Job ID = 6367476 SRX = SRX331233 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:26:36 prefetch.2.10.7: 1) Downloading 'SRR947465'... 2020-06-15T23:26:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:27:29 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:27:29 prefetch.2.10.7: 'SRR947465' is valid 2020-06-15T23:27:29 prefetch.2.10.7: 1) 'SRR947465' was downloaded successfully Read 7229842 spots for SRR947465/SRR947465.sra Written 7229842 spots for SRR947465/SRR947465.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: 00:01:13 7229842 reads; of these: 7229842 (100.00%) were unpaired; of these: 146861 (2.03%) aligned 0 times 5621383 (77.75%) aligned exactly 1 time 1461598 (20.22%) aligned >1 times 97.97% overall alignment rate Time searching: 00:01:13 Overall time: 00:01:13 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] 962227 / 7082981 = 0.1359 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 08:30:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331233/SRX331233.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331233/SRX331233.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331233/SRX331233.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331233/SRX331233.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 08:30:50: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:30:50: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:30:54: 1000000 INFO @ Tue, 16 Jun 2020 08:30:58: 2000000 INFO @ Tue, 16 Jun 2020 08:31:03: 3000000 INFO @ Tue, 16 Jun 2020 08:31:07: 4000000 INFO @ Tue, 16 Jun 2020 08:31:11: 5000000 INFO @ Tue, 16 Jun 2020 08:31:16: 6000000 INFO @ Tue, 16 Jun 2020 08:31:17: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:31:17: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:31:17: #1 total tags in treatment: 6120754 INFO @ Tue, 16 Jun 2020 08:31:17: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:31:17: #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 08:31:17: #1 tags after filtering in treatment: 6120754 INFO @ Tue, 16 Jun 2020 08:31:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:31:17: #1 finished! INFO @ Tue, 16 Jun 2020 08:31:17: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:31:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:31:17: #2 number of paired peaks: 559 WARNING @ Tue, 16 Jun 2020 08:31:17: Fewer paired peaks (559) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 559 pairs to build model! INFO @ Tue, 16 Jun 2020 08:31:17: start model_add_line... INFO @ Tue, 16 Jun 2020 08:31:17: start X-correlation... INFO @ Tue, 16 Jun 2020 08:31:17: end of X-cor INFO @ Tue, 16 Jun 2020 08:31:17: #2 finished! INFO @ Tue, 16 Jun 2020 08:31:17: #2 predicted fragment length is 32 bps INFO @ Tue, 16 Jun 2020 08:31:17: #2 alternative fragment length(s) may be 2,32,527,558,582 bps INFO @ Tue, 16 Jun 2020 08:31:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331233/SRX331233.05_model.r WARNING @ Tue, 16 Jun 2020 08:31:17: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:31:17: #2 You may need to consider one of the other alternative d(s): 2,32,527,558,582 WARNING @ Tue, 16 Jun 2020 08:31:17: #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 08:31:17: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:31:17: #3 Pre-compute pvalue-qvalue table... 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 08:31:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331233/SRX331233.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331233/SRX331233.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331233/SRX331233.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331233/SRX331233.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 08:31:19: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:31:19: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:31:24: 1000000 INFO @ Tue, 16 Jun 2020 08:31:28: 2000000 INFO @ Tue, 16 Jun 2020 08:31:29: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:31:33: 3000000 INFO @ Tue, 16 Jun 2020 08:31:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331233/SRX331233.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:31:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331233/SRX331233.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:31:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331233/SRX331233.05_summits.bed INFO @ Tue, 16 Jun 2020 08:31:35: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (617 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:31:37: 4000000 INFO @ Tue, 16 Jun 2020 08:31:42: 5000000 INFO @ Tue, 16 Jun 2020 08:31:46: 6000000 INFO @ Tue, 16 Jun 2020 08:31:47: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:31:47: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:31:47: #1 total tags in treatment: 6120754 INFO @ Tue, 16 Jun 2020 08:31:47: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:31:47: #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 08:31:47: #1 tags after filtering in treatment: 6120754 INFO @ Tue, 16 Jun 2020 08:31:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:31:47: #1 finished! INFO @ Tue, 16 Jun 2020 08:31:47: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:31:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:31:47: #2 number of paired peaks: 559 WARNING @ Tue, 16 Jun 2020 08:31:47: Fewer paired peaks (559) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 559 pairs to build model! INFO @ Tue, 16 Jun 2020 08:31:47: start model_add_line... INFO @ Tue, 16 Jun 2020 08:31:47: start X-correlation... INFO @ Tue, 16 Jun 2020 08:31:47: end of X-cor INFO @ Tue, 16 Jun 2020 08:31:47: #2 finished! INFO @ Tue, 16 Jun 2020 08:31:47: #2 predicted fragment length is 32 bps INFO @ Tue, 16 Jun 2020 08:31:47: #2 alternative fragment length(s) may be 2,32,527,558,582 bps INFO @ Tue, 16 Jun 2020 08:31:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331233/SRX331233.10_model.r WARNING @ Tue, 16 Jun 2020 08:31:47: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:31:47: #2 You may need to consider one of the other alternative d(s): 2,32,527,558,582 WARNING @ Tue, 16 Jun 2020 08:31:47: #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 08:31:47: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:31:47: #3 Pre-compute pvalue-qvalue table... 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 08:31:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331233/SRX331233.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331233/SRX331233.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331233/SRX331233.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331233/SRX331233.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 08:31:49: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:31:49: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:31:54: 1000000 INFO @ Tue, 16 Jun 2020 08:31:58: 2000000 INFO @ Tue, 16 Jun 2020 08:31:59: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:32:03: 3000000 INFO @ Tue, 16 Jun 2020 08:32:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331233/SRX331233.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:32:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331233/SRX331233.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:32:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331233/SRX331233.10_summits.bed INFO @ Tue, 16 Jun 2020 08:32:05: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (310 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:32:07: 4000000 INFO @ Tue, 16 Jun 2020 08:32:12: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:32:16: 6000000 INFO @ Tue, 16 Jun 2020 08:32:17: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:32:17: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:32:17: #1 total tags in treatment: 6120754 INFO @ Tue, 16 Jun 2020 08:32:17: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:32:17: #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 08:32:17: #1 tags after filtering in treatment: 6120754 INFO @ Tue, 16 Jun 2020 08:32:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:32:17: #1 finished! INFO @ Tue, 16 Jun 2020 08:32:17: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:32:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:32:17: #2 number of paired peaks: 559 WARNING @ Tue, 16 Jun 2020 08:32:17: Fewer paired peaks (559) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 559 pairs to build model! INFO @ Tue, 16 Jun 2020 08:32:17: start model_add_line... INFO @ Tue, 16 Jun 2020 08:32:17: start X-correlation... INFO @ Tue, 16 Jun 2020 08:32:17: end of X-cor INFO @ Tue, 16 Jun 2020 08:32:17: #2 finished! INFO @ Tue, 16 Jun 2020 08:32:17: #2 predicted fragment length is 32 bps INFO @ Tue, 16 Jun 2020 08:32:17: #2 alternative fragment length(s) may be 2,32,527,558,582 bps INFO @ Tue, 16 Jun 2020 08:32:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331233/SRX331233.20_model.r WARNING @ Tue, 16 Jun 2020 08:32:17: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:32:17: #2 You may need to consider one of the other alternative d(s): 2,32,527,558,582 WARNING @ Tue, 16 Jun 2020 08:32:17: #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 08:32:17: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:32:17: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:32:29: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:32:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331233/SRX331233.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:32:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331233/SRX331233.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:32:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331233/SRX331233.20_summits.bed INFO @ Tue, 16 Jun 2020 08:32:35: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (62 records, 4 fields): 1 millis CompletedMACS2peakCalling