Job ID = 6368976 SRX = SRX7971801 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:36:49 prefetch.2.10.7: 1) Downloading 'SRR11392687'... 2020-06-16T00:36:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:38:45 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:38:45 prefetch.2.10.7: 1) 'SRR11392687' was downloaded successfully 2020-06-16T00:38:45 prefetch.2.10.7: 'SRR11392687' has 0 unresolved dependencies Read 23156320 spots for SRR11392687/SRR11392687.sra Written 23156320 spots for SRR11392687/SRR11392687.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: 00:07:32 23156320 reads; of these: 23156320 (100.00%) were unpaired; of these: 1194092 (5.16%) aligned 0 times 18399057 (79.46%) aligned exactly 1 time 3563171 (15.39%) aligned >1 times 94.84% overall alignment rate Time searching: 00:07:32 Overall time: 00:07:32 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] 2252064 / 21962228 = 0.1025 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 09:53:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7971801/SRX7971801.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7971801/SRX7971801.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7971801/SRX7971801.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7971801/SRX7971801.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 09:53:04: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:53:04: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:53:10: 1000000 INFO @ Tue, 16 Jun 2020 09:53:15: 2000000 INFO @ Tue, 16 Jun 2020 09:53:21: 3000000 INFO @ Tue, 16 Jun 2020 09:53:26: 4000000 INFO @ Tue, 16 Jun 2020 09:53:32: 5000000 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 09:53:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7971801/SRX7971801.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7971801/SRX7971801.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7971801/SRX7971801.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7971801/SRX7971801.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 09:53:34: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:53:34: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:53:38: 6000000 INFO @ Tue, 16 Jun 2020 09:53:42: 1000000 INFO @ Tue, 16 Jun 2020 09:53:45: 7000000 INFO @ Tue, 16 Jun 2020 09:53:49: 2000000 INFO @ Tue, 16 Jun 2020 09:53:51: 8000000 INFO @ Tue, 16 Jun 2020 09:53:57: 3000000 INFO @ Tue, 16 Jun 2020 09:53:58: 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 09:54:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7971801/SRX7971801.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7971801/SRX7971801.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7971801/SRX7971801.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7971801/SRX7971801.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 09:54:04: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:54:04: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:54:04: 4000000 INFO @ Tue, 16 Jun 2020 09:54:05: 10000000 INFO @ Tue, 16 Jun 2020 09:54:11: 1000000 INFO @ Tue, 16 Jun 2020 09:54:11: 11000000 INFO @ Tue, 16 Jun 2020 09:54:11: 5000000 INFO @ Tue, 16 Jun 2020 09:54:18: 2000000 INFO @ Tue, 16 Jun 2020 09:54:18: 12000000 INFO @ Tue, 16 Jun 2020 09:54:19: 6000000 INFO @ Tue, 16 Jun 2020 09:54:25: 3000000 INFO @ Tue, 16 Jun 2020 09:54:25: 13000000 INFO @ Tue, 16 Jun 2020 09:54:27: 7000000 INFO @ Tue, 16 Jun 2020 09:54:32: 14000000 INFO @ Tue, 16 Jun 2020 09:54:32: 4000000 INFO @ Tue, 16 Jun 2020 09:54:34: 8000000 INFO @ Tue, 16 Jun 2020 09:54:39: 15000000 INFO @ Tue, 16 Jun 2020 09:54:39: 5000000 INFO @ Tue, 16 Jun 2020 09:54:42: 9000000 INFO @ Tue, 16 Jun 2020 09:54:45: 16000000 INFO @ Tue, 16 Jun 2020 09:54:46: 6000000 INFO @ Tue, 16 Jun 2020 09:54:50: 10000000 INFO @ Tue, 16 Jun 2020 09:54:52: 17000000 INFO @ Tue, 16 Jun 2020 09:54:53: 7000000 INFO @ Tue, 16 Jun 2020 09:54:57: 11000000 INFO @ Tue, 16 Jun 2020 09:54:59: 18000000 INFO @ Tue, 16 Jun 2020 09:55:00: 8000000 INFO @ Tue, 16 Jun 2020 09:55:05: 12000000 INFO @ Tue, 16 Jun 2020 09:55:06: 19000000 INFO @ Tue, 16 Jun 2020 09:55:07: 9000000 INFO @ Tue, 16 Jun 2020 09:55:11: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:55:11: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:55:11: #1 total tags in treatment: 19710164 INFO @ Tue, 16 Jun 2020 09:55:11: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:55:11: #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 09:55:11: #1 tags after filtering in treatment: 19710164 INFO @ Tue, 16 Jun 2020 09:55:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:55:11: #1 finished! INFO @ Tue, 16 Jun 2020 09:55:11: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:55:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:55:12: #2 number of paired peaks: 178 WARNING @ Tue, 16 Jun 2020 09:55:12: Fewer paired peaks (178) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 178 pairs to build model! INFO @ Tue, 16 Jun 2020 09:55:12: start model_add_line... INFO @ Tue, 16 Jun 2020 09:55:12: start X-correlation... INFO @ Tue, 16 Jun 2020 09:55:12: end of X-cor INFO @ Tue, 16 Jun 2020 09:55:12: #2 finished! INFO @ Tue, 16 Jun 2020 09:55:12: #2 predicted fragment length is 70 bps INFO @ Tue, 16 Jun 2020 09:55:12: #2 alternative fragment length(s) may be 1,70 bps INFO @ Tue, 16 Jun 2020 09:55:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7971801/SRX7971801.05_model.r WARNING @ Tue, 16 Jun 2020 09:55:12: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:55:12: #2 You may need to consider one of the other alternative d(s): 1,70 WARNING @ Tue, 16 Jun 2020 09:55:12: #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 09:55:12: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:55:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:55:13: 13000000 INFO @ Tue, 16 Jun 2020 09:55:14: 10000000 INFO @ Tue, 16 Jun 2020 09:55:20: 11000000 INFO @ Tue, 16 Jun 2020 09:55:21: 14000000 INFO @ Tue, 16 Jun 2020 09:55:27: 12000000 INFO @ Tue, 16 Jun 2020 09:55:29: 15000000 INFO @ Tue, 16 Jun 2020 09:55:34: 13000000 INFO @ Tue, 16 Jun 2020 09:55:37: 16000000 INFO @ Tue, 16 Jun 2020 09:55:41: 14000000 INFO @ Tue, 16 Jun 2020 09:55:44: 17000000 INFO @ Tue, 16 Jun 2020 09:55:45: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:55:48: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:55:52: 18000000 INFO @ Tue, 16 Jun 2020 09:55:55: 16000000 INFO @ Tue, 16 Jun 2020 09:56:00: 19000000 INFO @ Tue, 16 Jun 2020 09:56:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7971801/SRX7971801.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:56:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7971801/SRX7971801.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:56:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7971801/SRX7971801.05_summits.bed INFO @ Tue, 16 Jun 2020 09:56:00: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (615 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:56:01: 17000000 INFO @ Tue, 16 Jun 2020 09:56:05: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:56:05: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:56:05: #1 total tags in treatment: 19710164 INFO @ Tue, 16 Jun 2020 09:56:05: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:56:05: #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 09:56:05: #1 tags after filtering in treatment: 19710164 INFO @ Tue, 16 Jun 2020 09:56:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:56:05: #1 finished! INFO @ Tue, 16 Jun 2020 09:56:05: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:56:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:56:07: #2 number of paired peaks: 178 WARNING @ Tue, 16 Jun 2020 09:56:07: Fewer paired peaks (178) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 178 pairs to build model! INFO @ Tue, 16 Jun 2020 09:56:07: start model_add_line... INFO @ Tue, 16 Jun 2020 09:56:07: start X-correlation... INFO @ Tue, 16 Jun 2020 09:56:07: end of X-cor INFO @ Tue, 16 Jun 2020 09:56:07: #2 finished! INFO @ Tue, 16 Jun 2020 09:56:07: #2 predicted fragment length is 70 bps INFO @ Tue, 16 Jun 2020 09:56:07: #2 alternative fragment length(s) may be 1,70 bps INFO @ Tue, 16 Jun 2020 09:56:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7971801/SRX7971801.10_model.r WARNING @ Tue, 16 Jun 2020 09:56:07: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:56:07: #2 You may need to consider one of the other alternative d(s): 1,70 WARNING @ Tue, 16 Jun 2020 09:56:07: #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 09:56:07: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:56:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:56:08: 18000000 INFO @ Tue, 16 Jun 2020 09:56:14: 19000000 INFO @ Tue, 16 Jun 2020 09:56:19: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:56:19: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:56:19: #1 total tags in treatment: 19710164 INFO @ Tue, 16 Jun 2020 09:56:19: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:56:19: #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 09:56:19: #1 tags after filtering in treatment: 19710164 INFO @ Tue, 16 Jun 2020 09:56:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:56:19: #1 finished! INFO @ Tue, 16 Jun 2020 09:56:19: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:56:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:56:20: #2 number of paired peaks: 178 WARNING @ Tue, 16 Jun 2020 09:56:20: Fewer paired peaks (178) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 178 pairs to build model! INFO @ Tue, 16 Jun 2020 09:56:20: start model_add_line... INFO @ Tue, 16 Jun 2020 09:56:20: start X-correlation... INFO @ Tue, 16 Jun 2020 09:56:20: end of X-cor INFO @ Tue, 16 Jun 2020 09:56:20: #2 finished! INFO @ Tue, 16 Jun 2020 09:56:20: #2 predicted fragment length is 70 bps INFO @ Tue, 16 Jun 2020 09:56:20: #2 alternative fragment length(s) may be 1,70 bps INFO @ Tue, 16 Jun 2020 09:56:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7971801/SRX7971801.20_model.r WARNING @ Tue, 16 Jun 2020 09:56:20: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:56:20: #2 You may need to consider one of the other alternative d(s): 1,70 WARNING @ Tue, 16 Jun 2020 09:56:20: #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 09:56:20: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:56:20: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:56:40: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:56:54: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:56:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7971801/SRX7971801.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:56:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7971801/SRX7971801.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:56:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7971801/SRX7971801.10_summits.bed INFO @ Tue, 16 Jun 2020 09:56:56: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (460 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:57:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7971801/SRX7971801.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:57:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7971801/SRX7971801.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:57:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7971801/SRX7971801.20_summits.bed INFO @ Tue, 16 Jun 2020 09:57:10: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (229 records, 4 fields): 2 millis CompletedMACS2peakCalling