Job ID = 6368739 SRX = SRX5402763 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:32:46 prefetch.2.10.7: 1) Downloading 'SRR8602997'... 2020-06-16T00:32:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:36:58 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:36:58 prefetch.2.10.7: 1) 'SRR8602997' was downloaded successfully Read 44731113 spots for SRR8602997/SRR8602997.sra Written 44731113 spots for SRR8602997/SRR8602997.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: 00:08:34 44731113 reads; of these: 44731113 (100.00%) were unpaired; of these: 11047979 (24.70%) aligned 0 times 27955797 (62.50%) aligned exactly 1 time 5727337 (12.80%) aligned >1 times 75.30% overall alignment rate Time searching: 00:08:34 Overall time: 00:08:34 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 16 files... [bam_rmdupse_core] 5720539 / 33683134 = 0.1698 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 09:55:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402763/SRX5402763.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402763/SRX5402763.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402763/SRX5402763.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402763/SRX5402763.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 09:55:30: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:55:30: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:55:37: 1000000 INFO @ Tue, 16 Jun 2020 09:55:44: 2000000 INFO @ Tue, 16 Jun 2020 09:55:50: 3000000 INFO @ Tue, 16 Jun 2020 09:55:57: 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 09:56:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402763/SRX5402763.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402763/SRX5402763.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402763/SRX5402763.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402763/SRX5402763.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 09:56:00: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:56:00: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:56:04: 5000000 INFO @ Tue, 16 Jun 2020 09:56:08: 1000000 INFO @ Tue, 16 Jun 2020 09:56:11: 6000000 INFO @ Tue, 16 Jun 2020 09:56:15: 2000000 INFO @ Tue, 16 Jun 2020 09:56:18: 7000000 INFO @ Tue, 16 Jun 2020 09:56:22: 3000000 INFO @ Tue, 16 Jun 2020 09:56:25: 8000000 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 09:56:29: 4000000 INFO @ Tue, 16 Jun 2020 09:56:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402763/SRX5402763.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402763/SRX5402763.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402763/SRX5402763.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402763/SRX5402763.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 09:56:30: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:56:30: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:56:32: 9000000 INFO @ Tue, 16 Jun 2020 09:56:36: 5000000 INFO @ Tue, 16 Jun 2020 09:56:38: 1000000 INFO @ Tue, 16 Jun 2020 09:56:39: 10000000 INFO @ Tue, 16 Jun 2020 09:56:44: 6000000 INFO @ Tue, 16 Jun 2020 09:56:45: 2000000 INFO @ Tue, 16 Jun 2020 09:56:46: 11000000 INFO @ Tue, 16 Jun 2020 09:56:51: 7000000 INFO @ Tue, 16 Jun 2020 09:56:52: 3000000 INFO @ Tue, 16 Jun 2020 09:56:53: 12000000 INFO @ Tue, 16 Jun 2020 09:56:58: 8000000 INFO @ Tue, 16 Jun 2020 09:56:59: 4000000 INFO @ Tue, 16 Jun 2020 09:57:01: 13000000 INFO @ Tue, 16 Jun 2020 09:57:05: 9000000 INFO @ Tue, 16 Jun 2020 09:57:07: 5000000 INFO @ Tue, 16 Jun 2020 09:57:08: 14000000 INFO @ Tue, 16 Jun 2020 09:57:12: 10000000 INFO @ Tue, 16 Jun 2020 09:57:14: 6000000 INFO @ Tue, 16 Jun 2020 09:57:15: 15000000 INFO @ Tue, 16 Jun 2020 09:57:19: 11000000 INFO @ Tue, 16 Jun 2020 09:57:21: 7000000 INFO @ Tue, 16 Jun 2020 09:57:22: 16000000 INFO @ Tue, 16 Jun 2020 09:57:26: 12000000 INFO @ Tue, 16 Jun 2020 09:57:28: 8000000 INFO @ Tue, 16 Jun 2020 09:57:29: 17000000 INFO @ Tue, 16 Jun 2020 09:57:33: 13000000 INFO @ Tue, 16 Jun 2020 09:57:35: 9000000 INFO @ Tue, 16 Jun 2020 09:57:36: 18000000 INFO @ Tue, 16 Jun 2020 09:57:40: 14000000 INFO @ Tue, 16 Jun 2020 09:57:42: 10000000 INFO @ Tue, 16 Jun 2020 09:57:43: 19000000 INFO @ Tue, 16 Jun 2020 09:57:47: 15000000 INFO @ Tue, 16 Jun 2020 09:57:49: 11000000 INFO @ Tue, 16 Jun 2020 09:57:50: 20000000 INFO @ Tue, 16 Jun 2020 09:57:54: 16000000 INFO @ Tue, 16 Jun 2020 09:57:56: 12000000 INFO @ Tue, 16 Jun 2020 09:57:57: 21000000 INFO @ Tue, 16 Jun 2020 09:58:01: 17000000 INFO @ Tue, 16 Jun 2020 09:58:03: 13000000 INFO @ Tue, 16 Jun 2020 09:58:03: 22000000 INFO @ Tue, 16 Jun 2020 09:58:08: 18000000 INFO @ Tue, 16 Jun 2020 09:58:10: 14000000 INFO @ Tue, 16 Jun 2020 09:58:10: 23000000 INFO @ Tue, 16 Jun 2020 09:58:15: 19000000 INFO @ Tue, 16 Jun 2020 09:58:17: 15000000 INFO @ Tue, 16 Jun 2020 09:58:17: 24000000 INFO @ Tue, 16 Jun 2020 09:58:21: 20000000 INFO @ Tue, 16 Jun 2020 09:58:24: 16000000 INFO @ Tue, 16 Jun 2020 09:58:24: 25000000 INFO @ Tue, 16 Jun 2020 09:58:28: 21000000 INFO @ Tue, 16 Jun 2020 09:58:31: 17000000 INFO @ Tue, 16 Jun 2020 09:58:31: 26000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:58:35: 22000000 INFO @ Tue, 16 Jun 2020 09:58:37: 18000000 INFO @ Tue, 16 Jun 2020 09:58:38: 27000000 INFO @ Tue, 16 Jun 2020 09:58:42: 23000000 INFO @ Tue, 16 Jun 2020 09:58:44: 19000000 INFO @ Tue, 16 Jun 2020 09:58:44: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:58:44: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:58:44: #1 total tags in treatment: 27962595 INFO @ Tue, 16 Jun 2020 09:58:44: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:58:44: #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 09:58:45: #1 tags after filtering in treatment: 27962595 INFO @ Tue, 16 Jun 2020 09:58:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:58:45: #1 finished! INFO @ Tue, 16 Jun 2020 09:58:45: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:58:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:58:46: #2 number of paired peaks: 125 WARNING @ Tue, 16 Jun 2020 09:58:46: Fewer paired peaks (125) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 125 pairs to build model! INFO @ Tue, 16 Jun 2020 09:58:46: start model_add_line... INFO @ Tue, 16 Jun 2020 09:58:47: start X-correlation... INFO @ Tue, 16 Jun 2020 09:58:47: end of X-cor INFO @ Tue, 16 Jun 2020 09:58:47: #2 finished! INFO @ Tue, 16 Jun 2020 09:58:47: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:58:47: #2 alternative fragment length(s) may be 1,48,102,535,554 bps INFO @ Tue, 16 Jun 2020 09:58:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402763/SRX5402763.05_model.r WARNING @ Tue, 16 Jun 2020 09:58:47: #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 09:58:47: #2 You may need to consider one of the other alternative d(s): 1,48,102,535,554 WARNING @ Tue, 16 Jun 2020 09:58:47: #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 09:58:47: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:58:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:58:48: 24000000 INFO @ Tue, 16 Jun 2020 09:58:51: 20000000 INFO @ Tue, 16 Jun 2020 09:58:55: 25000000 INFO @ Tue, 16 Jun 2020 09:58:57: 21000000 INFO @ Tue, 16 Jun 2020 09:59:01: 26000000 INFO @ Tue, 16 Jun 2020 09:59:04: 22000000 INFO @ Tue, 16 Jun 2020 09:59:08: 27000000 INFO @ Tue, 16 Jun 2020 09:59:10: 23000000 INFO @ Tue, 16 Jun 2020 09:59:14: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:59:14: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:59:14: #1 total tags in treatment: 27962595 INFO @ Tue, 16 Jun 2020 09:59:14: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:59:14: #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 09:59:15: #1 tags after filtering in treatment: 27962595 INFO @ Tue, 16 Jun 2020 09:59:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:59:15: #1 finished! INFO @ Tue, 16 Jun 2020 09:59:15: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:59:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:59:17: #2 number of paired peaks: 125 WARNING @ Tue, 16 Jun 2020 09:59:17: Fewer paired peaks (125) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 125 pairs to build model! INFO @ Tue, 16 Jun 2020 09:59:17: start model_add_line... INFO @ Tue, 16 Jun 2020 09:59:17: start X-correlation... INFO @ Tue, 16 Jun 2020 09:59:17: end of X-cor INFO @ Tue, 16 Jun 2020 09:59:17: #2 finished! INFO @ Tue, 16 Jun 2020 09:59:17: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:59:17: #2 alternative fragment length(s) may be 1,48,102,535,554 bps INFO @ Tue, 16 Jun 2020 09:59:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402763/SRX5402763.10_model.r WARNING @ Tue, 16 Jun 2020 09:59:17: #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 09:59:17: #2 You may need to consider one of the other alternative d(s): 1,48,102,535,554 WARNING @ Tue, 16 Jun 2020 09:59:17: #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 09:59:17: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:59:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:59:17: 24000000 INFO @ Tue, 16 Jun 2020 09:59:23: 25000000 INFO @ Tue, 16 Jun 2020 09:59:25: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:59:29: 26000000 INFO @ Tue, 16 Jun 2020 09:59:36: 27000000 INFO @ Tue, 16 Jun 2020 09:59:42: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:59:42: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:59:42: #1 total tags in treatment: 27962595 INFO @ Tue, 16 Jun 2020 09:59:42: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:59:42: #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 09:59:42: #1 tags after filtering in treatment: 27962595 INFO @ Tue, 16 Jun 2020 09:59:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:59:42: #1 finished! INFO @ Tue, 16 Jun 2020 09:59:42: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:59:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:59:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402763/SRX5402763.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:59:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402763/SRX5402763.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:59:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402763/SRX5402763.05_summits.bed INFO @ Tue, 16 Jun 2020 09:59:43: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:59:44: #2 number of paired peaks: 125 WARNING @ Tue, 16 Jun 2020 09:59:44: Fewer paired peaks (125) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 125 pairs to build model! INFO @ Tue, 16 Jun 2020 09:59:44: start model_add_line... INFO @ Tue, 16 Jun 2020 09:59:44: start X-correlation... INFO @ Tue, 16 Jun 2020 09:59:44: end of X-cor INFO @ Tue, 16 Jun 2020 09:59:44: #2 finished! INFO @ Tue, 16 Jun 2020 09:59:44: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:59:44: #2 alternative fragment length(s) may be 1,48,102,535,554 bps INFO @ Tue, 16 Jun 2020 09:59:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402763/SRX5402763.20_model.r WARNING @ Tue, 16 Jun 2020 09:59:44: #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 09:59:44: #2 You may need to consider one of the other alternative d(s): 1,48,102,535,554 WARNING @ Tue, 16 Jun 2020 09:59:44: #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 09:59:44: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:59:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:59:55: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:00:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402763/SRX5402763.10_peaks.xls INFO @ Tue, 16 Jun 2020 10:00:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402763/SRX5402763.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:00:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402763/SRX5402763.10_summits.bed INFO @ Tue, 16 Jun 2020 10:00:14: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:00:23: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:00:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402763/SRX5402763.20_peaks.xls INFO @ Tue, 16 Jun 2020 10:00:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402763/SRX5402763.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:00:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402763/SRX5402763.20_summits.bed INFO @ Tue, 16 Jun 2020 10:00:41: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling