Job ID = 6368622 SRX = SRX5020846 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:35:31 prefetch.2.10.7: 1) Downloading 'SRR8201469'... 2020-06-16T00:35:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:37:56 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:37:56 prefetch.2.10.7: 'SRR8201469' is valid 2020-06-16T00:37:56 prefetch.2.10.7: 1) 'SRR8201469' was downloaded successfully Read 15030186 spots for SRR8201469/SRR8201469.sra Written 15030186 spots for SRR8201469/SRR8201469.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: 00:03:34 15030186 reads; of these: 15030186 (100.00%) were unpaired; of these: 183360 (1.22%) aligned 0 times 12282971 (81.72%) aligned exactly 1 time 2563855 (17.06%) aligned >1 times 98.78% overall alignment rate Time searching: 00:03:34 Overall time: 00:03:34 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] 2221418 / 14846826 = 0.1496 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 09:46:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020846/SRX5020846.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020846/SRX5020846.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020846/SRX5020846.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020846/SRX5020846.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 09:46:10: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:46:10: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:46:15: 1000000 INFO @ Tue, 16 Jun 2020 09:46:20: 2000000 INFO @ Tue, 16 Jun 2020 09:46:25: 3000000 INFO @ Tue, 16 Jun 2020 09:46:29: 4000000 INFO @ Tue, 16 Jun 2020 09:46:34: 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 09:46:39: 6000000 INFO @ Tue, 16 Jun 2020 09:46:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020846/SRX5020846.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020846/SRX5020846.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020846/SRX5020846.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020846/SRX5020846.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 09:46:40: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:46:40: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:46:44: 7000000 INFO @ Tue, 16 Jun 2020 09:46:45: 1000000 INFO @ Tue, 16 Jun 2020 09:46:49: 8000000 INFO @ Tue, 16 Jun 2020 09:46:50: 2000000 INFO @ Tue, 16 Jun 2020 09:46:54: 9000000 INFO @ Tue, 16 Jun 2020 09:46:55: 3000000 INFO @ Tue, 16 Jun 2020 09:46:59: 10000000 INFO @ Tue, 16 Jun 2020 09:47:00: 4000000 INFO @ Tue, 16 Jun 2020 09:47:04: 11000000 INFO @ Tue, 16 Jun 2020 09:47:05: 5000000 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 09:47:09: 12000000 INFO @ Tue, 16 Jun 2020 09:47:10: 6000000 INFO @ Tue, 16 Jun 2020 09:47:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020846/SRX5020846.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020846/SRX5020846.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020846/SRX5020846.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020846/SRX5020846.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 09:47:10: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:47:10: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:47:12: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:47:12: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:47:12: #1 total tags in treatment: 12625408 INFO @ Tue, 16 Jun 2020 09:47:12: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:47:12: #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 09:47:12: #1 tags after filtering in treatment: 12625408 INFO @ Tue, 16 Jun 2020 09:47:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:47:12: #1 finished! INFO @ Tue, 16 Jun 2020 09:47:12: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:47:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:47:13: #2 number of paired peaks: 348 WARNING @ Tue, 16 Jun 2020 09:47:13: Fewer paired peaks (348) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 348 pairs to build model! INFO @ Tue, 16 Jun 2020 09:47:13: start model_add_line... INFO @ Tue, 16 Jun 2020 09:47:13: start X-correlation... INFO @ Tue, 16 Jun 2020 09:47:13: end of X-cor INFO @ Tue, 16 Jun 2020 09:47:13: #2 finished! INFO @ Tue, 16 Jun 2020 09:47:13: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 09:47:13: #2 alternative fragment length(s) may be 2,49,542 bps INFO @ Tue, 16 Jun 2020 09:47:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020846/SRX5020846.05_model.r WARNING @ Tue, 16 Jun 2020 09:47:13: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:47:13: #2 You may need to consider one of the other alternative d(s): 2,49,542 WARNING @ Tue, 16 Jun 2020 09:47:13: #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 09:47:13: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:47:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:47:15: 7000000 INFO @ Tue, 16 Jun 2020 09:47:16: 1000000 INFO @ Tue, 16 Jun 2020 09:47:20: 8000000 INFO @ Tue, 16 Jun 2020 09:47:22: 2000000 INFO @ Tue, 16 Jun 2020 09:47:25: 9000000 INFO @ Tue, 16 Jun 2020 09:47:28: 3000000 INFO @ Tue, 16 Jun 2020 09:47:30: 10000000 INFO @ Tue, 16 Jun 2020 09:47:34: 4000000 INFO @ Tue, 16 Jun 2020 09:47:35: 11000000 INFO @ Tue, 16 Jun 2020 09:47:36: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:47:40: 5000000 INFO @ Tue, 16 Jun 2020 09:47:41: 12000000 INFO @ Tue, 16 Jun 2020 09:47:44: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:47:44: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:47:44: #1 total tags in treatment: 12625408 INFO @ Tue, 16 Jun 2020 09:47:44: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:47:44: #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 09:47:44: #1 tags after filtering in treatment: 12625408 INFO @ Tue, 16 Jun 2020 09:47:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:47:44: #1 finished! INFO @ Tue, 16 Jun 2020 09:47:44: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:47:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:47:45: #2 number of paired peaks: 348 WARNING @ Tue, 16 Jun 2020 09:47:45: Fewer paired peaks (348) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 348 pairs to build model! INFO @ Tue, 16 Jun 2020 09:47:45: start model_add_line... INFO @ Tue, 16 Jun 2020 09:47:45: start X-correlation... INFO @ Tue, 16 Jun 2020 09:47:45: end of X-cor INFO @ Tue, 16 Jun 2020 09:47:45: #2 finished! INFO @ Tue, 16 Jun 2020 09:47:45: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 09:47:45: #2 alternative fragment length(s) may be 2,49,542 bps INFO @ Tue, 16 Jun 2020 09:47:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020846/SRX5020846.10_model.r WARNING @ Tue, 16 Jun 2020 09:47:45: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:47:45: #2 You may need to consider one of the other alternative d(s): 2,49,542 WARNING @ Tue, 16 Jun 2020 09:47:45: #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 09:47:45: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:47:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:47:46: 6000000 INFO @ Tue, 16 Jun 2020 09:47:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020846/SRX5020846.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:47:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020846/SRX5020846.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:47:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020846/SRX5020846.05_summits.bed INFO @ Tue, 16 Jun 2020 09:47:48: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (701 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:47:52: 7000000 INFO @ Tue, 16 Jun 2020 09:47:57: 8000000 INFO @ Tue, 16 Jun 2020 09:48:03: 9000000 INFO @ Tue, 16 Jun 2020 09:48:07: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:48:09: 10000000 INFO @ Tue, 16 Jun 2020 09:48:15: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:48:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020846/SRX5020846.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:48:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020846/SRX5020846.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:48:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020846/SRX5020846.10_summits.bed INFO @ Tue, 16 Jun 2020 09:48:19: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (498 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:48:21: 12000000 INFO @ Tue, 16 Jun 2020 09:48:24: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:48:24: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:48:24: #1 total tags in treatment: 12625408 INFO @ Tue, 16 Jun 2020 09:48:24: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:48:24: #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 09:48:25: #1 tags after filtering in treatment: 12625408 INFO @ Tue, 16 Jun 2020 09:48:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:48:25: #1 finished! INFO @ Tue, 16 Jun 2020 09:48:25: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:48:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:48:25: #2 number of paired peaks: 348 WARNING @ Tue, 16 Jun 2020 09:48:25: Fewer paired peaks (348) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 348 pairs to build model! INFO @ Tue, 16 Jun 2020 09:48:25: start model_add_line... INFO @ Tue, 16 Jun 2020 09:48:26: start X-correlation... INFO @ Tue, 16 Jun 2020 09:48:26: end of X-cor INFO @ Tue, 16 Jun 2020 09:48:26: #2 finished! INFO @ Tue, 16 Jun 2020 09:48:26: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 09:48:26: #2 alternative fragment length(s) may be 2,49,542 bps INFO @ Tue, 16 Jun 2020 09:48:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020846/SRX5020846.20_model.r WARNING @ Tue, 16 Jun 2020 09:48:26: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:48:26: #2 You may need to consider one of the other alternative d(s): 2,49,542 WARNING @ Tue, 16 Jun 2020 09:48:26: #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 09:48:26: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:48:26: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:48:49: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:49:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020846/SRX5020846.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:49:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020846/SRX5020846.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:49:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020846/SRX5020846.20_summits.bed INFO @ Tue, 16 Jun 2020 09:49:01: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (206 records, 4 fields): 2 millis CompletedMACS2peakCalling