Job ID = 6368531 SRX = SRX5020760 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:18:51 prefetch.2.10.7: 1) Downloading 'SRR8201383'... 2020-06-16T00:18:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:21:33 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:21:33 prefetch.2.10.7: 1) 'SRR8201383' was downloaded successfully 2020-06-16T00:21:33 prefetch.2.10.7: 'SRR8201383' has 0 unresolved dependencies Read 20732212 spots for SRR8201383/SRR8201383.sra Written 20732212 spots for SRR8201383/SRR8201383.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: 00:06:00 20732212 reads; of these: 20732212 (100.00%) were unpaired; of these: 3471436 (16.74%) aligned 0 times 14303289 (68.99%) aligned exactly 1 time 2957487 (14.27%) aligned >1 times 83.26% overall alignment rate Time searching: 00:06:00 Overall time: 00:06:00 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] 3674827 / 17260776 = 0.2129 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 09:34:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020760/SRX5020760.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020760/SRX5020760.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020760/SRX5020760.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020760/SRX5020760.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 09:34:37: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:34:37: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:34:43: 1000000 INFO @ Tue, 16 Jun 2020 09:34:50: 2000000 INFO @ Tue, 16 Jun 2020 09:34:57: 3000000 INFO @ Tue, 16 Jun 2020 09:35:03: 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 09:35:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020760/SRX5020760.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020760/SRX5020760.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020760/SRX5020760.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020760/SRX5020760.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 09:35:07: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:35:07: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:35:10: 5000000 INFO @ Tue, 16 Jun 2020 09:35:14: 1000000 INFO @ Tue, 16 Jun 2020 09:35:17: 6000000 INFO @ Tue, 16 Jun 2020 09:35:21: 2000000 INFO @ Tue, 16 Jun 2020 09:35:24: 7000000 INFO @ Tue, 16 Jun 2020 09:35:28: 3000000 INFO @ Tue, 16 Jun 2020 09:35:31: 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 09:35:35: 4000000 INFO @ Tue, 16 Jun 2020 09:35:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020760/SRX5020760.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020760/SRX5020760.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020760/SRX5020760.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020760/SRX5020760.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 09:35:37: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:35:37: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:35:39: 9000000 INFO @ Tue, 16 Jun 2020 09:35:42: 5000000 INFO @ Tue, 16 Jun 2020 09:35:45: 1000000 INFO @ Tue, 16 Jun 2020 09:35:46: 10000000 INFO @ Tue, 16 Jun 2020 09:35:50: 6000000 INFO @ Tue, 16 Jun 2020 09:35:52: 2000000 INFO @ Tue, 16 Jun 2020 09:35:53: 11000000 INFO @ Tue, 16 Jun 2020 09:35:57: 7000000 INFO @ Tue, 16 Jun 2020 09:36:00: 3000000 INFO @ Tue, 16 Jun 2020 09:36:00: 12000000 INFO @ Tue, 16 Jun 2020 09:36:05: 8000000 INFO @ Tue, 16 Jun 2020 09:36:07: 4000000 INFO @ Tue, 16 Jun 2020 09:36:08: 13000000 INFO @ Tue, 16 Jun 2020 09:36:12: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:36:12: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:36:12: #1 total tags in treatment: 13585949 INFO @ Tue, 16 Jun 2020 09:36:12: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:36:12: #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 09:36:12: #1 tags after filtering in treatment: 13585949 INFO @ Tue, 16 Jun 2020 09:36:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:36:12: #1 finished! INFO @ Tue, 16 Jun 2020 09:36:12: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:36:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:36:13: 9000000 INFO @ Tue, 16 Jun 2020 09:36:13: #2 number of paired peaks: 426 WARNING @ Tue, 16 Jun 2020 09:36:13: Fewer paired peaks (426) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 426 pairs to build model! INFO @ Tue, 16 Jun 2020 09:36:13: start model_add_line... INFO @ Tue, 16 Jun 2020 09:36:13: start X-correlation... INFO @ Tue, 16 Jun 2020 09:36:13: end of X-cor INFO @ Tue, 16 Jun 2020 09:36:13: #2 finished! INFO @ Tue, 16 Jun 2020 09:36:13: #2 predicted fragment length is 111 bps INFO @ Tue, 16 Jun 2020 09:36:13: #2 alternative fragment length(s) may be 111 bps INFO @ Tue, 16 Jun 2020 09:36:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020760/SRX5020760.05_model.r WARNING @ Tue, 16 Jun 2020 09:36:13: #2 Since the d (111) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:36:13: #2 You may need to consider one of the other alternative d(s): 111 WARNING @ Tue, 16 Jun 2020 09:36:13: #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 09:36:13: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:36:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:36:15: 5000000 INFO @ Tue, 16 Jun 2020 09:36:20: 10000000 INFO @ Tue, 16 Jun 2020 09:36:22: 6000000 INFO @ Tue, 16 Jun 2020 09:36:27: 11000000 INFO @ Tue, 16 Jun 2020 09:36:29: 7000000 INFO @ Tue, 16 Jun 2020 09:36:34: 12000000 INFO @ Tue, 16 Jun 2020 09:36:36: 8000000 INFO @ Tue, 16 Jun 2020 09:36:39: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:36:41: 13000000 INFO @ Tue, 16 Jun 2020 09:36:44: 9000000 INFO @ Tue, 16 Jun 2020 09:36:45: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:36:45: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:36:45: #1 total tags in treatment: 13585949 INFO @ Tue, 16 Jun 2020 09:36:45: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:36:45: #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 09:36:46: #1 tags after filtering in treatment: 13585949 INFO @ Tue, 16 Jun 2020 09:36:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:36:46: #1 finished! INFO @ Tue, 16 Jun 2020 09:36:46: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:36:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:36:47: #2 number of paired peaks: 426 WARNING @ Tue, 16 Jun 2020 09:36:47: Fewer paired peaks (426) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 426 pairs to build model! INFO @ Tue, 16 Jun 2020 09:36:47: start model_add_line... INFO @ Tue, 16 Jun 2020 09:36:47: start X-correlation... INFO @ Tue, 16 Jun 2020 09:36:47: end of X-cor INFO @ Tue, 16 Jun 2020 09:36:47: #2 finished! INFO @ Tue, 16 Jun 2020 09:36:47: #2 predicted fragment length is 111 bps INFO @ Tue, 16 Jun 2020 09:36:47: #2 alternative fragment length(s) may be 111 bps INFO @ Tue, 16 Jun 2020 09:36:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020760/SRX5020760.10_model.r WARNING @ Tue, 16 Jun 2020 09:36:47: #2 Since the d (111) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:36:47: #2 You may need to consider one of the other alternative d(s): 111 WARNING @ Tue, 16 Jun 2020 09:36:47: #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 09:36:47: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:36:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:36:50: 10000000 INFO @ Tue, 16 Jun 2020 09:36:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020760/SRX5020760.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:36:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020760/SRX5020760.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:36:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020760/SRX5020760.05_summits.bed INFO @ Tue, 16 Jun 2020 09:36:51: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1737 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:36:57: 11000000 INFO @ Tue, 16 Jun 2020 09:37:05: 12000000 INFO @ Tue, 16 Jun 2020 09:37:12: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:37:13: 13000000 INFO @ Tue, 16 Jun 2020 09:37:18: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:37:18: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:37:18: #1 total tags in treatment: 13585949 INFO @ Tue, 16 Jun 2020 09:37:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:37:18: #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 09:37:18: #1 tags after filtering in treatment: 13585949 INFO @ Tue, 16 Jun 2020 09:37:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:37:18: #1 finished! INFO @ Tue, 16 Jun 2020 09:37:18: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:37:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:37:19: #2 number of paired peaks: 426 WARNING @ Tue, 16 Jun 2020 09:37:19: Fewer paired peaks (426) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 426 pairs to build model! INFO @ Tue, 16 Jun 2020 09:37:19: start model_add_line... INFO @ Tue, 16 Jun 2020 09:37:19: start X-correlation... INFO @ Tue, 16 Jun 2020 09:37:19: end of X-cor INFO @ Tue, 16 Jun 2020 09:37:19: #2 finished! INFO @ Tue, 16 Jun 2020 09:37:19: #2 predicted fragment length is 111 bps INFO @ Tue, 16 Jun 2020 09:37:19: #2 alternative fragment length(s) may be 111 bps INFO @ Tue, 16 Jun 2020 09:37:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020760/SRX5020760.20_model.r WARNING @ Tue, 16 Jun 2020 09:37:19: #2 Since the d (111) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:37:19: #2 You may need to consider one of the other alternative d(s): 111 WARNING @ Tue, 16 Jun 2020 09:37:19: #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 09:37:19: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:37:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:37:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020760/SRX5020760.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:37:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020760/SRX5020760.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:37:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020760/SRX5020760.10_summits.bed INFO @ Tue, 16 Jun 2020 09:37:24: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1007 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:37:45: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:37:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020760/SRX5020760.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:37:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020760/SRX5020760.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:37:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020760/SRX5020760.20_summits.bed INFO @ Tue, 16 Jun 2020 09:37:57: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (554 records, 4 fields): 2 millis CompletedMACS2peakCalling