Job ID = 6368478 SRX = SRX5020708 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:13:20 prefetch.2.10.7: 1) Downloading 'SRR8201331'... 2020-06-16T00:13:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:14:57 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:14:58 prefetch.2.10.7: 'SRR8201331' is valid 2020-06-16T00:14:58 prefetch.2.10.7: 1) 'SRR8201331' was downloaded successfully Read 6891148 spots for SRR8201331/SRR8201331.sra Written 6891148 spots for SRR8201331/SRR8201331.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: 00:01:25 6891148 reads; of these: 6891148 (100.00%) were unpaired; of these: 148805 (2.16%) aligned 0 times 5719649 (83.00%) aligned exactly 1 time 1022694 (14.84%) aligned >1 times 97.84% overall alignment rate Time searching: 00:01:25 Overall time: 00:01:25 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_rmdupse_core] 265536 / 6742343 = 0.0394 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 09:19:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020708/SRX5020708.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020708/SRX5020708.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020708/SRX5020708.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020708/SRX5020708.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 09:19:31: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:19:31: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:19:37: 1000000 INFO @ Tue, 16 Jun 2020 09:19:44: 2000000 INFO @ Tue, 16 Jun 2020 09:19:50: 3000000 INFO @ Tue, 16 Jun 2020 09:19:56: 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 09:20:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020708/SRX5020708.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020708/SRX5020708.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020708/SRX5020708.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020708/SRX5020708.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 09:20:01: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:20:01: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:20:02: 5000000 INFO @ Tue, 16 Jun 2020 09:20:09: 1000000 INFO @ Tue, 16 Jun 2020 09:20:10: 6000000 INFO @ Tue, 16 Jun 2020 09:20:13: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:20:13: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:20:13: #1 total tags in treatment: 6476807 INFO @ Tue, 16 Jun 2020 09:20:13: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:20:13: #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 09:20:13: #1 tags after filtering in treatment: 6476807 INFO @ Tue, 16 Jun 2020 09:20:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:20:13: #1 finished! INFO @ Tue, 16 Jun 2020 09:20:13: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:20:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:20:14: #2 number of paired peaks: 266 WARNING @ Tue, 16 Jun 2020 09:20:14: Fewer paired peaks (266) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 266 pairs to build model! INFO @ Tue, 16 Jun 2020 09:20:14: start model_add_line... INFO @ Tue, 16 Jun 2020 09:20:14: start X-correlation... INFO @ Tue, 16 Jun 2020 09:20:14: end of X-cor INFO @ Tue, 16 Jun 2020 09:20:14: #2 finished! INFO @ Tue, 16 Jun 2020 09:20:14: #2 predicted fragment length is 52 bps INFO @ Tue, 16 Jun 2020 09:20:14: #2 alternative fragment length(s) may be 4,52,498 bps INFO @ Tue, 16 Jun 2020 09:20:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020708/SRX5020708.05_model.r WARNING @ Tue, 16 Jun 2020 09:20:14: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:20:14: #2 You may need to consider one of the other alternative d(s): 4,52,498 WARNING @ Tue, 16 Jun 2020 09:20:14: #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 09:20:14: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:20:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:20:15: 2000000 INFO @ Tue, 16 Jun 2020 09:20:21: 3000000 INFO @ Tue, 16 Jun 2020 09:20:26: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:20:28: 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 09:20:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020708/SRX5020708.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020708/SRX5020708.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020708/SRX5020708.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020708/SRX5020708.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 09:20:31: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:20:31: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:20:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020708/SRX5020708.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:20:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020708/SRX5020708.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:20:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020708/SRX5020708.05_summits.bed INFO @ Tue, 16 Jun 2020 09:20:32: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (404 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:20:35: 5000000 INFO @ Tue, 16 Jun 2020 09:20:39: 1000000 INFO @ Tue, 16 Jun 2020 09:20:42: 6000000 INFO @ Tue, 16 Jun 2020 09:20:45: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:20:45: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:20:45: #1 total tags in treatment: 6476807 INFO @ Tue, 16 Jun 2020 09:20:45: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:20:45: #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 09:20:45: #1 tags after filtering in treatment: 6476807 INFO @ Tue, 16 Jun 2020 09:20:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:20:45: #1 finished! INFO @ Tue, 16 Jun 2020 09:20:45: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:20:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:20:46: #2 number of paired peaks: 266 WARNING @ Tue, 16 Jun 2020 09:20:46: Fewer paired peaks (266) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 266 pairs to build model! INFO @ Tue, 16 Jun 2020 09:20:46: start model_add_line... INFO @ Tue, 16 Jun 2020 09:20:46: start X-correlation... INFO @ Tue, 16 Jun 2020 09:20:46: end of X-cor INFO @ Tue, 16 Jun 2020 09:20:46: #2 finished! INFO @ Tue, 16 Jun 2020 09:20:46: #2 predicted fragment length is 52 bps INFO @ Tue, 16 Jun 2020 09:20:46: #2 alternative fragment length(s) may be 4,52,498 bps INFO @ Tue, 16 Jun 2020 09:20:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020708/SRX5020708.10_model.r WARNING @ Tue, 16 Jun 2020 09:20:46: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:20:46: #2 You may need to consider one of the other alternative d(s): 4,52,498 WARNING @ Tue, 16 Jun 2020 09:20:46: #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 09:20:46: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:20:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:20:46: 2000000 INFO @ Tue, 16 Jun 2020 09:20:53: 3000000 INFO @ Tue, 16 Jun 2020 09:20:58: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:20:59: 4000000 INFO @ Tue, 16 Jun 2020 09:21:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020708/SRX5020708.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:21:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020708/SRX5020708.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:21:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020708/SRX5020708.10_summits.bed INFO @ Tue, 16 Jun 2020 09:21:05: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (235 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:21:06: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:21:12: 6000000 INFO @ Tue, 16 Jun 2020 09:21:15: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:21:15: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:21:15: #1 total tags in treatment: 6476807 INFO @ Tue, 16 Jun 2020 09:21:15: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:21:15: #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 09:21:15: #1 tags after filtering in treatment: 6476807 INFO @ Tue, 16 Jun 2020 09:21:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:21:15: #1 finished! INFO @ Tue, 16 Jun 2020 09:21:15: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:21:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:21:16: #2 number of paired peaks: 266 WARNING @ Tue, 16 Jun 2020 09:21:16: Fewer paired peaks (266) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 266 pairs to build model! INFO @ Tue, 16 Jun 2020 09:21:16: start model_add_line... INFO @ Tue, 16 Jun 2020 09:21:16: start X-correlation... INFO @ Tue, 16 Jun 2020 09:21:16: end of X-cor INFO @ Tue, 16 Jun 2020 09:21:16: #2 finished! INFO @ Tue, 16 Jun 2020 09:21:16: #2 predicted fragment length is 52 bps INFO @ Tue, 16 Jun 2020 09:21:16: #2 alternative fragment length(s) may be 4,52,498 bps INFO @ Tue, 16 Jun 2020 09:21:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020708/SRX5020708.20_model.r WARNING @ Tue, 16 Jun 2020 09:21:16: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:21:16: #2 You may need to consider one of the other alternative d(s): 4,52,498 WARNING @ Tue, 16 Jun 2020 09:21:16: #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 09:21:16: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:21:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:21:28: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:21:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020708/SRX5020708.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:21:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020708/SRX5020708.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:21:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020708/SRX5020708.20_summits.bed INFO @ Tue, 16 Jun 2020 09:21:34: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (97 records, 4 fields): 1 millis CompletedMACS2peakCalling