Job ID = 6507948 SRX = SRX495108 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T13:26:33 prefetch.2.10.7: 1) Downloading 'SRR1198640'... 2020-06-26T13:26:33 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:29:34 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:29:34 prefetch.2.10.7: 1) 'SRR1198640' was downloaded successfully Read 28380011 spots for SRR1198640/SRR1198640.sra Written 28380011 spots for SRR1198640/SRR1198640.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: 00:06:39 28380011 reads; of these: 28380011 (100.00%) were unpaired; of these: 2424990 (8.54%) aligned 0 times 20668364 (72.83%) aligned exactly 1 time 5286657 (18.63%) aligned >1 times 91.46% overall alignment rate Time searching: 00:06:39 Overall time: 00:06:39 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 12 files... [bam_rmdupse_core] 5627531 / 25955021 = 0.2168 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 @ Fri, 26 Jun 2020 22:44:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495108/SRX495108.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495108/SRX495108.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495108/SRX495108.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495108/SRX495108.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 @ Fri, 26 Jun 2020 22:44:21: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:44:21: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:44:27: 1000000 INFO @ Fri, 26 Jun 2020 22:44:33: 2000000 INFO @ Fri, 26 Jun 2020 22:44:38: 3000000 INFO @ Fri, 26 Jun 2020 22:44:44: 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 @ Fri, 26 Jun 2020 22:44:50: 5000000 INFO @ Fri, 26 Jun 2020 22:44:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495108/SRX495108.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495108/SRX495108.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495108/SRX495108.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495108/SRX495108.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 @ Fri, 26 Jun 2020 22:44:52: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:44:52: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:44:56: 6000000 INFO @ Fri, 26 Jun 2020 22:44:57: 1000000 INFO @ Fri, 26 Jun 2020 22:45:01: 7000000 INFO @ Fri, 26 Jun 2020 22:45:03: 2000000 INFO @ Fri, 26 Jun 2020 22:45:07: 8000000 INFO @ Fri, 26 Jun 2020 22:45:09: 3000000 INFO @ Fri, 26 Jun 2020 22:45:13: 9000000 INFO @ Fri, 26 Jun 2020 22:45:15: 4000000 INFO @ Fri, 26 Jun 2020 22:45:19: 10000000 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 @ Fri, 26 Jun 2020 22:45:21: 5000000 INFO @ Fri, 26 Jun 2020 22:45:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495108/SRX495108.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495108/SRX495108.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495108/SRX495108.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495108/SRX495108.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 @ Fri, 26 Jun 2020 22:45:21: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:45:21: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:45:25: 11000000 INFO @ Fri, 26 Jun 2020 22:45:26: 6000000 INFO @ Fri, 26 Jun 2020 22:45:27: 1000000 INFO @ Fri, 26 Jun 2020 22:45:31: 12000000 INFO @ Fri, 26 Jun 2020 22:45:32: 7000000 INFO @ Fri, 26 Jun 2020 22:45:33: 2000000 INFO @ Fri, 26 Jun 2020 22:45:37: 13000000 INFO @ Fri, 26 Jun 2020 22:45:38: 8000000 INFO @ Fri, 26 Jun 2020 22:45:40: 3000000 INFO @ Fri, 26 Jun 2020 22:45:43: 14000000 INFO @ Fri, 26 Jun 2020 22:45:44: 9000000 INFO @ Fri, 26 Jun 2020 22:45:46: 4000000 INFO @ Fri, 26 Jun 2020 22:45:49: 15000000 INFO @ Fri, 26 Jun 2020 22:45:50: 10000000 INFO @ Fri, 26 Jun 2020 22:45:52: 5000000 INFO @ Fri, 26 Jun 2020 22:45:55: 11000000 INFO @ Fri, 26 Jun 2020 22:45:55: 16000000 INFO @ Fri, 26 Jun 2020 22:45:59: 6000000 INFO @ Fri, 26 Jun 2020 22:46:01: 12000000 INFO @ Fri, 26 Jun 2020 22:46:02: 17000000 INFO @ Fri, 26 Jun 2020 22:46:05: 7000000 INFO @ Fri, 26 Jun 2020 22:46:07: 13000000 INFO @ Fri, 26 Jun 2020 22:46:08: 18000000 INFO @ Fri, 26 Jun 2020 22:46:11: 8000000 INFO @ Fri, 26 Jun 2020 22:46:13: 14000000 INFO @ Fri, 26 Jun 2020 22:46:14: 19000000 INFO @ Fri, 26 Jun 2020 22:46:18: 9000000 INFO @ Fri, 26 Jun 2020 22:46:19: 15000000 INFO @ Fri, 26 Jun 2020 22:46:20: 20000000 INFO @ Fri, 26 Jun 2020 22:46:22: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 22:46:22: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 22:46:22: #1 total tags in treatment: 20327490 INFO @ Fri, 26 Jun 2020 22:46:22: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:46:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:46:23: #1 tags after filtering in treatment: 20327490 INFO @ Fri, 26 Jun 2020 22:46:23: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:46:23: #1 finished! INFO @ Fri, 26 Jun 2020 22:46:23: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:46:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:46:24: 10000000 INFO @ Fri, 26 Jun 2020 22:46:24: #2 number of paired peaks: 252 WARNING @ Fri, 26 Jun 2020 22:46:24: Fewer paired peaks (252) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 252 pairs to build model! INFO @ Fri, 26 Jun 2020 22:46:24: start model_add_line... INFO @ Fri, 26 Jun 2020 22:46:24: start X-correlation... INFO @ Fri, 26 Jun 2020 22:46:24: end of X-cor INFO @ Fri, 26 Jun 2020 22:46:24: #2 finished! INFO @ Fri, 26 Jun 2020 22:46:24: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 22:46:24: #2 alternative fragment length(s) may be 1,34,578,585,591 bps INFO @ Fri, 26 Jun 2020 22:46:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495108/SRX495108.05_model.r WARNING @ Fri, 26 Jun 2020 22:46:24: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:46:24: #2 You may need to consider one of the other alternative d(s): 1,34,578,585,591 WARNING @ Fri, 26 Jun 2020 22:46:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 22:46:24: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:46:24: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:46:25: 16000000 INFO @ Fri, 26 Jun 2020 22:46:30: 11000000 INFO @ Fri, 26 Jun 2020 22:46:31: 17000000 INFO @ Fri, 26 Jun 2020 22:46:36: 18000000 INFO @ Fri, 26 Jun 2020 22:46:37: 12000000 INFO @ Fri, 26 Jun 2020 22:46:42: 19000000 INFO @ Fri, 26 Jun 2020 22:46:43: 13000000 INFO @ Fri, 26 Jun 2020 22:46:48: 20000000 INFO @ Fri, 26 Jun 2020 22:46:49: 14000000 INFO @ Fri, 26 Jun 2020 22:46:50: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 22:46:50: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 22:46:50: #1 total tags in treatment: 20327490 INFO @ Fri, 26 Jun 2020 22:46:50: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:46:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:46:51: #1 tags after filtering in treatment: 20327490 INFO @ Fri, 26 Jun 2020 22:46:51: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:46:51: #1 finished! INFO @ Fri, 26 Jun 2020 22:46:51: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:46:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:46:52: #2 number of paired peaks: 252 WARNING @ Fri, 26 Jun 2020 22:46:52: Fewer paired peaks (252) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 252 pairs to build model! INFO @ Fri, 26 Jun 2020 22:46:52: start model_add_line... INFO @ Fri, 26 Jun 2020 22:46:52: start X-correlation... INFO @ Fri, 26 Jun 2020 22:46:52: end of X-cor INFO @ Fri, 26 Jun 2020 22:46:52: #2 finished! INFO @ Fri, 26 Jun 2020 22:46:52: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 22:46:52: #2 alternative fragment length(s) may be 1,34,578,585,591 bps INFO @ Fri, 26 Jun 2020 22:46:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495108/SRX495108.10_model.r WARNING @ Fri, 26 Jun 2020 22:46:52: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:46:52: #2 You may need to consider one of the other alternative d(s): 1,34,578,585,591 WARNING @ Fri, 26 Jun 2020 22:46:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 22:46:52: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:46:52: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:46:56: 15000000 INFO @ Fri, 26 Jun 2020 22:47:02: 16000000 INFO @ Fri, 26 Jun 2020 22:47:02: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 22:47:08: 17000000 INFO @ Fri, 26 Jun 2020 22:47:14: 18000000 INFO @ Fri, 26 Jun 2020 22:47:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495108/SRX495108.05_peaks.xls INFO @ Fri, 26 Jun 2020 22:47:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495108/SRX495108.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:47:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495108/SRX495108.05_summits.bed INFO @ Fri, 26 Jun 2020 22:47:20: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:47:21: 19000000 INFO @ Fri, 26 Jun 2020 22:47:27: 20000000 INFO @ Fri, 26 Jun 2020 22:47:29: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 22:47:29: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 22:47:29: #1 total tags in treatment: 20327490 INFO @ Fri, 26 Jun 2020 22:47:29: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:47:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:47:30: #1 tags after filtering in treatment: 20327490 INFO @ Fri, 26 Jun 2020 22:47:30: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:47:30: #1 finished! INFO @ Fri, 26 Jun 2020 22:47:30: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:47:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:47:30: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:47:31: #2 number of paired peaks: 252 WARNING @ Fri, 26 Jun 2020 22:47:31: Fewer paired peaks (252) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 252 pairs to build model! INFO @ Fri, 26 Jun 2020 22:47:31: start model_add_line... INFO @ Fri, 26 Jun 2020 22:47:31: start X-correlation... INFO @ Fri, 26 Jun 2020 22:47:31: end of X-cor INFO @ Fri, 26 Jun 2020 22:47:31: #2 finished! INFO @ Fri, 26 Jun 2020 22:47:31: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 22:47:31: #2 alternative fragment length(s) may be 1,34,578,585,591 bps INFO @ Fri, 26 Jun 2020 22:47:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495108/SRX495108.20_model.r WARNING @ Fri, 26 Jun 2020 22:47:31: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:47:31: #2 You may need to consider one of the other alternative d(s): 1,34,578,585,591 WARNING @ Fri, 26 Jun 2020 22:47:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 22:47:31: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:47:31: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:47:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495108/SRX495108.10_peaks.xls INFO @ Fri, 26 Jun 2020 22:47:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495108/SRX495108.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:47:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495108/SRX495108.10_summits.bed INFO @ Fri, 26 Jun 2020 22:47:47: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 22:48:06: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:48:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495108/SRX495108.20_peaks.xls INFO @ Fri, 26 Jun 2020 22:48:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495108/SRX495108.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:48:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495108/SRX495108.20_summits.bed INFO @ Fri, 26 Jun 2020 22:48:24: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling