Job ID = 6368084 SRX = SRX466547 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:52:03 prefetch.2.10.7: 1) Downloading 'SRR1163613'... 2020-06-15T23:52:03 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:54:14 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:54:14 prefetch.2.10.7: 1) 'SRR1163613' was downloaded successfully Read 30788149 spots for SRR1163613/SRR1163613.sra Written 30788149 spots for SRR1163613/SRR1163613.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: 00:05:07 30788149 reads; of these: 30788149 (100.00%) were unpaired; of these: 169790 (0.55%) aligned 0 times 25275390 (82.09%) aligned exactly 1 time 5342969 (17.35%) aligned >1 times 99.45% overall alignment rate Time searching: 00:05:07 Overall time: 00:05:07 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] 4711751 / 30618359 = 0.1539 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 09:06:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466547/SRX466547.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466547/SRX466547.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466547/SRX466547.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466547/SRX466547.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 09:06:59: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:06:59: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:07:05: 1000000 INFO @ Tue, 16 Jun 2020 09:07:11: 2000000 INFO @ Tue, 16 Jun 2020 09:07:17: 3000000 INFO @ Tue, 16 Jun 2020 09:07:22: 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, 16 Jun 2020 09:07:28: 5000000 INFO @ Tue, 16 Jun 2020 09:07:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466547/SRX466547.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466547/SRX466547.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466547/SRX466547.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466547/SRX466547.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 09:07:29: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:07:29: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:07:34: 6000000 INFO @ Tue, 16 Jun 2020 09:07:35: 1000000 INFO @ Tue, 16 Jun 2020 09:07:41: 2000000 INFO @ Tue, 16 Jun 2020 09:07:41: 7000000 INFO @ Tue, 16 Jun 2020 09:07:46: 3000000 INFO @ Tue, 16 Jun 2020 09:07:47: 8000000 INFO @ Tue, 16 Jun 2020 09:07:52: 4000000 INFO @ Tue, 16 Jun 2020 09:07:53: 9000000 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 09:07:58: 5000000 INFO @ Tue, 16 Jun 2020 09:07:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466547/SRX466547.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466547/SRX466547.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466547/SRX466547.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466547/SRX466547.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 09:07:59: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:07:59: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:07:59: 10000000 INFO @ Tue, 16 Jun 2020 09:08:03: 6000000 INFO @ Tue, 16 Jun 2020 09:08:05: 1000000 INFO @ Tue, 16 Jun 2020 09:08:06: 11000000 INFO @ Tue, 16 Jun 2020 09:08:09: 7000000 INFO @ Tue, 16 Jun 2020 09:08:12: 2000000 INFO @ Tue, 16 Jun 2020 09:08:12: 12000000 INFO @ Tue, 16 Jun 2020 09:08:15: 8000000 INFO @ Tue, 16 Jun 2020 09:08:18: 3000000 INFO @ Tue, 16 Jun 2020 09:08:18: 13000000 INFO @ Tue, 16 Jun 2020 09:08:21: 9000000 INFO @ Tue, 16 Jun 2020 09:08:24: 4000000 INFO @ Tue, 16 Jun 2020 09:08:24: 14000000 INFO @ Tue, 16 Jun 2020 09:08:27: 10000000 INFO @ Tue, 16 Jun 2020 09:08:30: 5000000 INFO @ Tue, 16 Jun 2020 09:08:31: 15000000 INFO @ Tue, 16 Jun 2020 09:08:32: 11000000 INFO @ Tue, 16 Jun 2020 09:08:37: 6000000 INFO @ Tue, 16 Jun 2020 09:08:37: 16000000 INFO @ Tue, 16 Jun 2020 09:08:38: 12000000 INFO @ Tue, 16 Jun 2020 09:08:43: 7000000 INFO @ Tue, 16 Jun 2020 09:08:43: 17000000 INFO @ Tue, 16 Jun 2020 09:08:44: 13000000 INFO @ Tue, 16 Jun 2020 09:08:49: 8000000 INFO @ Tue, 16 Jun 2020 09:08:50: 18000000 INFO @ Tue, 16 Jun 2020 09:08:50: 14000000 INFO @ Tue, 16 Jun 2020 09:08:55: 15000000 INFO @ Tue, 16 Jun 2020 09:08:56: 9000000 INFO @ Tue, 16 Jun 2020 09:08:56: 19000000 INFO @ Tue, 16 Jun 2020 09:09:01: 16000000 INFO @ Tue, 16 Jun 2020 09:09:02: 10000000 INFO @ Tue, 16 Jun 2020 09:09:02: 20000000 INFO @ Tue, 16 Jun 2020 09:09:07: 17000000 INFO @ Tue, 16 Jun 2020 09:09:08: 11000000 INFO @ Tue, 16 Jun 2020 09:09:08: 21000000 INFO @ Tue, 16 Jun 2020 09:09:12: 18000000 INFO @ Tue, 16 Jun 2020 09:09:14: 12000000 INFO @ Tue, 16 Jun 2020 09:09:15: 22000000 INFO @ Tue, 16 Jun 2020 09:09:18: 19000000 INFO @ Tue, 16 Jun 2020 09:09:21: 13000000 INFO @ Tue, 16 Jun 2020 09:09:21: 23000000 INFO @ Tue, 16 Jun 2020 09:09:24: 20000000 INFO @ Tue, 16 Jun 2020 09:09:27: 14000000 INFO @ Tue, 16 Jun 2020 09:09:27: 24000000 INFO @ Tue, 16 Jun 2020 09:09:29: 21000000 INFO @ Tue, 16 Jun 2020 09:09:33: 15000000 INFO @ Tue, 16 Jun 2020 09:09:34: 25000000 INFO @ Tue, 16 Jun 2020 09:09:35: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:09:39: 16000000 INFO @ Tue, 16 Jun 2020 09:09:39: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:09:39: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:09:39: #1 total tags in treatment: 25906608 INFO @ Tue, 16 Jun 2020 09:09:39: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:09:39: #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 09:09:40: #1 tags after filtering in treatment: 25906608 INFO @ Tue, 16 Jun 2020 09:09:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:09:40: #1 finished! INFO @ Tue, 16 Jun 2020 09:09:40: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:09:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:09:41: 23000000 INFO @ Tue, 16 Jun 2020 09:09:41: #2 number of paired peaks: 140 WARNING @ Tue, 16 Jun 2020 09:09:41: Fewer paired peaks (140) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 140 pairs to build model! INFO @ Tue, 16 Jun 2020 09:09:41: start model_add_line... INFO @ Tue, 16 Jun 2020 09:09:41: start X-correlation... INFO @ Tue, 16 Jun 2020 09:09:41: end of X-cor INFO @ Tue, 16 Jun 2020 09:09:41: #2 finished! INFO @ Tue, 16 Jun 2020 09:09:41: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 09:09:41: #2 alternative fragment length(s) may be 0,33,93,442,464,498,552 bps INFO @ Tue, 16 Jun 2020 09:09:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466547/SRX466547.05_model.r WARNING @ Tue, 16 Jun 2020 09:09:41: #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 09:09:41: #2 You may need to consider one of the other alternative d(s): 0,33,93,442,464,498,552 WARNING @ Tue, 16 Jun 2020 09:09:41: #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 09:09:41: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:09:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:09:45: 17000000 INFO @ Tue, 16 Jun 2020 09:09:46: 24000000 INFO @ Tue, 16 Jun 2020 09:09:52: 18000000 INFO @ Tue, 16 Jun 2020 09:09:52: 25000000 INFO @ Tue, 16 Jun 2020 09:09:57: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:09:57: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:09:57: #1 total tags in treatment: 25906608 INFO @ Tue, 16 Jun 2020 09:09:57: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:09:57: #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 09:09:58: #1 tags after filtering in treatment: 25906608 INFO @ Tue, 16 Jun 2020 09:09:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:09:58: #1 finished! INFO @ Tue, 16 Jun 2020 09:09:58: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:09:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:09:58: 19000000 INFO @ Tue, 16 Jun 2020 09:09:59: #2 number of paired peaks: 140 WARNING @ Tue, 16 Jun 2020 09:09:59: Fewer paired peaks (140) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 140 pairs to build model! INFO @ Tue, 16 Jun 2020 09:09:59: start model_add_line... INFO @ Tue, 16 Jun 2020 09:10:00: start X-correlation... INFO @ Tue, 16 Jun 2020 09:10:00: end of X-cor INFO @ Tue, 16 Jun 2020 09:10:00: #2 finished! INFO @ Tue, 16 Jun 2020 09:10:00: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 09:10:00: #2 alternative fragment length(s) may be 0,33,93,442,464,498,552 bps INFO @ Tue, 16 Jun 2020 09:10:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466547/SRX466547.10_model.r WARNING @ Tue, 16 Jun 2020 09:10:00: #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 09:10:00: #2 You may need to consider one of the other alternative d(s): 0,33,93,442,464,498,552 WARNING @ Tue, 16 Jun 2020 09:10:00: #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 09:10:00: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:10:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:10:04: 20000000 INFO @ Tue, 16 Jun 2020 09:10:10: 21000000 INFO @ Tue, 16 Jun 2020 09:10:16: 22000000 INFO @ Tue, 16 Jun 2020 09:10:22: 23000000 INFO @ Tue, 16 Jun 2020 09:10:27: 24000000 BigWig に変換しました。 /var/spool/uge/at153/job_scripts/6368084: line 271: 123301 Terminated MACS $i /var/spool/uge/at153/job_scripts/6368084: line 271: 123516 Terminated MACS $i /var/spool/uge/at153/job_scripts/6368084: line 271: 123838 Terminated MACS $i ls: cannot access SRX466547.05.bed: No such file or directory mv: cannot stat ‘SRX466547.05.bed’: No such file or directory mv: cannot stat ‘SRX466547.05.bb’: No such file or directory ls: cannot access SRX466547.10.bed: No such file or directory mv: cannot stat ‘SRX466547.10.bed’: No such file or directory mv: cannot stat ‘SRX466547.10.bb’: No such file or directory ls: cannot access SRX466547.20.bed: No such file or directory mv: cannot stat ‘SRX466547.20.bed’: No such file or directory mv: cannot stat ‘SRX466547.20.bb’: No such file or directory