16 Jun 2020 08:33:14: start X-correlation... INFO @ Tue, 16 Jun 2020 08:33:14: end of X-cor INFO @ Tue, 16 Jun 2020 08:33:14: #2 finished! INFO @ Tue, 16 Jun 2020 08:33:14: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 08:33:14: #2 alternative fragment length(s) may be 0,46,464,491,541 bps INFO @ Tue, 16 Jun 2020 08:33:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2737086/SRX2737086.20_model.r WARNING @ Tue, 16 Jun 2020 08:33:14: #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, 16 Jun 2020 08:33:14: #2 You may need to consider one of the other alternative d(s): 0,46,464,491,541 WARNING @ Tue, 16 Jun 2020 08:33:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:33:14: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:33:14: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 /var/spool/uge/at146/job_scripts/6367027: line 271: 85816 Terminated MACS $i /var/spool/uge/at146/job_scripts/6367027: line 271: 87047 Terminated MACS $i /var/spool/uge/at146/job_scripts/6367027: line 271: 87834 Terminated MACS $i ls: cannot access SRX2737086.05.bed: No such file or directory mv: cannot stat ‘SRX2737086.05.bed’: No such file or directory mv: cannot stat ‘SRX2737086.05.bb’: No such file or directory ls: cannot access SRX2737086.10.bed: No such file or directory mv: cannot stat ‘SRX2737086.10.bed’: No such file or directory mv: cannot stat ‘SRX2737086.10.bb’: No such file or directory ls: cannot access SRX2737086.20.bed: No such file or directory mv: cannot stat ‘SRX2737086.20.bed’: No such file or directory mv: cannot stat ‘SRX2737086.20.bb’: No such file or directory