Job ID = 6527415 SRX = SRX495113 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T12:38:26 prefetch.2.10.7: 1) Downloading 'SRR1198645'... 2020-06-29T12:38:26 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:41:39 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:41:39 prefetch.2.10.7: 1) 'SRR1198645' was downloaded successfully Read 30788149 spots for SRR1198645/SRR1198645.sra Written 30788149 spots for SRR1198645/SRR1198645.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: 00:05:06 30788149 reads; of these: 30788149 (100.00%) were unpaired; of these: 171815 (0.56%) aligned 0 times 25273614 (82.09%) aligned exactly 1 time 5342720 (17.35%) aligned >1 times 99.44% overall alignment rate Time searching: 00:05:06 Overall time: 00:05:06 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] 4711139 / 30616334 = 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 @ Mon, 29 Jun 2020 21:59:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495113/SRX495113.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495113/SRX495113.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495113/SRX495113.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495113/SRX495113.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 21:59:33: #1 read tag files... INFO @ Mon, 29 Jun 2020 21:59:33: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 21:59:39: 1000000 INFO @ Mon, 29 Jun 2020 21:59:44: 2000000 INFO @ Mon, 29 Jun 2020 21:59:50: 3000000 INFO @ Mon, 29 Jun 2020 21:59:55: 4000000 INFO @ Mon, 29 Jun 2020 22:00:01: 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 22:00:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495113/SRX495113.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495113/SRX495113.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495113/SRX495113.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495113/SRX495113.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 22:00:03: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:00:03: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:00:06: 6000000 INFO @ Mon, 29 Jun 2020 22:00:08: 1000000 INFO @ Mon, 29 Jun 2020 22:00:12: 7000000 INFO @ Mon, 29 Jun 2020 22:00:14: 2000000 INFO @ Mon, 29 Jun 2020 22:00:18: 8000000 INFO @ Mon, 29 Jun 2020 22:00:19: 3000000 INFO @ Mon, 29 Jun 2020 22:00:24: 9000000 INFO @ Mon, 29 Jun 2020 22:00:25: 4000000 INFO @ Mon, 29 Jun 2020 22:00:29: 10000000 INFO @ Mon, 29 Jun 2020 22:00:30: 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 @ Mon, 29 Jun 2020 22:00:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495113/SRX495113.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495113/SRX495113.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495113/SRX495113.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495113/SRX495113.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 22:00:33: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:00:33: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:00:35: 11000000 INFO @ Mon, 29 Jun 2020 22:00:35: 6000000 INFO @ Mon, 29 Jun 2020 22:00:39: 1000000 INFO @ Mon, 29 Jun 2020 22:00:41: 7000000 INFO @ Mon, 29 Jun 2020 22:00:41: 12000000 INFO @ Mon, 29 Jun 2020 22:00:45: 2000000 INFO @ Mon, 29 Jun 2020 22:00:46: 8000000 INFO @ Mon, 29 Jun 2020 22:00:47: 13000000 INFO @ Mon, 29 Jun 2020 22:00:51: 3000000 INFO @ Mon, 29 Jun 2020 22:00:51: 9000000 INFO @ Mon, 29 Jun 2020 22:00:53: 14000000 INFO @ Mon, 29 Jun 2020 22:00:56: 4000000 INFO @ Mon, 29 Jun 2020 22:00:57: 10000000 INFO @ Mon, 29 Jun 2020 22:00:59: 15000000 INFO @ Mon, 29 Jun 2020 22:01:02: 5000000 INFO @ Mon, 29 Jun 2020 22:01:02: 11000000 INFO @ Mon, 29 Jun 2020 22:01:05: 16000000 INFO @ Mon, 29 Jun 2020 22:01:08: 12000000 INFO @ Mon, 29 Jun 2020 22:01:08: 6000000 INFO @ Mon, 29 Jun 2020 22:01:11: 17000000 INFO @ Mon, 29 Jun 2020 22:01:13: 13000000 INFO @ Mon, 29 Jun 2020 22:01:13: 7000000 INFO @ Mon, 29 Jun 2020 22:01:17: 18000000 INFO @ Mon, 29 Jun 2020 22:01:19: 14000000 INFO @ Mon, 29 Jun 2020 22:01:19: 8000000 INFO @ Mon, 29 Jun 2020 22:01:23: 19000000 INFO @ Mon, 29 Jun 2020 22:01:24: 15000000 INFO @ Mon, 29 Jun 2020 22:01:25: 9000000 INFO @ Mon, 29 Jun 2020 22:01:29: 20000000 INFO @ Mon, 29 Jun 2020 22:01:30: 16000000 INFO @ Mon, 29 Jun 2020 22:01:31: 10000000 INFO @ Mon, 29 Jun 2020 22:01:35: 21000000 INFO @ Mon, 29 Jun 2020 22:01:35: 17000000 INFO @ Mon, 29 Jun 2020 22:01:37: 11000000 INFO @ Mon, 29 Jun 2020 22:01:41: 22000000 INFO @ Mon, 29 Jun 2020 22:01:41: 18000000 INFO @ Mon, 29 Jun 2020 22:01:43: 12000000 INFO @ Mon, 29 Jun 2020 22:01:46: 19000000 INFO @ Mon, 29 Jun 2020 22:01:46: 23000000 INFO @ Mon, 29 Jun 2020 22:01:49: 13000000 INFO @ Mon, 29 Jun 2020 22:01:52: 20000000 INFO @ Mon, 29 Jun 2020 22:01:52: 24000000 INFO @ Mon, 29 Jun 2020 22:01:55: 14000000 INFO @ Mon, 29 Jun 2020 22:01:57: 21000000 INFO @ Mon, 29 Jun 2020 22:01:58: 25000000 INFO @ Mon, 29 Jun 2020 22:02:01: 15000000 INFO @ Mon, 29 Jun 2020 22:02:03: 22000000 INFO @ Mon, 29 Jun 2020 22:02:04: #1 tag size is determined as 36 bps INFO @ Mon, 29 Jun 2020 22:02:04: #1 tag size = 36 INFO @ Mon, 29 Jun 2020 22:02:04: #1 total tags in treatment: 25905195 INFO @ Mon, 29 Jun 2020 22:02:04: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:02:04: #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 22:02:04: #1 tags after filtering in treatment: 25905195 INFO @ Mon, 29 Jun 2020 22:02:04: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:02:04: #1 finished! INFO @ Mon, 29 Jun 2020 22:02:04: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:02:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:02:06: #2 number of paired peaks: 146 WARNING @ Mon, 29 Jun 2020 22:02:06: Fewer paired peaks (146) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 146 pairs to build model! INFO @ Mon, 29 Jun 2020 22:02:06: start model_add_line... INFO @ Mon, 29 Jun 2020 22:02:06: start X-correlation... INFO @ Mon, 29 Jun 2020 22:02:06: end of X-cor INFO @ Mon, 29 Jun 2020 22:02:06: #2 finished! INFO @ Mon, 29 Jun 2020 22:02:06: #2 predicted fragment length is 0 bps INFO @ Mon, 29 Jun 2020 22:02:06: #2 alternative fragment length(s) may be 0,14,32,213,437,439,476,478,572 bps INFO @ Mon, 29 Jun 2020 22:02:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495113/SRX495113.05_model.r WARNING @ Mon, 29 Jun 2020 22:02:06: #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 22:02:06: #2 You may need to consider one of the other alternative d(s): 0,14,32,213,437,439,476,478,572 WARNING @ Mon, 29 Jun 2020 22:02:06: #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 22:02:06: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:02:06: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:02:07: 16000000 INFO @ Mon, 29 Jun 2020 22:02:09: 23000000 INFO @ Mon, 29 Jun 2020 22:02:13: 17000000 INFO @ Mon, 29 Jun 2020 22:02:14: 24000000 INFO @ Mon, 29 Jun 2020 22:02:19: 18000000 INFO @ Mon, 29 Jun 2020 22:02:20: 25000000 INFO @ Mon, 29 Jun 2020 22:02:25: #1 tag size is determined as 36 bps INFO @ Mon, 29 Jun 2020 22:02:25: #1 tag size = 36 INFO @ Mon, 29 Jun 2020 22:02:25: #1 total tags in treatment: 25905195 INFO @ Mon, 29 Jun 2020 22:02:25: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:02:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 22:02:25: #1 tags after filtering in treatment: 25905195 INFO @ Mon, 29 Jun 2020 22:02:25: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:02:25: #1 finished! INFO @ Mon, 29 Jun 2020 22:02:25: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:02:25: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:02:25: 19000000 INFO @ Mon, 29 Jun 2020 22:02:27: #2 number of paired peaks: 146 WARNING @ Mon, 29 Jun 2020 22:02:27: Fewer paired peaks (146) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 146 pairs to build model! INFO @ Mon, 29 Jun 2020 22:02:27: start model_add_line... INFO @ Mon, 29 Jun 2020 22:02:27: start X-correlation... INFO @ Mon, 29 Jun 2020 22:02:27: end of X-cor INFO @ Mon, 29 Jun 2020 22:02:27: #2 finished! INFO @ Mon, 29 Jun 2020 22:02:27: #2 predicted fragment length is 0 bps INFO @ Mon, 29 Jun 2020 22:02:27: #2 alternative fragment length(s) may be 0,14,32,213,437,439,476,478,572 bps INFO @ Mon, 29 Jun 2020 22:02:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495113/SRX495113.10_model.r WARNING @ Mon, 29 Jun 2020 22:02:27: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:02:27: #2 You may need to consider one of the other alternative d(s): 0,14,32,213,437,439,476,478,572 WARNING @ Mon, 29 Jun 2020 22:02:27: #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 22:02:27: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:02:27: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:02:31: 20000000 INFO @ Mon, 29 Jun 2020 22:02:36: 21000000 INFO @ Mon, 29 Jun 2020 22:02:41: 22000000 INFO @ Mon, 29 Jun 2020 22:02:47: 23000000 INFO @ Mon, 29 Jun 2020 22:02:52: 24000000 INFO @ Mon, 29 Jun 2020 22:02:58: 25000000 INFO @ Mon, 29 Jun 2020 22:03:03: #1 tag size is determined as 36 bps INFO @ Mon, 29 Jun 2020 22:03:03: #1 tag size = 36 INFO @ Mon, 29 Jun 2020 22:03:03: #1 total tags in treatment: 25905195 INFO @ Mon, 29 Jun 2020 22:03:03: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:03:03: #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 22:03:03: #1 tags after filtering in treatment: 25905195 INFO @ Mon, 29 Jun 2020 22:03:03: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:03:03: #1 finished! INFO @ Mon, 29 Jun 2020 22:03:03: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:03:03: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:03:05: #2 number of paired peaks: 146 WARNING @ Mon, 29 Jun 2020 22:03:05: Fewer paired peaks (146) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 146 pairs to build model! INFO @ Mon, 29 Jun 2020 22:03:05: start model_add_line... INFO @ Mon, 29 Jun 2020 22:03:05: start X-correlation... INFO @ Mon, 29 Jun 2020 22:03:05: end of X-cor INFO @ Mon, 29 Jun 2020 22:03:05: #2 finished! INFO @ Mon, 29 Jun 2020 22:03:05: #2 predicted fragment length is 0 bps INFO @ Mon, 29 Jun 2020 22:03:05: #2 alternative fragment length(s) may be 0,14,32,213,437,439,476,478,572 bps INFO @ Mon, 29 Jun 2020 22:03:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495113/SRX495113.20_model.r WARNING @ Mon, 29 Jun 2020 22:03:05: #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 22:03:05: #2 You may need to consider one of the other alternative d(s): 0,14,32,213,437,439,476,478,572 WARNING @ Mon, 29 Jun 2020 22:03:05: #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 22:03:05: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:03:05: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 /var/spool/uge/at163/job_scripts/6527415: line 293: 80428 Terminated MACS $i /var/spool/uge/at163/job_scripts/6527415: line 293: 83212 Terminated MACS $i /var/spool/uge/at163/job_scripts/6527415: line 293: 85624 Terminated MACS $i ls: cannot access SRX495113.05.bed: No such file or directory mv: cannot stat ‘SRX495113.05.bed’: No such file or directory mv: cannot stat ‘SRX495113.05.bb’: No such file or directory ls: cannot access SRX495113.10.bed: No such file or directory mv: cannot stat ‘SRX495113.10.bed’: No such file or directory mv: cannot stat ‘SRX495113.10.bb’: No such file or directory ls: cannot access SRX495113.20.bed: No such file or directory mv: cannot stat ‘SRX495113.20.bed’: No such file or directory mv: cannot stat ‘SRX495113.20.bb’: No such file or directory