Job ID = 6368689 SRX = SRX5402715 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:26:19 prefetch.2.10.7: 1) Downloading 'SRR8602949'... 2020-06-16T00:26:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:28:46 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:28:46 prefetch.2.10.7: 1) 'SRR8602949' was downloaded successfully Read 32668453 spots for SRR8602949/SRR8602949.sra Written 32668453 spots for SRR8602949/SRR8602949.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: 00:05:34 32668453 reads; of these: 32668453 (100.00%) were unpaired; of these: 6741867 (20.64%) aligned 0 times 22061612 (67.53%) aligned exactly 1 time 3864974 (11.83%) aligned >1 times 79.36% overall alignment rate Time searching: 00:05:34 Overall time: 00:05:34 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 12 files... [bam_rmdupse_core] 4182436 / 25926586 = 0.1613 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 09:43:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402715/SRX5402715.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402715/SRX5402715.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402715/SRX5402715.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402715/SRX5402715.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 09:43:23: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:43:23: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:43:29: 1000000 INFO @ Tue, 16 Jun 2020 09:43:35: 2000000 INFO @ Tue, 16 Jun 2020 09:43:41: 3000000 INFO @ Tue, 16 Jun 2020 09:43:48: 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 09:43:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402715/SRX5402715.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402715/SRX5402715.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402715/SRX5402715.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402715/SRX5402715.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 09:43:53: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:43:53: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:43:54: 5000000 INFO @ Tue, 16 Jun 2020 09:43:59: 1000000 INFO @ Tue, 16 Jun 2020 09:44:01: 6000000 INFO @ Tue, 16 Jun 2020 09:44:06: 2000000 INFO @ Tue, 16 Jun 2020 09:44:07: 7000000 INFO @ Tue, 16 Jun 2020 09:44:13: 3000000 INFO @ Tue, 16 Jun 2020 09:44:14: 8000000 INFO @ Tue, 16 Jun 2020 09:44:19: 4000000 INFO @ Tue, 16 Jun 2020 09:44:20: 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 09:44:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402715/SRX5402715.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402715/SRX5402715.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402715/SRX5402715.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402715/SRX5402715.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 09:44:23: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:44:23: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:44:26: 5000000 INFO @ Tue, 16 Jun 2020 09:44:27: 10000000 INFO @ Tue, 16 Jun 2020 09:44:31: 1000000 INFO @ Tue, 16 Jun 2020 09:44:33: 6000000 INFO @ Tue, 16 Jun 2020 09:44:33: 11000000 INFO @ Tue, 16 Jun 2020 09:44:39: 2000000 INFO @ Tue, 16 Jun 2020 09:44:39: 7000000 INFO @ Tue, 16 Jun 2020 09:44:40: 12000000 INFO @ Tue, 16 Jun 2020 09:44:46: 8000000 INFO @ Tue, 16 Jun 2020 09:44:47: 13000000 INFO @ Tue, 16 Jun 2020 09:44:47: 3000000 INFO @ Tue, 16 Jun 2020 09:44:53: 9000000 INFO @ Tue, 16 Jun 2020 09:44:54: 14000000 INFO @ Tue, 16 Jun 2020 09:44:55: 4000000 INFO @ Tue, 16 Jun 2020 09:45:00: 10000000 INFO @ Tue, 16 Jun 2020 09:45:01: 15000000 INFO @ Tue, 16 Jun 2020 09:45:03: 5000000 INFO @ Tue, 16 Jun 2020 09:45:07: 11000000 INFO @ Tue, 16 Jun 2020 09:45:08: 16000000 INFO @ Tue, 16 Jun 2020 09:45:11: 6000000 INFO @ Tue, 16 Jun 2020 09:45:14: 12000000 INFO @ Tue, 16 Jun 2020 09:45:15: 17000000 INFO @ Tue, 16 Jun 2020 09:45:19: 7000000 INFO @ Tue, 16 Jun 2020 09:45:20: 13000000 INFO @ Tue, 16 Jun 2020 09:45:21: 18000000 INFO @ Tue, 16 Jun 2020 09:45:27: 8000000 INFO @ Tue, 16 Jun 2020 09:45:27: 14000000 INFO @ Tue, 16 Jun 2020 09:45:28: 19000000 INFO @ Tue, 16 Jun 2020 09:45:34: 15000000 INFO @ Tue, 16 Jun 2020 09:45:35: 9000000 INFO @ Tue, 16 Jun 2020 09:45:35: 20000000 INFO @ Tue, 16 Jun 2020 09:45:41: 16000000 INFO @ Tue, 16 Jun 2020 09:45:42: 21000000 INFO @ Tue, 16 Jun 2020 09:45:43: 10000000 INFO @ Tue, 16 Jun 2020 09:45:47: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:45:47: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:45:47: #1 total tags in treatment: 21744150 INFO @ Tue, 16 Jun 2020 09:45:47: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:45:47: #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 09:45:48: #1 tags after filtering in treatment: 21744150 INFO @ Tue, 16 Jun 2020 09:45:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:45:48: #1 finished! INFO @ Tue, 16 Jun 2020 09:45:48: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:45:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:45:48: 17000000 INFO @ Tue, 16 Jun 2020 09:45:49: #2 number of paired peaks: 152 WARNING @ Tue, 16 Jun 2020 09:45:49: Fewer paired peaks (152) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 152 pairs to build model! INFO @ Tue, 16 Jun 2020 09:45:49: start model_add_line... INFO @ Tue, 16 Jun 2020 09:45:49: start X-correlation... INFO @ Tue, 16 Jun 2020 09:45:49: end of X-cor INFO @ Tue, 16 Jun 2020 09:45:49: #2 finished! INFO @ Tue, 16 Jun 2020 09:45:49: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:45:49: #2 alternative fragment length(s) may be 1,26,45,499,567,597 bps INFO @ Tue, 16 Jun 2020 09:45:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402715/SRX5402715.05_model.r WARNING @ Tue, 16 Jun 2020 09:45:49: #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 09:45:49: #2 You may need to consider one of the other alternative d(s): 1,26,45,499,567,597 WARNING @ Tue, 16 Jun 2020 09:45:49: #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 09:45:49: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:45:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:45:51: 11000000 INFO @ Tue, 16 Jun 2020 09:45:55: 18000000 INFO @ Tue, 16 Jun 2020 09:45:59: 12000000 INFO @ Tue, 16 Jun 2020 09:46:02: 19000000 INFO @ Tue, 16 Jun 2020 09:46:07: 13000000 INFO @ Tue, 16 Jun 2020 09:46:08: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:46:15: 21000000 INFO @ Tue, 16 Jun 2020 09:46:15: 14000000 INFO @ Tue, 16 Jun 2020 09:46:19: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:46:20: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:46:20: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:46:20: #1 total tags in treatment: 21744150 INFO @ Tue, 16 Jun 2020 09:46:20: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:46:20: #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 09:46:21: #1 tags after filtering in treatment: 21744150 INFO @ Tue, 16 Jun 2020 09:46:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:46:21: #1 finished! INFO @ Tue, 16 Jun 2020 09:46:21: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:46:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:46:22: #2 number of paired peaks: 152 WARNING @ Tue, 16 Jun 2020 09:46:22: Fewer paired peaks (152) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 152 pairs to build model! INFO @ Tue, 16 Jun 2020 09:46:22: start model_add_line... INFO @ Tue, 16 Jun 2020 09:46:22: start X-correlation... INFO @ Tue, 16 Jun 2020 09:46:22: end of X-cor INFO @ Tue, 16 Jun 2020 09:46:22: #2 finished! INFO @ Tue, 16 Jun 2020 09:46:22: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:46:22: #2 alternative fragment length(s) may be 1,26,45,499,567,597 bps INFO @ Tue, 16 Jun 2020 09:46:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402715/SRX5402715.10_model.r WARNING @ Tue, 16 Jun 2020 09:46:22: #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 09:46:22: #2 You may need to consider one of the other alternative d(s): 1,26,45,499,567,597 WARNING @ Tue, 16 Jun 2020 09:46:22: #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 09:46:22: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:46:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:46:23: 15000000 INFO @ Tue, 16 Jun 2020 09:46:32: 16000000 INFO @ Tue, 16 Jun 2020 09:46:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402715/SRX5402715.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:46:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402715/SRX5402715.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:46:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402715/SRX5402715.05_summits.bed INFO @ Tue, 16 Jun 2020 09:46:34: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:46:40: 17000000 INFO @ Tue, 16 Jun 2020 09:46:48: 18000000 INFO @ Tue, 16 Jun 2020 09:46:52: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:46:55: 19000000 INFO @ Tue, 16 Jun 2020 09:47:03: 20000000 INFO @ Tue, 16 Jun 2020 09:47:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402715/SRX5402715.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:47:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402715/SRX5402715.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:47:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402715/SRX5402715.10_summits.bed INFO @ Tue, 16 Jun 2020 09:47:06: 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 @ Tue, 16 Jun 2020 09:47:11: 21000000 INFO @ Tue, 16 Jun 2020 09:47:16: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:47:16: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:47:16: #1 total tags in treatment: 21744150 INFO @ Tue, 16 Jun 2020 09:47:16: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:47:16: #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 09:47:17: #1 tags after filtering in treatment: 21744150 INFO @ Tue, 16 Jun 2020 09:47:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:47:17: #1 finished! INFO @ Tue, 16 Jun 2020 09:47:17: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:47:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:47:18: #2 number of paired peaks: 152 WARNING @ Tue, 16 Jun 2020 09:47:18: Fewer paired peaks (152) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 152 pairs to build model! INFO @ Tue, 16 Jun 2020 09:47:18: start model_add_line... INFO @ Tue, 16 Jun 2020 09:47:18: start X-correlation... INFO @ Tue, 16 Jun 2020 09:47:18: end of X-cor INFO @ Tue, 16 Jun 2020 09:47:18: #2 finished! INFO @ Tue, 16 Jun 2020 09:47:18: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:47:18: #2 alternative fragment length(s) may be 1,26,45,499,567,597 bps INFO @ Tue, 16 Jun 2020 09:47:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402715/SRX5402715.20_model.r WARNING @ Tue, 16 Jun 2020 09:47:18: #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 09:47:18: #2 You may need to consider one of the other alternative d(s): 1,26,45,499,567,597 WARNING @ Tue, 16 Jun 2020 09:47:18: #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 09:47:18: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:47:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:47:47: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:48:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402715/SRX5402715.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:48:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402715/SRX5402715.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:48:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402715/SRX5402715.20_summits.bed INFO @ Tue, 16 Jun 2020 09:48:02: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling