Job ID = 6368500 SRX = SRX5020730 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:10:21 prefetch.2.10.7: 1) Downloading 'SRR8201353'... 2020-06-16T00:10:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:12:16 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:12:17 prefetch.2.10.7: 'SRR8201353' is valid 2020-06-16T00:12:17 prefetch.2.10.7: 1) 'SRR8201353' was downloaded successfully Read 11566894 spots for SRR8201353/SRR8201353.sra Written 11566894 spots for SRR8201353/SRR8201353.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: 00:02:30 11566894 reads; of these: 11566894 (100.00%) were unpaired; of these: 820383 (7.09%) aligned 0 times 8983483 (77.67%) aligned exactly 1 time 1763028 (15.24%) aligned >1 times 92.91% overall alignment rate Time searching: 00:02:30 Overall time: 00:02:30 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] 819561 / 10746511 = 0.0763 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 09:19:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020730/SRX5020730.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020730/SRX5020730.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020730/SRX5020730.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020730/SRX5020730.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 09:19:30: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:19:30: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:19:35: 1000000 INFO @ Tue, 16 Jun 2020 09:19:41: 2000000 INFO @ Tue, 16 Jun 2020 09:19:46: 3000000 INFO @ Tue, 16 Jun 2020 09:19:51: 4000000 INFO @ Tue, 16 Jun 2020 09:19:57: 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 09:19:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020730/SRX5020730.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020730/SRX5020730.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020730/SRX5020730.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020730/SRX5020730.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 09:19:59: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:19:59: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:20:03: 6000000 INFO @ Tue, 16 Jun 2020 09:20:05: 1000000 INFO @ Tue, 16 Jun 2020 09:20:09: 7000000 INFO @ Tue, 16 Jun 2020 09:20:11: 2000000 INFO @ Tue, 16 Jun 2020 09:20:14: 8000000 INFO @ Tue, 16 Jun 2020 09:20:17: 3000000 INFO @ Tue, 16 Jun 2020 09:20:20: 9000000 INFO @ Tue, 16 Jun 2020 09:20:22: 4000000 INFO @ Tue, 16 Jun 2020 09:20:25: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:20:25: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:20:25: #1 total tags in treatment: 9926950 INFO @ Tue, 16 Jun 2020 09:20:25: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:20:25: #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 09:20:26: #1 tags after filtering in treatment: 9926950 INFO @ Tue, 16 Jun 2020 09:20:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:20:26: #1 finished! INFO @ Tue, 16 Jun 2020 09:20:26: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:20:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:20:26: #2 number of paired peaks: 309 WARNING @ Tue, 16 Jun 2020 09:20:26: Fewer paired peaks (309) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 309 pairs to build model! INFO @ Tue, 16 Jun 2020 09:20:26: start model_add_line... INFO @ Tue, 16 Jun 2020 09:20:26: start X-correlation... INFO @ Tue, 16 Jun 2020 09:20:26: end of X-cor INFO @ Tue, 16 Jun 2020 09:20:26: #2 finished! INFO @ Tue, 16 Jun 2020 09:20:26: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 09:20:26: #2 alternative fragment length(s) may be 3,50,546 bps INFO @ Tue, 16 Jun 2020 09:20:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020730/SRX5020730.05_model.r WARNING @ Tue, 16 Jun 2020 09:20:26: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:20:26: #2 You may need to consider one of the other alternative d(s): 3,50,546 WARNING @ Tue, 16 Jun 2020 09:20:26: #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 09:20:26: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:20:26: #3 Pre-compute pvalue-qvalue table... 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 09:20:28: 5000000 INFO @ Tue, 16 Jun 2020 09:20:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020730/SRX5020730.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020730/SRX5020730.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020730/SRX5020730.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020730/SRX5020730.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 09:20:29: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:20:29: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:20:34: 6000000 INFO @ Tue, 16 Jun 2020 09:20:35: 1000000 INFO @ Tue, 16 Jun 2020 09:20:40: 7000000 INFO @ Tue, 16 Jun 2020 09:20:40: 2000000 INFO @ Tue, 16 Jun 2020 09:20:44: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:20:45: 8000000 INFO @ Tue, 16 Jun 2020 09:20:46: 3000000 INFO @ Tue, 16 Jun 2020 09:20:51: 9000000 INFO @ Tue, 16 Jun 2020 09:20:51: 4000000 INFO @ Tue, 16 Jun 2020 09:20:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020730/SRX5020730.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:20:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020730/SRX5020730.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:20:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020730/SRX5020730.05_summits.bed INFO @ Tue, 16 Jun 2020 09:20:54: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (575 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:20:56: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:20:56: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:20:56: #1 total tags in treatment: 9926950 INFO @ Tue, 16 Jun 2020 09:20:56: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:20:56: #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 09:20:56: #1 tags after filtering in treatment: 9926950 INFO @ Tue, 16 Jun 2020 09:20:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:20:56: #1 finished! INFO @ Tue, 16 Jun 2020 09:20:56: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:20:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:20:57: 5000000 INFO @ Tue, 16 Jun 2020 09:20:57: #2 number of paired peaks: 309 WARNING @ Tue, 16 Jun 2020 09:20:57: Fewer paired peaks (309) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 309 pairs to build model! INFO @ Tue, 16 Jun 2020 09:20:57: start model_add_line... INFO @ Tue, 16 Jun 2020 09:20:57: start X-correlation... INFO @ Tue, 16 Jun 2020 09:20:57: end of X-cor INFO @ Tue, 16 Jun 2020 09:20:57: #2 finished! INFO @ Tue, 16 Jun 2020 09:20:57: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 09:20:57: #2 alternative fragment length(s) may be 3,50,546 bps INFO @ Tue, 16 Jun 2020 09:20:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020730/SRX5020730.10_model.r WARNING @ Tue, 16 Jun 2020 09:20:57: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:20:57: #2 You may need to consider one of the other alternative d(s): 3,50,546 WARNING @ Tue, 16 Jun 2020 09:20:57: #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 09:20:57: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:20:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:21:03: 6000000 INFO @ Tue, 16 Jun 2020 09:21:09: 7000000 INFO @ Tue, 16 Jun 2020 09:21:14: 8000000 INFO @ Tue, 16 Jun 2020 09:21:14: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:21:20: 9000000 INFO @ Tue, 16 Jun 2020 09:21:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020730/SRX5020730.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:21:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020730/SRX5020730.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:21:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020730/SRX5020730.10_summits.bed INFO @ Tue, 16 Jun 2020 09:21:24: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (356 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:21:25: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:21:25: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:21:25: #1 total tags in treatment: 9926950 INFO @ Tue, 16 Jun 2020 09:21:25: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:21:25: #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 09:21:25: #1 tags after filtering in treatment: 9926950 INFO @ Tue, 16 Jun 2020 09:21:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:21:25: #1 finished! INFO @ Tue, 16 Jun 2020 09:21:25: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:21:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:21:26: #2 number of paired peaks: 309 WARNING @ Tue, 16 Jun 2020 09:21:26: Fewer paired peaks (309) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 309 pairs to build model! INFO @ Tue, 16 Jun 2020 09:21:26: start model_add_line... INFO @ Tue, 16 Jun 2020 09:21:26: start X-correlation... INFO @ Tue, 16 Jun 2020 09:21:26: end of X-cor INFO @ Tue, 16 Jun 2020 09:21:26: #2 finished! INFO @ Tue, 16 Jun 2020 09:21:26: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 09:21:26: #2 alternative fragment length(s) may be 3,50,546 bps INFO @ Tue, 16 Jun 2020 09:21:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020730/SRX5020730.20_model.r WARNING @ Tue, 16 Jun 2020 09:21:26: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:21:26: #2 You may need to consider one of the other alternative d(s): 3,50,546 WARNING @ Tue, 16 Jun 2020 09:21:26: #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 09:21:26: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:21:26: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:21:44: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:21:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020730/SRX5020730.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:21:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020730/SRX5020730.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:21:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020730/SRX5020730.20_summits.bed INFO @ Tue, 16 Jun 2020 09:21:53: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (147 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。