Job ID = 6368534 SRX = SRX5020762 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:24:06 prefetch.2.10.7: 1) Downloading 'SRR8201385'... 2020-06-16T00:24:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:26:18 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:26:19 prefetch.2.10.7: 'SRR8201385' is valid 2020-06-16T00:26:19 prefetch.2.10.7: 1) 'SRR8201385' was downloaded successfully 2020-06-16T00:26:19 prefetch.2.10.7: 'SRR8201385' has 0 unresolved dependencies Read 12014281 spots for SRR8201385/SRR8201385.sra Written 12014281 spots for SRR8201385/SRR8201385.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: 00:03:45 12014281 reads; of these: 12014281 (100.00%) were unpaired; of these: 1914336 (15.93%) aligned 0 times 8389274 (69.83%) aligned exactly 1 time 1710671 (14.24%) aligned >1 times 84.07% overall alignment rate Time searching: 00:03:45 Overall time: 00:03:45 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] 1336265 / 10099945 = 0.1323 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 09:34:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020762/SRX5020762.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020762/SRX5020762.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020762/SRX5020762.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020762/SRX5020762.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 09:34:03: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:34:03: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:34:10: 1000000 INFO @ Tue, 16 Jun 2020 09:34:16: 2000000 INFO @ Tue, 16 Jun 2020 09:34:23: 3000000 INFO @ Tue, 16 Jun 2020 09:34:30: 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 09:34:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020762/SRX5020762.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020762/SRX5020762.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020762/SRX5020762.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020762/SRX5020762.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 09:34:33: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:34:33: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:34:37: 5000000 INFO @ Tue, 16 Jun 2020 09:34:40: 1000000 INFO @ Tue, 16 Jun 2020 09:34:44: 6000000 INFO @ Tue, 16 Jun 2020 09:34:48: 2000000 INFO @ Tue, 16 Jun 2020 09:34:52: 7000000 INFO @ Tue, 16 Jun 2020 09:34:55: 3000000 INFO @ Tue, 16 Jun 2020 09:34:59: 8000000 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 09:35:03: 4000000 INFO @ Tue, 16 Jun 2020 09:35:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020762/SRX5020762.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020762/SRX5020762.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020762/SRX5020762.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020762/SRX5020762.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 09:35:03: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:35:03: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:35:05: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:35:05: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:35:05: #1 total tags in treatment: 8763680 INFO @ Tue, 16 Jun 2020 09:35:05: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:35:05: #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 09:35:05: #1 tags after filtering in treatment: 8763680 INFO @ Tue, 16 Jun 2020 09:35:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:35:05: #1 finished! INFO @ Tue, 16 Jun 2020 09:35:05: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:35:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:35:06: #2 number of paired peaks: 509 WARNING @ Tue, 16 Jun 2020 09:35:06: Fewer paired peaks (509) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 509 pairs to build model! INFO @ Tue, 16 Jun 2020 09:35:06: start model_add_line... INFO @ Tue, 16 Jun 2020 09:35:06: start X-correlation... INFO @ Tue, 16 Jun 2020 09:35:06: end of X-cor INFO @ Tue, 16 Jun 2020 09:35:06: #2 finished! INFO @ Tue, 16 Jun 2020 09:35:06: #2 predicted fragment length is 99 bps INFO @ Tue, 16 Jun 2020 09:35:06: #2 alternative fragment length(s) may be 99 bps INFO @ Tue, 16 Jun 2020 09:35:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020762/SRX5020762.05_model.r WARNING @ Tue, 16 Jun 2020 09:35:06: #2 Since the d (99) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:35:06: #2 You may need to consider one of the other alternative d(s): 99 WARNING @ Tue, 16 Jun 2020 09:35:06: #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 09:35:06: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:35:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:35:11: 5000000 INFO @ Tue, 16 Jun 2020 09:35:13: 1000000 INFO @ Tue, 16 Jun 2020 09:35:20: 6000000 INFO @ Tue, 16 Jun 2020 09:35:23: 2000000 INFO @ Tue, 16 Jun 2020 09:35:25: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:35:28: 7000000 INFO @ Tue, 16 Jun 2020 09:35:32: 3000000 INFO @ Tue, 16 Jun 2020 09:35:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020762/SRX5020762.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:35:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020762/SRX5020762.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:35:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020762/SRX5020762.05_summits.bed INFO @ Tue, 16 Jun 2020 09:35:34: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1543 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:35:37: 8000000 INFO @ Tue, 16 Jun 2020 09:35:42: 4000000 INFO @ Tue, 16 Jun 2020 09:35:43: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:35:43: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:35:43: #1 total tags in treatment: 8763680 INFO @ Tue, 16 Jun 2020 09:35:43: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:35:43: #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 09:35:43: #1 tags after filtering in treatment: 8763680 INFO @ Tue, 16 Jun 2020 09:35:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:35:43: #1 finished! INFO @ Tue, 16 Jun 2020 09:35:43: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:35:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:35:44: #2 number of paired peaks: 509 WARNING @ Tue, 16 Jun 2020 09:35:44: Fewer paired peaks (509) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 509 pairs to build model! INFO @ Tue, 16 Jun 2020 09:35:44: start model_add_line... INFO @ Tue, 16 Jun 2020 09:35:44: start X-correlation... INFO @ Tue, 16 Jun 2020 09:35:44: end of X-cor INFO @ Tue, 16 Jun 2020 09:35:44: #2 finished! INFO @ Tue, 16 Jun 2020 09:35:44: #2 predicted fragment length is 99 bps INFO @ Tue, 16 Jun 2020 09:35:44: #2 alternative fragment length(s) may be 99 bps INFO @ Tue, 16 Jun 2020 09:35:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020762/SRX5020762.10_model.r WARNING @ Tue, 16 Jun 2020 09:35:44: #2 Since the d (99) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:35:44: #2 You may need to consider one of the other alternative d(s): 99 WARNING @ Tue, 16 Jun 2020 09:35:44: #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 09:35:44: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:35:44: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:35:51: 5000000 INFO @ Tue, 16 Jun 2020 09:35:59: 6000000 INFO @ Tue, 16 Jun 2020 09:36:03: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:36:07: 7000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:36:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020762/SRX5020762.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:36:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020762/SRX5020762.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:36:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020762/SRX5020762.10_summits.bed INFO @ Tue, 16 Jun 2020 09:36:13: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (968 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:36:16: 8000000 INFO @ Tue, 16 Jun 2020 09:36:22: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:36:22: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:36:22: #1 total tags in treatment: 8763680 INFO @ Tue, 16 Jun 2020 09:36:22: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:36:22: #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 09:36:22: #1 tags after filtering in treatment: 8763680 INFO @ Tue, 16 Jun 2020 09:36:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:36:22: #1 finished! INFO @ Tue, 16 Jun 2020 09:36:22: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:36:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:36:23: #2 number of paired peaks: 509 WARNING @ Tue, 16 Jun 2020 09:36:23: Fewer paired peaks (509) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 509 pairs to build model! INFO @ Tue, 16 Jun 2020 09:36:23: start model_add_line... INFO @ Tue, 16 Jun 2020 09:36:23: start X-correlation... INFO @ Tue, 16 Jun 2020 09:36:23: end of X-cor INFO @ Tue, 16 Jun 2020 09:36:23: #2 finished! INFO @ Tue, 16 Jun 2020 09:36:23: #2 predicted fragment length is 99 bps INFO @ Tue, 16 Jun 2020 09:36:23: #2 alternative fragment length(s) may be 99 bps INFO @ Tue, 16 Jun 2020 09:36:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020762/SRX5020762.20_model.r WARNING @ Tue, 16 Jun 2020 09:36:23: #2 Since the d (99) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:36:23: #2 You may need to consider one of the other alternative d(s): 99 WARNING @ Tue, 16 Jun 2020 09:36:23: #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 09:36:23: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:36:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:36:41: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:36:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020762/SRX5020762.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:36:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020762/SRX5020762.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:36:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020762/SRX5020762.20_summits.bed INFO @ Tue, 16 Jun 2020 09:36:51: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (571 records, 4 fields): 2 millis CompletedMACS2peakCalling