Job ID = 6367650 SRX = SRX373272 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:33:05 prefetch.2.10.7: 1) Downloading 'SRR1024190'... 2020-06-15T23:33:05 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:38:55 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:38:55 prefetch.2.10.7: 1) 'SRR1024190' was downloaded successfully Read 26510838 spots for SRR1024190/SRR1024190.sra Written 26510838 spots for SRR1024190/SRR1024190.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: 00:03:27 26510838 reads; of these: 26510838 (100.00%) were unpaired; of these: 19345231 (72.97%) aligned 0 times 5867806 (22.13%) aligned exactly 1 time 1297801 (4.90%) aligned >1 times 27.03% overall alignment rate Time searching: 00:03:27 Overall time: 00:03:27 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] 619473 / 7165607 = 0.0865 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 08:45:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX373272/SRX373272.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX373272/SRX373272.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX373272/SRX373272.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX373272/SRX373272.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 08:45:53: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:45:53: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:45:58: 1000000 INFO @ Tue, 16 Jun 2020 08:46:03: 2000000 INFO @ Tue, 16 Jun 2020 08:46:08: 3000000 INFO @ Tue, 16 Jun 2020 08:46:13: 4000000 INFO @ Tue, 16 Jun 2020 08:46:18: 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 08:46:23: 6000000 INFO @ Tue, 16 Jun 2020 08:46:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX373272/SRX373272.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX373272/SRX373272.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX373272/SRX373272.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX373272/SRX373272.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 08:46:23: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:46:23: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:46:26: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:46:26: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:46:26: #1 total tags in treatment: 6546134 INFO @ Tue, 16 Jun 2020 08:46:26: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:46:26: #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 08:46:26: #1 tags after filtering in treatment: 6546134 INFO @ Tue, 16 Jun 2020 08:46:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:46:26: #1 finished! INFO @ Tue, 16 Jun 2020 08:46:26: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:46:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:46:26: #2 number of paired peaks: 371 WARNING @ Tue, 16 Jun 2020 08:46:26: Fewer paired peaks (371) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 371 pairs to build model! INFO @ Tue, 16 Jun 2020 08:46:26: start model_add_line... INFO @ Tue, 16 Jun 2020 08:46:26: start X-correlation... INFO @ Tue, 16 Jun 2020 08:46:26: end of X-cor INFO @ Tue, 16 Jun 2020 08:46:26: #2 finished! INFO @ Tue, 16 Jun 2020 08:46:26: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 08:46:26: #2 alternative fragment length(s) may be 4,49,514,569 bps INFO @ Tue, 16 Jun 2020 08:46:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX373272/SRX373272.05_model.r WARNING @ Tue, 16 Jun 2020 08:46:26: #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 08:46:26: #2 You may need to consider one of the other alternative d(s): 4,49,514,569 WARNING @ Tue, 16 Jun 2020 08:46:26: #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 08:46:26: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:46:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:46:29: 1000000 INFO @ Tue, 16 Jun 2020 08:46:35: 2000000 INFO @ Tue, 16 Jun 2020 08:46:40: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:46:40: 3000000 INFO @ Tue, 16 Jun 2020 08:46:46: 4000000 INFO @ Tue, 16 Jun 2020 08:46:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX373272/SRX373272.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:46:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX373272/SRX373272.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:46:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX373272/SRX373272.05_summits.bed INFO @ Tue, 16 Jun 2020 08:46:47: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (585 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 08:46:51: 5000000 INFO @ Tue, 16 Jun 2020 08:46:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX373272/SRX373272.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX373272/SRX373272.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX373272/SRX373272.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX373272/SRX373272.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 08:46:53: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:46:53: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:46:57: 6000000 INFO @ Tue, 16 Jun 2020 08:46:59: 1000000 INFO @ Tue, 16 Jun 2020 08:47:00: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:47:00: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:47:00: #1 total tags in treatment: 6546134 INFO @ Tue, 16 Jun 2020 08:47:00: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:47:00: #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 08:47:01: #1 tags after filtering in treatment: 6546134 INFO @ Tue, 16 Jun 2020 08:47:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:47:01: #1 finished! INFO @ Tue, 16 Jun 2020 08:47:01: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:47:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:47:01: #2 number of paired peaks: 371 WARNING @ Tue, 16 Jun 2020 08:47:01: Fewer paired peaks (371) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 371 pairs to build model! INFO @ Tue, 16 Jun 2020 08:47:01: start model_add_line... INFO @ Tue, 16 Jun 2020 08:47:01: start X-correlation... INFO @ Tue, 16 Jun 2020 08:47:01: end of X-cor INFO @ Tue, 16 Jun 2020 08:47:01: #2 finished! INFO @ Tue, 16 Jun 2020 08:47:01: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 08:47:01: #2 alternative fragment length(s) may be 4,49,514,569 bps INFO @ Tue, 16 Jun 2020 08:47:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX373272/SRX373272.10_model.r WARNING @ Tue, 16 Jun 2020 08:47:01: #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 08:47:01: #2 You may need to consider one of the other alternative d(s): 4,49,514,569 WARNING @ Tue, 16 Jun 2020 08:47:01: #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 08:47:01: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:47:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:47:05: 2000000 INFO @ Tue, 16 Jun 2020 08:47:11: 3000000 INFO @ Tue, 16 Jun 2020 08:47:14: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:47:16: 4000000 INFO @ Tue, 16 Jun 2020 08:47:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX373272/SRX373272.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:47:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX373272/SRX373272.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:47:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX373272/SRX373272.10_summits.bed INFO @ Tue, 16 Jun 2020 08:47:21: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (342 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:47:22: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:47:28: 6000000 INFO @ Tue, 16 Jun 2020 08:47:31: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:47:31: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:47:31: #1 total tags in treatment: 6546134 INFO @ Tue, 16 Jun 2020 08:47:31: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:47:31: #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 08:47:31: #1 tags after filtering in treatment: 6546134 INFO @ Tue, 16 Jun 2020 08:47:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:47:31: #1 finished! INFO @ Tue, 16 Jun 2020 08:47:31: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:47:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:47:31: #2 number of paired peaks: 371 WARNING @ Tue, 16 Jun 2020 08:47:31: Fewer paired peaks (371) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 371 pairs to build model! INFO @ Tue, 16 Jun 2020 08:47:31: start model_add_line... INFO @ Tue, 16 Jun 2020 08:47:31: start X-correlation... INFO @ Tue, 16 Jun 2020 08:47:31: end of X-cor INFO @ Tue, 16 Jun 2020 08:47:31: #2 finished! INFO @ Tue, 16 Jun 2020 08:47:31: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 08:47:31: #2 alternative fragment length(s) may be 4,49,514,569 bps INFO @ Tue, 16 Jun 2020 08:47:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX373272/SRX373272.20_model.r WARNING @ Tue, 16 Jun 2020 08:47:31: #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 08:47:31: #2 You may need to consider one of the other alternative d(s): 4,49,514,569 WARNING @ Tue, 16 Jun 2020 08:47:31: #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 08:47:31: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:47:31: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:47:44: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:47:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX373272/SRX373272.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:47:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX373272/SRX373272.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:47:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX373272/SRX373272.20_summits.bed INFO @ Tue, 16 Jun 2020 08:47:51: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (125 records, 4 fields): 1 millis CompletedMACS2peakCalling