Job ID = 6367471 SRX = SRX331228 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:27:36 prefetch.2.10.7: 1) Downloading 'SRR947460'... 2020-06-15T23:27:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:29:01 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:29:01 prefetch.2.10.7: 'SRR947460' is valid 2020-06-15T23:29:01 prefetch.2.10.7: 1) 'SRR947460' was downloaded successfully Read 7646519 spots for SRR947460/SRR947460.sra Written 7646519 spots for SRR947460/SRR947460.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: 00:01:08 7646519 reads; of these: 7646519 (100.00%) were unpaired; of these: 1192039 (15.59%) aligned 0 times 5331911 (69.73%) aligned exactly 1 time 1122569 (14.68%) aligned >1 times 84.41% overall alignment rate Time searching: 00:01:08 Overall time: 00:01:08 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] 564940 / 6454480 = 0.0875 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 08:32:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331228/SRX331228.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331228/SRX331228.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331228/SRX331228.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331228/SRX331228.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 08:32:18: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:32:18: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:32:23: 1000000 INFO @ Tue, 16 Jun 2020 08:32:29: 2000000 INFO @ Tue, 16 Jun 2020 08:32:35: 3000000 INFO @ Tue, 16 Jun 2020 08:32:41: 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 08:32:47: 5000000 INFO @ Tue, 16 Jun 2020 08:32:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331228/SRX331228.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331228/SRX331228.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331228/SRX331228.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331228/SRX331228.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 08:32:48: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:32:48: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:32:53: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:32:53: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:32:53: #1 total tags in treatment: 5889540 INFO @ Tue, 16 Jun 2020 08:32:53: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:32:53: #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 08:32:53: #1 tags after filtering in treatment: 5889540 INFO @ Tue, 16 Jun 2020 08:32:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:32:53: #1 finished! INFO @ Tue, 16 Jun 2020 08:32:53: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:32:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:32:54: #2 number of paired peaks: 457 WARNING @ Tue, 16 Jun 2020 08:32:54: Fewer paired peaks (457) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 457 pairs to build model! INFO @ Tue, 16 Jun 2020 08:32:54: start model_add_line... INFO @ Tue, 16 Jun 2020 08:32:54: start X-correlation... INFO @ Tue, 16 Jun 2020 08:32:54: end of X-cor INFO @ Tue, 16 Jun 2020 08:32:54: #2 finished! INFO @ Tue, 16 Jun 2020 08:32:54: #2 predicted fragment length is 30 bps INFO @ Tue, 16 Jun 2020 08:32:54: #2 alternative fragment length(s) may be 2,30,509 bps INFO @ Tue, 16 Jun 2020 08:32:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331228/SRX331228.05_model.r WARNING @ Tue, 16 Jun 2020 08:32:54: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:32:54: #2 You may need to consider one of the other alternative d(s): 2,30,509 WARNING @ Tue, 16 Jun 2020 08:32:54: #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 08:32:54: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:32:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:32:54: 1000000 INFO @ Tue, 16 Jun 2020 08:33:00: 2000000 INFO @ Tue, 16 Jun 2020 08:33:05: 3000000 INFO @ Tue, 16 Jun 2020 08:33:06: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:33:11: 4000000 INFO @ Tue, 16 Jun 2020 08:33:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331228/SRX331228.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:33:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331228/SRX331228.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:33:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331228/SRX331228.05_summits.bed INFO @ Tue, 16 Jun 2020 08:33:12: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (594 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 08:33:17: 5000000 INFO @ Tue, 16 Jun 2020 08:33:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331228/SRX331228.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331228/SRX331228.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331228/SRX331228.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331228/SRX331228.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 08:33:18: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:33:18: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:33:23: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:33:23: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:33:23: #1 total tags in treatment: 5889540 INFO @ Tue, 16 Jun 2020 08:33:23: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:33:23: #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 08:33:23: #1 tags after filtering in treatment: 5889540 INFO @ Tue, 16 Jun 2020 08:33:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:33:23: #1 finished! INFO @ Tue, 16 Jun 2020 08:33:23: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:33:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:33:23: #2 number of paired peaks: 457 WARNING @ Tue, 16 Jun 2020 08:33:23: Fewer paired peaks (457) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 457 pairs to build model! INFO @ Tue, 16 Jun 2020 08:33:23: start model_add_line... INFO @ Tue, 16 Jun 2020 08:33:23: start X-correlation... INFO @ Tue, 16 Jun 2020 08:33:23: end of X-cor INFO @ Tue, 16 Jun 2020 08:33:23: #2 finished! INFO @ Tue, 16 Jun 2020 08:33:23: #2 predicted fragment length is 30 bps INFO @ Tue, 16 Jun 2020 08:33:23: #2 alternative fragment length(s) may be 2,30,509 bps INFO @ Tue, 16 Jun 2020 08:33:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331228/SRX331228.10_model.r WARNING @ Tue, 16 Jun 2020 08:33:23: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:33:23: #2 You may need to consider one of the other alternative d(s): 2,30,509 WARNING @ Tue, 16 Jun 2020 08:33:23: #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 08:33:23: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:33:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:33:24: 1000000 INFO @ Tue, 16 Jun 2020 08:33:29: 2000000 INFO @ Tue, 16 Jun 2020 08:33:35: 3000000 INFO @ Tue, 16 Jun 2020 08:33:36: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:33:41: 4000000 INFO @ Tue, 16 Jun 2020 08:33:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331228/SRX331228.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:33:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331228/SRX331228.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:33:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331228/SRX331228.10_summits.bed INFO @ Tue, 16 Jun 2020 08:33:42: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (277 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:33:47: 5000000 INFO @ Tue, 16 Jun 2020 08:33:52: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:33:52: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:33:52: #1 total tags in treatment: 5889540 INFO @ Tue, 16 Jun 2020 08:33:52: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:33:52: #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 08:33:52: #1 tags after filtering in treatment: 5889540 INFO @ Tue, 16 Jun 2020 08:33:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:33:52: #1 finished! INFO @ Tue, 16 Jun 2020 08:33:52: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:33:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:33:53: #2 number of paired peaks: 457 WARNING @ Tue, 16 Jun 2020 08:33:53: Fewer paired peaks (457) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 457 pairs to build model! INFO @ Tue, 16 Jun 2020 08:33:53: start model_add_line... INFO @ Tue, 16 Jun 2020 08:33:53: start X-correlation... INFO @ Tue, 16 Jun 2020 08:33:53: end of X-cor INFO @ Tue, 16 Jun 2020 08:33:53: #2 finished! INFO @ Tue, 16 Jun 2020 08:33:53: #2 predicted fragment length is 30 bps INFO @ Tue, 16 Jun 2020 08:33:53: #2 alternative fragment length(s) may be 2,30,509 bps INFO @ Tue, 16 Jun 2020 08:33:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331228/SRX331228.20_model.r WARNING @ Tue, 16 Jun 2020 08:33:53: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:33:53: #2 You may need to consider one of the other alternative d(s): 2,30,509 WARNING @ Tue, 16 Jun 2020 08:33:53: #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 08:33:53: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:33:53: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:34:05: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:34:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331228/SRX331228.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:34:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331228/SRX331228.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:34:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331228/SRX331228.20_summits.bed INFO @ Tue, 16 Jun 2020 08:34:11: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (77 records, 4 fields): 1 millis CompletedMACS2peakCalling