Job ID = 6527408 SRX = SRX3883438 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T12:18:40 prefetch.2.10.7: 1) Downloading 'SRR6938936'... 2020-06-29T12:18:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:20:23 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:20:24 prefetch.2.10.7: 'SRR6938936' is valid 2020-06-29T12:20:24 prefetch.2.10.7: 1) 'SRR6938936' was downloaded successfully 2020-06-29T12:20:24 prefetch.2.10.7: 'SRR6938936' has 0 unresolved dependencies Read 20455137 spots for SRR6938936/SRR6938936.sra Written 20455137 spots for SRR6938936/SRR6938936.sra 2020-06-29T12:21:40 prefetch.2.10.7: 1) Downloading 'SRR6938937'... 2020-06-29T12:21:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:23:22 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:23:22 prefetch.2.10.7: 1) 'SRR6938937' was downloaded successfully 2020-06-29T12:23:22 prefetch.2.10.7: 'SRR6938937' has 0 unresolved dependencies Read 27804801 spots for SRR6938937/SRR6938937.sra Written 27804801 spots for SRR6938937/SRR6938937.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: 00:08:26 48259938 reads; of these: 48259938 (100.00%) were unpaired; of these: 17192446 (35.62%) aligned 0 times 25733713 (53.32%) aligned exactly 1 time 5333779 (11.05%) aligned >1 times 64.38% overall alignment rate Time searching: 00:08:26 Overall time: 00:08:26 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] 5249722 / 31067492 = 0.1690 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 @ Mon, 29 Jun 2020 21:52:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3883438/SRX3883438.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3883438/SRX3883438.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3883438/SRX3883438.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3883438/SRX3883438.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 @ Mon, 29 Jun 2020 21:52:01: #1 read tag files... INFO @ Mon, 29 Jun 2020 21:52:01: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 21:52:06: 1000000 INFO @ Mon, 29 Jun 2020 21:52:11: 2000000 INFO @ Mon, 29 Jun 2020 21:52:16: 3000000 INFO @ Mon, 29 Jun 2020 21:52:20: 4000000 INFO @ Mon, 29 Jun 2020 21:52:25: 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 @ Mon, 29 Jun 2020 21:52:30: 6000000 INFO @ Mon, 29 Jun 2020 21:52:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3883438/SRX3883438.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3883438/SRX3883438.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3883438/SRX3883438.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3883438/SRX3883438.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 @ Mon, 29 Jun 2020 21:52:31: #1 read tag files... INFO @ Mon, 29 Jun 2020 21:52:31: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 21:52:35: 7000000 INFO @ Mon, 29 Jun 2020 21:52:36: 1000000 INFO @ Mon, 29 Jun 2020 21:52:41: 8000000 INFO @ Mon, 29 Jun 2020 21:52:42: 2000000 INFO @ Mon, 29 Jun 2020 21:52:46: 9000000 INFO @ Mon, 29 Jun 2020 21:52:48: 3000000 INFO @ Mon, 29 Jun 2020 21:52:51: 10000000 INFO @ Mon, 29 Jun 2020 21:52:54: 4000000 INFO @ Mon, 29 Jun 2020 21:52:57: 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 @ Mon, 29 Jun 2020 21:52:59: 5000000 INFO @ Mon, 29 Jun 2020 21:53:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3883438/SRX3883438.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3883438/SRX3883438.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3883438/SRX3883438.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3883438/SRX3883438.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 @ Mon, 29 Jun 2020 21:53:01: #1 read tag files... INFO @ Mon, 29 Jun 2020 21:53:01: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 21:53:02: 12000000 INFO @ Mon, 29 Jun 2020 21:53:04: 6000000 INFO @ Mon, 29 Jun 2020 21:53:06: 1000000 INFO @ Mon, 29 Jun 2020 21:53:07: 13000000 INFO @ Mon, 29 Jun 2020 21:53:10: 7000000 INFO @ Mon, 29 Jun 2020 21:53:12: 2000000 INFO @ Mon, 29 Jun 2020 21:53:13: 14000000 INFO @ Mon, 29 Jun 2020 21:53:16: 8000000 INFO @ Mon, 29 Jun 2020 21:53:17: 3000000 INFO @ Mon, 29 Jun 2020 21:53:18: 15000000 INFO @ Mon, 29 Jun 2020 21:53:21: 9000000 INFO @ Mon, 29 Jun 2020 21:53:23: 4000000 INFO @ Mon, 29 Jun 2020 21:53:24: 16000000 INFO @ Mon, 29 Jun 2020 21:53:27: 10000000 INFO @ Mon, 29 Jun 2020 21:53:28: 5000000 INFO @ Mon, 29 Jun 2020 21:53:30: 17000000 INFO @ Mon, 29 Jun 2020 21:53:32: 11000000 INFO @ Mon, 29 Jun 2020 21:53:33: 6000000 INFO @ Mon, 29 Jun 2020 21:53:35: 18000000 INFO @ Mon, 29 Jun 2020 21:53:38: 12000000 INFO @ Mon, 29 Jun 2020 21:53:39: 7000000 INFO @ Mon, 29 Jun 2020 21:53:41: 19000000 INFO @ Mon, 29 Jun 2020 21:53:44: 13000000 INFO @ Mon, 29 Jun 2020 21:53:44: 8000000 INFO @ Mon, 29 Jun 2020 21:53:46: 20000000 INFO @ Mon, 29 Jun 2020 21:53:49: 9000000 INFO @ Mon, 29 Jun 2020 21:53:49: 14000000 INFO @ Mon, 29 Jun 2020 21:53:51: 21000000 INFO @ Mon, 29 Jun 2020 21:53:55: 10000000 INFO @ Mon, 29 Jun 2020 21:53:55: 15000000 INFO @ Mon, 29 Jun 2020 21:53:57: 22000000 INFO @ Mon, 29 Jun 2020 21:54:00: 11000000 INFO @ Mon, 29 Jun 2020 21:54:01: 16000000 INFO @ Mon, 29 Jun 2020 21:54:02: 23000000 INFO @ Mon, 29 Jun 2020 21:54:06: 12000000 INFO @ Mon, 29 Jun 2020 21:54:06: 17000000 INFO @ Mon, 29 Jun 2020 21:54:07: 24000000 INFO @ Mon, 29 Jun 2020 21:54:11: 13000000 INFO @ Mon, 29 Jun 2020 21:54:12: 18000000 INFO @ Mon, 29 Jun 2020 21:54:13: 25000000 INFO @ Mon, 29 Jun 2020 21:54:17: 14000000 INFO @ Mon, 29 Jun 2020 21:54:17: 19000000 INFO @ Mon, 29 Jun 2020 21:54:17: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 21:54:17: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 21:54:17: #1 total tags in treatment: 25817770 INFO @ Mon, 29 Jun 2020 21:54:17: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 21:54:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 21:54:18: #1 tags after filtering in treatment: 25817770 INFO @ Mon, 29 Jun 2020 21:54:18: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 21:54:18: #1 finished! INFO @ Mon, 29 Jun 2020 21:54:18: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 21:54:18: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 21:54:19: #2 number of paired peaks: 130 WARNING @ Mon, 29 Jun 2020 21:54:19: Fewer paired peaks (130) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 130 pairs to build model! INFO @ Mon, 29 Jun 2020 21:54:19: start model_add_line... INFO @ Mon, 29 Jun 2020 21:54:20: start X-correlation... INFO @ Mon, 29 Jun 2020 21:54:20: end of X-cor INFO @ Mon, 29 Jun 2020 21:54:20: #2 finished! INFO @ Mon, 29 Jun 2020 21:54:20: #2 predicted fragment length is 0 bps INFO @ Mon, 29 Jun 2020 21:54:20: #2 alternative fragment length(s) may be 0,43,501,507,530,589 bps INFO @ Mon, 29 Jun 2020 21:54:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3883438/SRX3883438.05_model.r WARNING @ Mon, 29 Jun 2020 21:54:20: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 21:54:20: #2 You may need to consider one of the other alternative d(s): 0,43,501,507,530,589 WARNING @ Mon, 29 Jun 2020 21:54:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 21:54:20: #3 Call peaks... INFO @ Mon, 29 Jun 2020 21:54:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 21:54:22: 15000000 INFO @ Mon, 29 Jun 2020 21:54:23: 20000000 INFO @ Mon, 29 Jun 2020 21:54:27: 16000000 INFO @ Mon, 29 Jun 2020 21:54:28: 21000000 INFO @ Mon, 29 Jun 2020 21:54:33: 17000000 INFO @ Mon, 29 Jun 2020 21:54:34: 22000000 INFO @ Mon, 29 Jun 2020 21:54:38: 18000000 INFO @ Mon, 29 Jun 2020 21:54:39: 23000000 INFO @ Mon, 29 Jun 2020 21:54:44: 19000000 INFO @ Mon, 29 Jun 2020 21:54:44: 24000000 INFO @ Mon, 29 Jun 2020 21:54:49: 20000000 INFO @ Mon, 29 Jun 2020 21:54:50: 25000000 INFO @ Mon, 29 Jun 2020 21:54:54: 21000000 INFO @ Mon, 29 Jun 2020 21:54:55: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 21:54:55: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 21:54:55: #1 total tags in treatment: 25817770 INFO @ Mon, 29 Jun 2020 21:54:55: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 21:54:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 21:54:55: #1 tags after filtering in treatment: 25817770 INFO @ Mon, 29 Jun 2020 21:54:55: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 21:54:55: #1 finished! INFO @ Mon, 29 Jun 2020 21:54:55: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 21:54:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 21:54:57: #2 number of paired peaks: 130 WARNING @ Mon, 29 Jun 2020 21:54:57: Fewer paired peaks (130) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 130 pairs to build model! INFO @ Mon, 29 Jun 2020 21:54:57: start model_add_line... INFO @ Mon, 29 Jun 2020 21:54:57: start X-correlation... INFO @ Mon, 29 Jun 2020 21:54:57: end of X-cor INFO @ Mon, 29 Jun 2020 21:54:57: #2 finished! INFO @ Mon, 29 Jun 2020 21:54:57: #2 predicted fragment length is 0 bps INFO @ Mon, 29 Jun 2020 21:54:57: #2 alternative fragment length(s) may be 0,43,501,507,530,589 bps INFO @ Mon, 29 Jun 2020 21:54:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3883438/SRX3883438.10_model.r WARNING @ Mon, 29 Jun 2020 21:54:57: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 21:54:57: #2 You may need to consider one of the other alternative d(s): 0,43,501,507,530,589 WARNING @ Mon, 29 Jun 2020 21:54:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 21:54:57: #3 Call peaks... INFO @ Mon, 29 Jun 2020 21:54:57: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 21:55:00: 22000000 INFO @ Mon, 29 Jun 2020 21:55:05: 23000000 INFO @ Mon, 29 Jun 2020 21:55:10: 24000000 INFO @ Mon, 29 Jun 2020 21:55:15: 25000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 21:55:19: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 21:55:19: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 21:55:19: #1 total tags in treatment: 25817770 INFO @ Mon, 29 Jun 2020 21:55:19: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 21:55:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 21:55:20: #1 tags after filtering in treatment: 25817770 INFO @ Mon, 29 Jun 2020 21:55:20: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 21:55:20: #1 finished! INFO @ Mon, 29 Jun 2020 21:55:20: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 21:55:20: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 21:55:21: #2 number of paired peaks: 130 WARNING @ Mon, 29 Jun 2020 21:55:21: Fewer paired peaks (130) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 130 pairs to build model! INFO @ Mon, 29 Jun 2020 21:55:21: start model_add_line... INFO @ Mon, 29 Jun 2020 21:55:21: start X-correlation... INFO @ Mon, 29 Jun 2020 21:55:21: end of X-cor INFO @ Mon, 29 Jun 2020 21:55:21: #2 finished! INFO @ Mon, 29 Jun 2020 21:55:21: #2 predicted fragment length is 0 bps INFO @ Mon, 29 Jun 2020 21:55:21: #2 alternative fragment length(s) may be 0,43,501,507,530,589 bps INFO @ Mon, 29 Jun 2020 21:55:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3883438/SRX3883438.20_model.r WARNING @ Mon, 29 Jun 2020 21:55:21: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 21:55:21: #2 You may need to consider one of the other alternative d(s): 0,43,501,507,530,589 WARNING @ Mon, 29 Jun 2020 21:55:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 21:55:21: #3 Call peaks... INFO @ Mon, 29 Jun 2020 21:55:21: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 /var/spool/uge/at157/job_scripts/6527408: line 293: 64689 Terminated MACS $i /var/spool/uge/at157/job_scripts/6527408: line 293: 71717 Terminated MACS $i /var/spool/uge/at157/job_scripts/6527408: line 293: 76579 Terminated MACS $i ls: cannot access SRX3883438.05.bed: No such file or directory mv: cannot stat ‘SRX3883438.05.bed’: No such file or directory mv: cannot stat ‘SRX3883438.05.bb’: No such file or directory ls: cannot access SRX3883438.10.bed: No such file or directory mv: cannot stat ‘SRX3883438.10.bed’: No such file or directory mv: cannot stat ‘SRX3883438.10.bb’: No such file or directory ls: cannot access SRX3883438.20.bed: No such file or directory mv: cannot stat ‘SRX3883438.20.bed’: No such file or directory mv: cannot stat ‘SRX3883438.20.bb’: No such file or directory