Job ID = 6368370 SRX = SRX495050 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:09:39 prefetch.2.10.7: 1) Downloading 'SRR1198582'... 2020-06-16T00:09:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:11:41 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:11:42 prefetch.2.10.7: 'SRR1198582' is valid 2020-06-16T00:11:42 prefetch.2.10.7: 1) 'SRR1198582' was downloaded successfully Read 13338445 spots for SRR1198582/SRR1198582.sra Written 13338445 spots for SRR1198582/SRR1198582.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:33 13338445 reads; of these: 13338445 (100.00%) were unpaired; of these: 88328 (0.66%) aligned 0 times 10992865 (82.41%) aligned exactly 1 time 2257252 (16.92%) aligned >1 times 99.34% overall alignment rate Time searching: 00:02:34 Overall time: 00:02:34 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_rmdupse_core] 2114374 / 13250117 = 0.1596 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 09:18:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495050/SRX495050.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495050/SRX495050.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495050/SRX495050.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495050/SRX495050.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 09:18:15: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:18:15: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:18:21: 1000000 INFO @ Tue, 16 Jun 2020 09:18:26: 2000000 INFO @ Tue, 16 Jun 2020 09:18:31: 3000000 INFO @ Tue, 16 Jun 2020 09:18:37: 4000000 INFO @ Tue, 16 Jun 2020 09:18:42: 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 09:18:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495050/SRX495050.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495050/SRX495050.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495050/SRX495050.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495050/SRX495050.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 09:18:45: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:18:45: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:18:48: 6000000 INFO @ Tue, 16 Jun 2020 09:18:53: 1000000 INFO @ Tue, 16 Jun 2020 09:18:55: 7000000 INFO @ Tue, 16 Jun 2020 09:19:00: 2000000 INFO @ Tue, 16 Jun 2020 09:19:01: 8000000 INFO @ Tue, 16 Jun 2020 09:19:07: 3000000 INFO @ Tue, 16 Jun 2020 09:19:08: 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 09:19:14: 10000000 INFO @ Tue, 16 Jun 2020 09:19:15: 4000000 INFO @ Tue, 16 Jun 2020 09:19:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495050/SRX495050.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495050/SRX495050.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495050/SRX495050.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495050/SRX495050.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 09:19:15: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:19:15: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:19:21: 11000000 INFO @ Tue, 16 Jun 2020 09:19:22: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:19:22: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:19:22: #1 total tags in treatment: 11135743 INFO @ Tue, 16 Jun 2020 09:19:22: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:19:22: #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 09:19:22: 5000000 INFO @ Tue, 16 Jun 2020 09:19:22: #1 tags after filtering in treatment: 11135743 INFO @ Tue, 16 Jun 2020 09:19:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:19:22: #1 finished! INFO @ Tue, 16 Jun 2020 09:19:22: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:19:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:19:23: 1000000 INFO @ Tue, 16 Jun 2020 09:19:23: #2 number of paired peaks: 364 WARNING @ Tue, 16 Jun 2020 09:19:23: Fewer paired peaks (364) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 364 pairs to build model! INFO @ Tue, 16 Jun 2020 09:19:23: start model_add_line... INFO @ Tue, 16 Jun 2020 09:19:23: start X-correlation... INFO @ Tue, 16 Jun 2020 09:19:23: end of X-cor INFO @ Tue, 16 Jun 2020 09:19:23: #2 finished! INFO @ Tue, 16 Jun 2020 09:19:23: #2 predicted fragment length is 40 bps INFO @ Tue, 16 Jun 2020 09:19:23: #2 alternative fragment length(s) may be 2,40 bps INFO @ Tue, 16 Jun 2020 09:19:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495050/SRX495050.05_model.r WARNING @ Tue, 16 Jun 2020 09:19:23: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:19:23: #2 You may need to consider one of the other alternative d(s): 2,40 WARNING @ Tue, 16 Jun 2020 09:19:23: #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 09:19:23: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:19:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:19:29: 6000000 INFO @ Tue, 16 Jun 2020 09:19:30: 2000000 INFO @ Tue, 16 Jun 2020 09:19:37: 7000000 INFO @ Tue, 16 Jun 2020 09:19:37: 3000000 INFO @ Tue, 16 Jun 2020 09:19:44: 8000000 INFO @ Tue, 16 Jun 2020 09:19:44: 4000000 INFO @ Tue, 16 Jun 2020 09:19:45: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:19:51: 5000000 INFO @ Tue, 16 Jun 2020 09:19:51: 9000000 INFO @ Tue, 16 Jun 2020 09:19:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495050/SRX495050.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:19:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495050/SRX495050.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:19:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495050/SRX495050.05_summits.bed INFO @ Tue, 16 Jun 2020 09:19:56: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (914 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:19:58: 6000000 INFO @ Tue, 16 Jun 2020 09:19:58: 10000000 INFO @ Tue, 16 Jun 2020 09:20:05: 7000000 INFO @ Tue, 16 Jun 2020 09:20:06: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:20:07: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:20:07: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:20:07: #1 total tags in treatment: 11135743 INFO @ Tue, 16 Jun 2020 09:20:07: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:20:07: #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 09:20:07: #1 tags after filtering in treatment: 11135743 INFO @ Tue, 16 Jun 2020 09:20:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:20:07: #1 finished! INFO @ Tue, 16 Jun 2020 09:20:07: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:20:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:20:08: #2 number of paired peaks: 364 WARNING @ Tue, 16 Jun 2020 09:20:08: Fewer paired peaks (364) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 364 pairs to build model! INFO @ Tue, 16 Jun 2020 09:20:08: start model_add_line... INFO @ Tue, 16 Jun 2020 09:20:08: start X-correlation... INFO @ Tue, 16 Jun 2020 09:20:08: end of X-cor INFO @ Tue, 16 Jun 2020 09:20:08: #2 finished! INFO @ Tue, 16 Jun 2020 09:20:08: #2 predicted fragment length is 40 bps INFO @ Tue, 16 Jun 2020 09:20:08: #2 alternative fragment length(s) may be 2,40 bps INFO @ Tue, 16 Jun 2020 09:20:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495050/SRX495050.10_model.r WARNING @ Tue, 16 Jun 2020 09:20:08: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:20:08: #2 You may need to consider one of the other alternative d(s): 2,40 WARNING @ Tue, 16 Jun 2020 09:20:08: #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 09:20:08: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:20:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:20:12: 8000000 INFO @ Tue, 16 Jun 2020 09:20:19: 9000000 INFO @ Tue, 16 Jun 2020 09:20:26: 10000000 INFO @ Tue, 16 Jun 2020 09:20:29: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:20:32: 11000000 INFO @ Tue, 16 Jun 2020 09:20:33: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:20:33: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:20:33: #1 total tags in treatment: 11135743 INFO @ Tue, 16 Jun 2020 09:20:33: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:20:33: #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 09:20:33: #1 tags after filtering in treatment: 11135743 INFO @ Tue, 16 Jun 2020 09:20:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:20:33: #1 finished! INFO @ Tue, 16 Jun 2020 09:20:33: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:20:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:20:34: #2 number of paired peaks: 364 WARNING @ Tue, 16 Jun 2020 09:20:34: Fewer paired peaks (364) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 364 pairs to build model! INFO @ Tue, 16 Jun 2020 09:20:34: start model_add_line... INFO @ Tue, 16 Jun 2020 09:20:34: start X-correlation... INFO @ Tue, 16 Jun 2020 09:20:34: end of X-cor INFO @ Tue, 16 Jun 2020 09:20:34: #2 finished! INFO @ Tue, 16 Jun 2020 09:20:34: #2 predicted fragment length is 40 bps INFO @ Tue, 16 Jun 2020 09:20:34: #2 alternative fragment length(s) may be 2,40 bps INFO @ Tue, 16 Jun 2020 09:20:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495050/SRX495050.20_model.r WARNING @ Tue, 16 Jun 2020 09:20:34: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:20:34: #2 You may need to consider one of the other alternative d(s): 2,40 WARNING @ Tue, 16 Jun 2020 09:20:34: #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 09:20:34: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:20:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:20:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495050/SRX495050.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:20:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495050/SRX495050.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:20:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495050/SRX495050.10_summits.bed INFO @ Tue, 16 Jun 2020 09:20:40: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (362 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:20:54: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:21:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495050/SRX495050.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:21:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495050/SRX495050.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:21:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495050/SRX495050.20_summits.bed INFO @ Tue, 16 Jun 2020 09:21:05: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (129 records, 4 fields): 1 millis CompletedMACS2peakCalling