Job ID = 6368585 SRX = SRX5020811 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:19:21 prefetch.2.10.7: 1) Downloading 'SRR8201434'... 2020-06-16T00:19:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:22:34 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:22:34 prefetch.2.10.7: 1) 'SRR8201434' was downloaded successfully 2020-06-16T00:22:34 prefetch.2.10.7: 'SRR8201434' has 0 unresolved dependencies Read 19000462 spots for SRR8201434/SRR8201434.sra Written 19000462 spots for SRR8201434/SRR8201434.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: 00:06:41 19000462 reads; of these: 19000462 (100.00%) were unpaired; of these: 570843 (3.00%) aligned 0 times 15387704 (80.99%) aligned exactly 1 time 3041915 (16.01%) aligned >1 times 97.00% overall alignment rate Time searching: 00:06:41 Overall time: 00:06:41 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] 1908044 / 18429619 = 0.1035 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 09:37:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020811/SRX5020811.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020811/SRX5020811.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020811/SRX5020811.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020811/SRX5020811.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 09:37:00: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:37:00: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:37:07: 1000000 INFO @ Tue, 16 Jun 2020 09:37:14: 2000000 INFO @ Tue, 16 Jun 2020 09:37:21: 3000000 INFO @ Tue, 16 Jun 2020 09:37:27: 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 09:37:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020811/SRX5020811.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020811/SRX5020811.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020811/SRX5020811.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020811/SRX5020811.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 09:37:30: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:37:30: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:37:33: 5000000 INFO @ Tue, 16 Jun 2020 09:37:37: 1000000 INFO @ Tue, 16 Jun 2020 09:37:40: 6000000 INFO @ Tue, 16 Jun 2020 09:37:44: 2000000 INFO @ Tue, 16 Jun 2020 09:37:46: 7000000 INFO @ Tue, 16 Jun 2020 09:37:50: 3000000 INFO @ Tue, 16 Jun 2020 09:37:53: 8000000 INFO @ Tue, 16 Jun 2020 09:37:56: 4000000 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 09:37:59: 9000000 INFO @ Tue, 16 Jun 2020 09:38:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020811/SRX5020811.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020811/SRX5020811.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020811/SRX5020811.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020811/SRX5020811.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 09:38:00: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:38:00: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:38:03: 5000000 INFO @ Tue, 16 Jun 2020 09:38:07: 10000000 INFO @ Tue, 16 Jun 2020 09:38:08: 1000000 INFO @ Tue, 16 Jun 2020 09:38:10: 6000000 INFO @ Tue, 16 Jun 2020 09:38:15: 11000000 INFO @ Tue, 16 Jun 2020 09:38:16: 2000000 INFO @ Tue, 16 Jun 2020 09:38:17: 7000000 INFO @ Tue, 16 Jun 2020 09:38:22: 12000000 INFO @ Tue, 16 Jun 2020 09:38:23: 3000000 INFO @ Tue, 16 Jun 2020 09:38:24: 8000000 INFO @ Tue, 16 Jun 2020 09:38:28: 13000000 INFO @ Tue, 16 Jun 2020 09:38:30: 4000000 INFO @ Tue, 16 Jun 2020 09:38:31: 9000000 INFO @ Tue, 16 Jun 2020 09:38:35: 14000000 INFO @ Tue, 16 Jun 2020 09:38:37: 5000000 INFO @ Tue, 16 Jun 2020 09:38:39: 10000000 INFO @ Tue, 16 Jun 2020 09:38:42: 15000000 INFO @ Tue, 16 Jun 2020 09:38:44: 6000000 INFO @ Tue, 16 Jun 2020 09:38:47: 11000000 INFO @ Tue, 16 Jun 2020 09:38:48: 16000000 INFO @ Tue, 16 Jun 2020 09:38:52: 7000000 INFO @ Tue, 16 Jun 2020 09:38:52: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:38:52: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:38:52: #1 total tags in treatment: 16521575 INFO @ Tue, 16 Jun 2020 09:38:52: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:38:52: #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 09:38:52: #1 tags after filtering in treatment: 16521575 INFO @ Tue, 16 Jun 2020 09:38:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:38:52: #1 finished! INFO @ Tue, 16 Jun 2020 09:38:52: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:38:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:38:54: #2 number of paired peaks: 252 WARNING @ Tue, 16 Jun 2020 09:38:54: 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 @ Tue, 16 Jun 2020 09:38:54: start model_add_line... INFO @ Tue, 16 Jun 2020 09:38:54: start X-correlation... INFO @ Tue, 16 Jun 2020 09:38:54: end of X-cor INFO @ Tue, 16 Jun 2020 09:38:54: #2 finished! INFO @ Tue, 16 Jun 2020 09:38:54: #2 predicted fragment length is 73 bps INFO @ Tue, 16 Jun 2020 09:38:54: #2 alternative fragment length(s) may be 2,73,545 bps INFO @ Tue, 16 Jun 2020 09:38:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020811/SRX5020811.05_model.r WARNING @ Tue, 16 Jun 2020 09:38:54: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:38:54: #2 You may need to consider one of the other alternative d(s): 2,73,545 WARNING @ Tue, 16 Jun 2020 09:38:54: #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 09:38:54: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:38:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:38:55: 12000000 INFO @ Tue, 16 Jun 2020 09:38:59: 8000000 INFO @ Tue, 16 Jun 2020 09:39:02: 13000000 INFO @ Tue, 16 Jun 2020 09:39:06: 9000000 INFO @ Tue, 16 Jun 2020 09:39:10: 14000000 INFO @ Tue, 16 Jun 2020 09:39:15: 10000000 INFO @ Tue, 16 Jun 2020 09:39:18: 15000000 INFO @ Tue, 16 Jun 2020 09:39:21: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:39:22: 11000000 INFO @ Tue, 16 Jun 2020 09:39:26: 16000000 INFO @ Tue, 16 Jun 2020 09:39:30: 12000000 INFO @ Tue, 16 Jun 2020 09:39:30: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:39:30: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:39:30: #1 total tags in treatment: 16521575 INFO @ Tue, 16 Jun 2020 09:39:30: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:39:30: #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 09:39:30: #1 tags after filtering in treatment: 16521575 INFO @ Tue, 16 Jun 2020 09:39:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:39:30: #1 finished! INFO @ Tue, 16 Jun 2020 09:39:30: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:39:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:39:31: #2 number of paired peaks: 252 WARNING @ Tue, 16 Jun 2020 09:39:31: 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 @ Tue, 16 Jun 2020 09:39:31: start model_add_line... INFO @ Tue, 16 Jun 2020 09:39:32: start X-correlation... INFO @ Tue, 16 Jun 2020 09:39:32: end of X-cor INFO @ Tue, 16 Jun 2020 09:39:32: #2 finished! INFO @ Tue, 16 Jun 2020 09:39:32: #2 predicted fragment length is 73 bps INFO @ Tue, 16 Jun 2020 09:39:32: #2 alternative fragment length(s) may be 2,73,545 bps INFO @ Tue, 16 Jun 2020 09:39:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020811/SRX5020811.10_model.r WARNING @ Tue, 16 Jun 2020 09:39:32: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:39:32: #2 You may need to consider one of the other alternative d(s): 2,73,545 WARNING @ Tue, 16 Jun 2020 09:39:32: #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 09:39:32: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:39:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:39:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020811/SRX5020811.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:39:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020811/SRX5020811.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:39:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020811/SRX5020811.05_summits.bed INFO @ Tue, 16 Jun 2020 09:39:34: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (617 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:39:36: 13000000 INFO @ Tue, 16 Jun 2020 09:39:43: 14000000 INFO @ Tue, 16 Jun 2020 09:39:50: 15000000 INFO @ Tue, 16 Jun 2020 09:39:56: 16000000 INFO @ Tue, 16 Jun 2020 09:39:59: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:39:59: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:39:59: #1 total tags in treatment: 16521575 INFO @ Tue, 16 Jun 2020 09:39:59: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:39:59: #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 09:40:00: #1 tags after filtering in treatment: 16521575 INFO @ Tue, 16 Jun 2020 09:40:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:40:00: #1 finished! INFO @ Tue, 16 Jun 2020 09:40:00: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:40:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:40:00: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:40:01: #2 number of paired peaks: 252 WARNING @ Tue, 16 Jun 2020 09:40:01: 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 @ Tue, 16 Jun 2020 09:40:01: start model_add_line... INFO @ Tue, 16 Jun 2020 09:40:01: start X-correlation... INFO @ Tue, 16 Jun 2020 09:40:01: end of X-cor INFO @ Tue, 16 Jun 2020 09:40:01: #2 finished! INFO @ Tue, 16 Jun 2020 09:40:01: #2 predicted fragment length is 73 bps INFO @ Tue, 16 Jun 2020 09:40:01: #2 alternative fragment length(s) may be 2,73,545 bps INFO @ Tue, 16 Jun 2020 09:40:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020811/SRX5020811.20_model.r WARNING @ Tue, 16 Jun 2020 09:40:01: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:40:01: #2 You may need to consider one of the other alternative d(s): 2,73,545 WARNING @ Tue, 16 Jun 2020 09:40:01: #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 09:40:01: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:40:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:40:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020811/SRX5020811.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:40:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020811/SRX5020811.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:40:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020811/SRX5020811.10_summits.bed INFO @ Tue, 16 Jun 2020 09:40:13: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (448 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:40:28: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:40:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020811/SRX5020811.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:40:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020811/SRX5020811.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:40:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020811/SRX5020811.20_summits.bed INFO @ Tue, 16 Jun 2020 09:40:42: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (237 records, 4 fields): 1 millis CompletedMACS2peakCalling