Job ID = 6366104 SRX = SRX063961 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:44:52 prefetch.2.10.7: 1) Downloading 'SRR210889'... 2020-06-15T22:44:52 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:46:16 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:46:17 prefetch.2.10.7: 'SRR210889' is valid 2020-06-15T22:46:17 prefetch.2.10.7: 1) 'SRR210889' was downloaded successfully Read 24337237 spots for SRR210889/SRR210889.sra Written 24337237 spots for SRR210889/SRR210889.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: 00:04:39 24337237 reads; of these: 24337237 (100.00%) were unpaired; of these: 254482 (1.05%) aligned 0 times 18600046 (76.43%) aligned exactly 1 time 5482709 (22.53%) aligned >1 times 98.95% overall alignment rate Time searching: 00:04:39 Overall time: 00:04:39 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] 4524622 / 24082755 = 0.1879 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 07:56:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX063961/SRX063961.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX063961/SRX063961.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX063961/SRX063961.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX063961/SRX063961.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 07:56:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:56:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:56:44: 1000000 INFO @ Tue, 16 Jun 2020 07:56:49: 2000000 INFO @ Tue, 16 Jun 2020 07:56:55: 3000000 INFO @ Tue, 16 Jun 2020 07:57:00: 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 07:57:06: 5000000 INFO @ Tue, 16 Jun 2020 07:57:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX063961/SRX063961.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX063961/SRX063961.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX063961/SRX063961.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX063961/SRX063961.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 07:57:06: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:57:06: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:57:11: 6000000 INFO @ Tue, 16 Jun 2020 07:57:12: 1000000 INFO @ Tue, 16 Jun 2020 07:57:18: 7000000 INFO @ Tue, 16 Jun 2020 07:57:18: 2000000 INFO @ Tue, 16 Jun 2020 07:57:23: 8000000 INFO @ Tue, 16 Jun 2020 07:57:24: 3000000 INFO @ Tue, 16 Jun 2020 07:57:29: 9000000 INFO @ Tue, 16 Jun 2020 07:57:30: 4000000 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 07:57:35: 10000000 INFO @ Tue, 16 Jun 2020 07:57:36: 5000000 INFO @ Tue, 16 Jun 2020 07:57:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX063961/SRX063961.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX063961/SRX063961.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX063961/SRX063961.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX063961/SRX063961.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 07:57:36: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:57:36: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:57:42: 11000000 INFO @ Tue, 16 Jun 2020 07:57:42: 6000000 INFO @ Tue, 16 Jun 2020 07:57:43: 1000000 INFO @ Tue, 16 Jun 2020 07:57:48: 7000000 INFO @ Tue, 16 Jun 2020 07:57:48: 12000000 INFO @ Tue, 16 Jun 2020 07:57:49: 2000000 INFO @ Tue, 16 Jun 2020 07:57:55: 8000000 INFO @ Tue, 16 Jun 2020 07:57:55: 13000000 INFO @ Tue, 16 Jun 2020 07:57:55: 3000000 INFO @ Tue, 16 Jun 2020 07:58:01: 9000000 INFO @ Tue, 16 Jun 2020 07:58:01: 14000000 INFO @ Tue, 16 Jun 2020 07:58:01: 4000000 INFO @ Tue, 16 Jun 2020 07:58:07: 10000000 INFO @ Tue, 16 Jun 2020 07:58:07: 15000000 INFO @ Tue, 16 Jun 2020 07:58:08: 5000000 INFO @ Tue, 16 Jun 2020 07:58:13: 11000000 INFO @ Tue, 16 Jun 2020 07:58:14: 16000000 INFO @ Tue, 16 Jun 2020 07:58:14: 6000000 INFO @ Tue, 16 Jun 2020 07:58:19: 12000000 INFO @ Tue, 16 Jun 2020 07:58:20: 7000000 INFO @ Tue, 16 Jun 2020 07:58:20: 17000000 INFO @ Tue, 16 Jun 2020 07:58:26: 13000000 INFO @ Tue, 16 Jun 2020 07:58:26: 8000000 INFO @ Tue, 16 Jun 2020 07:58:26: 18000000 INFO @ Tue, 16 Jun 2020 07:58:32: 14000000 INFO @ Tue, 16 Jun 2020 07:58:32: 9000000 INFO @ Tue, 16 Jun 2020 07:58:33: 19000000 INFO @ Tue, 16 Jun 2020 07:58:36: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:58:36: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:58:36: #1 total tags in treatment: 19558133 INFO @ Tue, 16 Jun 2020 07:58:36: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:58:36: #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 07:58:37: #1 tags after filtering in treatment: 19558133 INFO @ Tue, 16 Jun 2020 07:58:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:58:37: #1 finished! INFO @ Tue, 16 Jun 2020 07:58:37: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:58:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:58:38: 15000000 INFO @ Tue, 16 Jun 2020 07:58:38: #2 number of paired peaks: 305 WARNING @ Tue, 16 Jun 2020 07:58:38: Fewer paired peaks (305) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 305 pairs to build model! INFO @ Tue, 16 Jun 2020 07:58:38: start model_add_line... INFO @ Tue, 16 Jun 2020 07:58:38: 10000000 INFO @ Tue, 16 Jun 2020 07:58:38: start X-correlation... INFO @ Tue, 16 Jun 2020 07:58:38: end of X-cor INFO @ Tue, 16 Jun 2020 07:58:38: #2 finished! INFO @ Tue, 16 Jun 2020 07:58:38: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 07:58:38: #2 alternative fragment length(s) may be 1,31,557,577 bps INFO @ Tue, 16 Jun 2020 07:58:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX063961/SRX063961.05_model.r WARNING @ Tue, 16 Jun 2020 07:58:38: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:58:38: #2 You may need to consider one of the other alternative d(s): 1,31,557,577 WARNING @ Tue, 16 Jun 2020 07:58:38: #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 07:58:38: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:58:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:58:44: 16000000 INFO @ Tue, 16 Jun 2020 07:58:44: 11000000 INFO @ Tue, 16 Jun 2020 07:58:50: 17000000 INFO @ Tue, 16 Jun 2020 07:58:50: 12000000 INFO @ Tue, 16 Jun 2020 07:58:56: 18000000 INFO @ Tue, 16 Jun 2020 07:58:56: 13000000 INFO @ Tue, 16 Jun 2020 07:59:02: 19000000 INFO @ Tue, 16 Jun 2020 07:59:02: 14000000 INFO @ Tue, 16 Jun 2020 07:59:05: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:59:05: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:59:05: #1 total tags in treatment: 19558133 INFO @ Tue, 16 Jun 2020 07:59:05: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:59:05: #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 07:59:06: #1 tags after filtering in treatment: 19558133 INFO @ Tue, 16 Jun 2020 07:59:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:59:06: #1 finished! INFO @ Tue, 16 Jun 2020 07:59:06: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:59:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:59:07: #2 number of paired peaks: 305 WARNING @ Tue, 16 Jun 2020 07:59:07: Fewer paired peaks (305) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 305 pairs to build model! INFO @ Tue, 16 Jun 2020 07:59:07: start model_add_line... INFO @ Tue, 16 Jun 2020 07:59:07: start X-correlation... INFO @ Tue, 16 Jun 2020 07:59:07: end of X-cor INFO @ Tue, 16 Jun 2020 07:59:07: #2 finished! INFO @ Tue, 16 Jun 2020 07:59:07: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 07:59:07: #2 alternative fragment length(s) may be 1,31,557,577 bps INFO @ Tue, 16 Jun 2020 07:59:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX063961/SRX063961.10_model.r WARNING @ Tue, 16 Jun 2020 07:59:07: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:59:07: #2 You may need to consider one of the other alternative d(s): 1,31,557,577 WARNING @ Tue, 16 Jun 2020 07:59:07: #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 07:59:07: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:59:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:59:08: 15000000 INFO @ Tue, 16 Jun 2020 07:59:13: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:59:14: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:59:19: 17000000 INFO @ Tue, 16 Jun 2020 07:59:25: 18000000 INFO @ Tue, 16 Jun 2020 07:59:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX063961/SRX063961.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:59:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX063961/SRX063961.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:59:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX063961/SRX063961.05_summits.bed INFO @ Tue, 16 Jun 2020 07:59:30: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:59:30: 19000000 INFO @ Tue, 16 Jun 2020 07:59:34: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:59:34: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:59:34: #1 total tags in treatment: 19558133 INFO @ Tue, 16 Jun 2020 07:59:34: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:59:34: #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 07:59:34: #1 tags after filtering in treatment: 19558133 INFO @ Tue, 16 Jun 2020 07:59:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:59:34: #1 finished! INFO @ Tue, 16 Jun 2020 07:59:34: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:59:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:59:35: #2 number of paired peaks: 305 WARNING @ Tue, 16 Jun 2020 07:59:35: Fewer paired peaks (305) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 305 pairs to build model! INFO @ Tue, 16 Jun 2020 07:59:35: start model_add_line... INFO @ Tue, 16 Jun 2020 07:59:35: start X-correlation... INFO @ Tue, 16 Jun 2020 07:59:35: end of X-cor INFO @ Tue, 16 Jun 2020 07:59:35: #2 finished! INFO @ Tue, 16 Jun 2020 07:59:35: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 07:59:35: #2 alternative fragment length(s) may be 1,31,557,577 bps INFO @ Tue, 16 Jun 2020 07:59:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX063961/SRX063961.20_model.r WARNING @ Tue, 16 Jun 2020 07:59:35: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:59:35: #2 You may need to consider one of the other alternative d(s): 1,31,557,577 WARNING @ Tue, 16 Jun 2020 07:59:35: #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 07:59:35: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:59:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:59:41: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:59:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX063961/SRX063961.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:59:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX063961/SRX063961.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:59:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX063961/SRX063961.10_summits.bed INFO @ Tue, 16 Jun 2020 07:59:57: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:00:08: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:00:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX063961/SRX063961.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:00:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX063961/SRX063961.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:00:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX063961/SRX063961.20_summits.bed INFO @ Tue, 16 Jun 2020 08:00:24: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling