Job ID = 6366276 SRX = SRX105310 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:48:37 prefetch.2.10.7: 1) Downloading 'SRR363997'... 2020-06-15T22:48:37 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:50:42 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:50:42 prefetch.2.10.7: 1) 'SRR363997' was downloaded successfully Read 27990405 spots for SRR363997/SRR363997.sra Written 27990405 spots for SRR363997/SRR363997.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: 00:04:28 27990405 reads; of these: 27990405 (100.00%) were unpaired; of these: 5468034 (19.54%) aligned 0 times 18598160 (66.44%) aligned exactly 1 time 3924211 (14.02%) aligned >1 times 80.46% overall alignment rate Time searching: 00:04:28 Overall time: 00:04:28 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] 2739416 / 22522371 = 0.1216 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 08:01:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX105310/SRX105310.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX105310/SRX105310.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX105310/SRX105310.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX105310/SRX105310.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 08:01:36: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:01:36: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:01:42: 1000000 INFO @ Tue, 16 Jun 2020 08:01:48: 2000000 INFO @ Tue, 16 Jun 2020 08:01:54: 3000000 INFO @ Tue, 16 Jun 2020 08:02:00: 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 08:02:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX105310/SRX105310.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX105310/SRX105310.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX105310/SRX105310.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX105310/SRX105310.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 08:02:06: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:02:06: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:02:07: 5000000 INFO @ Tue, 16 Jun 2020 08:02:12: 1000000 INFO @ Tue, 16 Jun 2020 08:02:13: 6000000 INFO @ Tue, 16 Jun 2020 08:02:18: 2000000 INFO @ Tue, 16 Jun 2020 08:02:20: 7000000 INFO @ Tue, 16 Jun 2020 08:02:24: 3000000 INFO @ Tue, 16 Jun 2020 08:02:26: 8000000 INFO @ Tue, 16 Jun 2020 08:02:30: 4000000 INFO @ Tue, 16 Jun 2020 08:02:33: 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 08:02:35: 5000000 INFO @ Tue, 16 Jun 2020 08:02:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX105310/SRX105310.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX105310/SRX105310.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX105310/SRX105310.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX105310/SRX105310.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 08:02:36: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:02:36: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:02:40: 10000000 INFO @ Tue, 16 Jun 2020 08:02:41: 6000000 INFO @ Tue, 16 Jun 2020 08:02:42: 1000000 INFO @ Tue, 16 Jun 2020 08:02:46: 11000000 INFO @ Tue, 16 Jun 2020 08:02:47: 7000000 INFO @ Tue, 16 Jun 2020 08:02:48: 2000000 INFO @ Tue, 16 Jun 2020 08:02:53: 12000000 INFO @ Tue, 16 Jun 2020 08:02:53: 8000000 INFO @ Tue, 16 Jun 2020 08:02:53: 3000000 INFO @ Tue, 16 Jun 2020 08:02:59: 9000000 INFO @ Tue, 16 Jun 2020 08:02:59: 4000000 INFO @ Tue, 16 Jun 2020 08:03:00: 13000000 INFO @ Tue, 16 Jun 2020 08:03:05: 10000000 INFO @ Tue, 16 Jun 2020 08:03:05: 5000000 INFO @ Tue, 16 Jun 2020 08:03:06: 14000000 INFO @ Tue, 16 Jun 2020 08:03:11: 11000000 INFO @ Tue, 16 Jun 2020 08:03:11: 6000000 INFO @ Tue, 16 Jun 2020 08:03:13: 15000000 INFO @ Tue, 16 Jun 2020 08:03:17: 12000000 INFO @ Tue, 16 Jun 2020 08:03:17: 7000000 INFO @ Tue, 16 Jun 2020 08:03:20: 16000000 INFO @ Tue, 16 Jun 2020 08:03:23: 8000000 INFO @ Tue, 16 Jun 2020 08:03:23: 13000000 INFO @ Tue, 16 Jun 2020 08:03:26: 17000000 INFO @ Tue, 16 Jun 2020 08:03:29: 9000000 INFO @ Tue, 16 Jun 2020 08:03:29: 14000000 INFO @ Tue, 16 Jun 2020 08:03:32: 18000000 INFO @ Tue, 16 Jun 2020 08:03:35: 10000000 INFO @ Tue, 16 Jun 2020 08:03:35: 15000000 INFO @ Tue, 16 Jun 2020 08:03:39: 19000000 INFO @ Tue, 16 Jun 2020 08:03:41: 11000000 INFO @ Tue, 16 Jun 2020 08:03:41: 16000000 INFO @ Tue, 16 Jun 2020 08:03:44: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 08:03:44: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 08:03:44: #1 total tags in treatment: 19782955 INFO @ Tue, 16 Jun 2020 08:03:44: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:03:44: #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 08:03:44: #1 tags after filtering in treatment: 19782955 INFO @ Tue, 16 Jun 2020 08:03:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:03:44: #1 finished! INFO @ Tue, 16 Jun 2020 08:03:44: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:03:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:03:46: #2 number of paired peaks: 183 WARNING @ Tue, 16 Jun 2020 08:03:46: Fewer paired peaks (183) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 183 pairs to build model! INFO @ Tue, 16 Jun 2020 08:03:46: start model_add_line... INFO @ Tue, 16 Jun 2020 08:03:46: start X-correlation... INFO @ Tue, 16 Jun 2020 08:03:46: end of X-cor INFO @ Tue, 16 Jun 2020 08:03:46: #2 finished! INFO @ Tue, 16 Jun 2020 08:03:46: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:03:46: #2 alternative fragment length(s) may be 1,31,534,568,593 bps INFO @ Tue, 16 Jun 2020 08:03:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX105310/SRX105310.05_model.r WARNING @ Tue, 16 Jun 2020 08:03:46: #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 08:03:46: #2 You may need to consider one of the other alternative d(s): 1,31,534,568,593 WARNING @ Tue, 16 Jun 2020 08:03:46: #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 08:03:46: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:03:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:03:47: 12000000 INFO @ Tue, 16 Jun 2020 08:03:47: 17000000 INFO @ Tue, 16 Jun 2020 08:03:52: 13000000 INFO @ Tue, 16 Jun 2020 08:03:53: 18000000 INFO @ Tue, 16 Jun 2020 08:03:58: 14000000 INFO @ Tue, 16 Jun 2020 08:03:58: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:04:03: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 08:04:03: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 08:04:03: #1 total tags in treatment: 19782955 INFO @ Tue, 16 Jun 2020 08:04:03: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:04:03: #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 08:04:03: #1 tags after filtering in treatment: 19782955 INFO @ Tue, 16 Jun 2020 08:04:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:04:03: #1 finished! INFO @ Tue, 16 Jun 2020 08:04:03: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:04:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:04:03: 15000000 INFO @ Tue, 16 Jun 2020 08:04:04: #2 number of paired peaks: 183 WARNING @ Tue, 16 Jun 2020 08:04:04: Fewer paired peaks (183) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 183 pairs to build model! INFO @ Tue, 16 Jun 2020 08:04:04: start model_add_line... INFO @ Tue, 16 Jun 2020 08:04:05: start X-correlation... INFO @ Tue, 16 Jun 2020 08:04:05: end of X-cor INFO @ Tue, 16 Jun 2020 08:04:05: #2 finished! INFO @ Tue, 16 Jun 2020 08:04:05: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:04:05: #2 alternative fragment length(s) may be 1,31,534,568,593 bps INFO @ Tue, 16 Jun 2020 08:04:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX105310/SRX105310.10_model.r WARNING @ Tue, 16 Jun 2020 08:04:05: #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 08:04:05: #2 You may need to consider one of the other alternative d(s): 1,31,534,568,593 WARNING @ Tue, 16 Jun 2020 08:04:05: #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 08:04:05: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:04:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:04:09: 16000000 INFO @ Tue, 16 Jun 2020 08:04:14: 17000000 INFO @ Tue, 16 Jun 2020 08:04:17: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:04:20: 18000000 INFO @ Tue, 16 Jun 2020 08:04:25: 19000000 INFO @ Tue, 16 Jun 2020 08:04:29: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 08:04:29: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 08:04:29: #1 total tags in treatment: 19782955 INFO @ Tue, 16 Jun 2020 08:04:29: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:04:29: #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 08:04:29: #1 tags after filtering in treatment: 19782955 INFO @ Tue, 16 Jun 2020 08:04:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:04:29: #1 finished! INFO @ Tue, 16 Jun 2020 08:04:29: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:04:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:04:31: #2 number of paired peaks: 183 WARNING @ Tue, 16 Jun 2020 08:04:31: Fewer paired peaks (183) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 183 pairs to build model! INFO @ Tue, 16 Jun 2020 08:04:31: start model_add_line... INFO @ Tue, 16 Jun 2020 08:04:31: start X-correlation... INFO @ Tue, 16 Jun 2020 08:04:31: end of X-cor INFO @ Tue, 16 Jun 2020 08:04:31: #2 finished! INFO @ Tue, 16 Jun 2020 08:04:31: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:04:31: #2 alternative fragment length(s) may be 1,31,534,568,593 bps INFO @ Tue, 16 Jun 2020 08:04:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX105310/SRX105310.20_model.r WARNING @ Tue, 16 Jun 2020 08:04:31: #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 08:04:31: #2 You may need to consider one of the other alternative d(s): 1,31,534,568,593 WARNING @ Tue, 16 Jun 2020 08:04:31: #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 08:04:31: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:04:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:04:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX105310/SRX105310.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:04:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX105310/SRX105310.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:04:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX105310/SRX105310.05_summits.bed INFO @ Tue, 16 Jun 2020 08:04:33: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:04:36: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:04:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX105310/SRX105310.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:04:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX105310/SRX105310.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:04:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX105310/SRX105310.10_summits.bed INFO @ Tue, 16 Jun 2020 08:04:51: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:05:02: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:05:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX105310/SRX105310.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:05:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX105310/SRX105310.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:05:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX105310/SRX105310.20_summits.bed INFO @ Tue, 16 Jun 2020 08:05:17: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling