Job ID = 6368801 SRX = SRX5709767 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:33:30 prefetch.2.10.7: 1) Downloading 'SRR8928717'... 2020-06-16T00:33:30 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:36:16 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:36:16 prefetch.2.10.7: 1) 'SRR8928717' was downloaded successfully 2020-06-16T00:36:16 prefetch.2.10.7: 'SRR8928717' has 0 unresolved dependencies Read 30139730 spots for SRR8928717/SRR8928717.sra Written 30139730 spots for SRR8928717/SRR8928717.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: 00:06:55 30139730 reads; of these: 30139730 (100.00%) were unpaired; of these: 989707 (3.28%) aligned 0 times 24346864 (80.78%) aligned exactly 1 time 4803159 (15.94%) aligned >1 times 96.72% overall alignment rate Time searching: 00:06:55 Overall time: 00:06:55 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 12 files... [bam_rmdupse_core] 6277791 / 29150023 = 0.2154 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 09:51:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5709767/SRX5709767.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5709767/SRX5709767.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5709767/SRX5709767.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5709767/SRX5709767.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 09:51:09: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:51:09: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:51:15: 1000000 INFO @ Tue, 16 Jun 2020 09:51:21: 2000000 INFO @ Tue, 16 Jun 2020 09:51:26: 3000000 INFO @ Tue, 16 Jun 2020 09:51:32: 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 09:51:38: 5000000 INFO @ Tue, 16 Jun 2020 09:51:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5709767/SRX5709767.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5709767/SRX5709767.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5709767/SRX5709767.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5709767/SRX5709767.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 09:51:39: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:51:39: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:51:44: 6000000 INFO @ Tue, 16 Jun 2020 09:51:45: 1000000 INFO @ Tue, 16 Jun 2020 09:51:50: 7000000 INFO @ Tue, 16 Jun 2020 09:51:51: 2000000 INFO @ Tue, 16 Jun 2020 09:51:57: 3000000 INFO @ Tue, 16 Jun 2020 09:51:57: 8000000 INFO @ Tue, 16 Jun 2020 09:52:02: 4000000 INFO @ Tue, 16 Jun 2020 09:52:03: 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 09:52:08: 5000000 INFO @ Tue, 16 Jun 2020 09:52:09: 10000000 INFO @ Tue, 16 Jun 2020 09:52:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5709767/SRX5709767.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5709767/SRX5709767.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5709767/SRX5709767.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5709767/SRX5709767.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 09:52:10: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:52:10: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:52:14: 6000000 INFO @ Tue, 16 Jun 2020 09:52:16: 11000000 INFO @ Tue, 16 Jun 2020 09:52:16: 1000000 INFO @ Tue, 16 Jun 2020 09:52:20: 7000000 INFO @ Tue, 16 Jun 2020 09:52:22: 2000000 INFO @ Tue, 16 Jun 2020 09:52:22: 12000000 INFO @ Tue, 16 Jun 2020 09:52:26: 8000000 INFO @ Tue, 16 Jun 2020 09:52:28: 3000000 INFO @ Tue, 16 Jun 2020 09:52:29: 13000000 INFO @ Tue, 16 Jun 2020 09:52:33: 9000000 INFO @ Tue, 16 Jun 2020 09:52:34: 4000000 INFO @ Tue, 16 Jun 2020 09:52:35: 14000000 INFO @ Tue, 16 Jun 2020 09:52:39: 10000000 INFO @ Tue, 16 Jun 2020 09:52:40: 5000000 INFO @ Tue, 16 Jun 2020 09:52:42: 15000000 INFO @ Tue, 16 Jun 2020 09:52:45: 11000000 INFO @ Tue, 16 Jun 2020 09:52:46: 6000000 INFO @ Tue, 16 Jun 2020 09:52:49: 16000000 INFO @ Tue, 16 Jun 2020 09:52:51: 12000000 INFO @ Tue, 16 Jun 2020 09:52:52: 7000000 INFO @ Tue, 16 Jun 2020 09:52:55: 17000000 INFO @ Tue, 16 Jun 2020 09:52:58: 13000000 INFO @ Tue, 16 Jun 2020 09:52:59: 8000000 INFO @ Tue, 16 Jun 2020 09:53:02: 18000000 INFO @ Tue, 16 Jun 2020 09:53:04: 14000000 INFO @ Tue, 16 Jun 2020 09:53:05: 9000000 INFO @ Tue, 16 Jun 2020 09:53:08: 19000000 INFO @ Tue, 16 Jun 2020 09:53:10: 15000000 INFO @ Tue, 16 Jun 2020 09:53:11: 10000000 INFO @ Tue, 16 Jun 2020 09:53:15: 20000000 INFO @ Tue, 16 Jun 2020 09:53:16: 16000000 INFO @ Tue, 16 Jun 2020 09:53:17: 11000000 INFO @ Tue, 16 Jun 2020 09:53:22: 21000000 INFO @ Tue, 16 Jun 2020 09:53:23: 17000000 INFO @ Tue, 16 Jun 2020 09:53:23: 12000000 INFO @ Tue, 16 Jun 2020 09:53:28: 22000000 INFO @ Tue, 16 Jun 2020 09:53:29: 18000000 INFO @ Tue, 16 Jun 2020 09:53:29: 13000000 INFO @ Tue, 16 Jun 2020 09:53:34: #1 tag size is determined as 49 bps INFO @ Tue, 16 Jun 2020 09:53:34: #1 tag size = 49 INFO @ Tue, 16 Jun 2020 09:53:34: #1 total tags in treatment: 22872232 INFO @ Tue, 16 Jun 2020 09:53:34: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:53:34: #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 09:53:34: #1 tags after filtering in treatment: 22872232 INFO @ Tue, 16 Jun 2020 09:53:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:53:34: #1 finished! INFO @ Tue, 16 Jun 2020 09:53:34: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:53:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:53:35: 19000000 INFO @ Tue, 16 Jun 2020 09:53:35: 14000000 INFO @ Tue, 16 Jun 2020 09:53:36: #2 number of paired peaks: 190 WARNING @ Tue, 16 Jun 2020 09:53:36: Fewer paired peaks (190) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 190 pairs to build model! INFO @ Tue, 16 Jun 2020 09:53:36: start model_add_line... INFO @ Tue, 16 Jun 2020 09:53:36: start X-correlation... INFO @ Tue, 16 Jun 2020 09:53:36: end of X-cor INFO @ Tue, 16 Jun 2020 09:53:36: #2 finished! INFO @ Tue, 16 Jun 2020 09:53:36: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 09:53:36: #2 alternative fragment length(s) may be 0,46,558,585 bps INFO @ Tue, 16 Jun 2020 09:53:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5709767/SRX5709767.05_model.r WARNING @ Tue, 16 Jun 2020 09:53:36: #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 09:53:36: #2 You may need to consider one of the other alternative d(s): 0,46,558,585 WARNING @ Tue, 16 Jun 2020 09:53:36: #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 09:53:36: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:53:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:53:41: 20000000 INFO @ Tue, 16 Jun 2020 09:53:41: 15000000 INFO @ Tue, 16 Jun 2020 09:53:47: 21000000 INFO @ Tue, 16 Jun 2020 09:53:47: 16000000 INFO @ Tue, 16 Jun 2020 09:53:52: 22000000 INFO @ Tue, 16 Jun 2020 09:53:53: 17000000 INFO @ Tue, 16 Jun 2020 09:53:57: #1 tag size is determined as 49 bps INFO @ Tue, 16 Jun 2020 09:53:57: #1 tag size = 49 INFO @ Tue, 16 Jun 2020 09:53:57: #1 total tags in treatment: 22872232 INFO @ Tue, 16 Jun 2020 09:53:57: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:53:57: #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 09:53:58: #1 tags after filtering in treatment: 22872232 INFO @ Tue, 16 Jun 2020 09:53:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:53:58: #1 finished! INFO @ Tue, 16 Jun 2020 09:53:58: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:53:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:53:58: 18000000 INFO @ Tue, 16 Jun 2020 09:53:59: #2 number of paired peaks: 190 WARNING @ Tue, 16 Jun 2020 09:53:59: Fewer paired peaks (190) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 190 pairs to build model! INFO @ Tue, 16 Jun 2020 09:53:59: start model_add_line... INFO @ Tue, 16 Jun 2020 09:54:00: start X-correlation... INFO @ Tue, 16 Jun 2020 09:54:00: end of X-cor INFO @ Tue, 16 Jun 2020 09:54:00: #2 finished! INFO @ Tue, 16 Jun 2020 09:54:00: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 09:54:00: #2 alternative fragment length(s) may be 0,46,558,585 bps INFO @ Tue, 16 Jun 2020 09:54:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5709767/SRX5709767.10_model.r WARNING @ Tue, 16 Jun 2020 09:54:00: #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 09:54:00: #2 You may need to consider one of the other alternative d(s): 0,46,558,585 WARNING @ Tue, 16 Jun 2020 09:54:00: #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 09:54:00: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:54:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:54:04: 19000000 INFO @ Tue, 16 Jun 2020 09:54:10: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:54:15: 21000000 INFO @ Tue, 16 Jun 2020 09:54:20: 22000000 INFO @ Tue, 16 Jun 2020 09:54:25: #1 tag size is determined as 49 bps INFO @ Tue, 16 Jun 2020 09:54:25: #1 tag size = 49 INFO @ Tue, 16 Jun 2020 09:54:25: #1 total tags in treatment: 22872232 INFO @ Tue, 16 Jun 2020 09:54:25: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:54:25: #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 09:54:26: #1 tags after filtering in treatment: 22872232 INFO @ Tue, 16 Jun 2020 09:54:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:54:26: #1 finished! INFO @ Tue, 16 Jun 2020 09:54:26: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:54:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:54:27: #2 number of paired peaks: 190 WARNING @ Tue, 16 Jun 2020 09:54:27: Fewer paired peaks (190) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 190 pairs to build model! INFO @ Tue, 16 Jun 2020 09:54:27: start model_add_line... INFO @ Tue, 16 Jun 2020 09:54:27: start X-correlation... INFO @ Tue, 16 Jun 2020 09:54:27: end of X-cor INFO @ Tue, 16 Jun 2020 09:54:27: #2 finished! INFO @ Tue, 16 Jun 2020 09:54:27: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 09:54:27: #2 alternative fragment length(s) may be 0,46,558,585 bps INFO @ Tue, 16 Jun 2020 09:54:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5709767/SRX5709767.20_model.r WARNING @ Tue, 16 Jun 2020 09:54:27: #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 09:54:27: #2 You may need to consider one of the other alternative d(s): 0,46,558,585 WARNING @ Tue, 16 Jun 2020 09:54:27: #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 09:54:27: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:54:27: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 /var/spool/uge/at150/job_scripts/6368801: line 271: 81229 Terminated MACS $i /var/spool/uge/at150/job_scripts/6368801: line 271: 81862 Terminated MACS $i /var/spool/uge/at150/job_scripts/6368801: line 271: 95929 Terminated MACS $i ls: cannot access SRX5709767.05.bed: No such file or directory mv: cannot stat ‘SRX5709767.05.bed’: No such file or directory mv: cannot stat ‘SRX5709767.05.bb’: No such file or directory ls: cannot access SRX5709767.10.bed: No such file or directory mv: cannot stat ‘SRX5709767.10.bed’: No such file or directory mv: cannot stat ‘SRX5709767.10.bb’: No such file or directory ls: cannot access SRX5709767.20.bed: No such file or directory mv: cannot stat ‘SRX5709767.20.bed’: No such file or directory mv: cannot stat ‘SRX5709767.20.bb’: No such file or directory