Job ID = 6366245 SRX = SRX080099 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:56:29 prefetch.2.10.7: 1) Downloading 'SRR298919'... 2020-06-15T22:56:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:56:56 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:56:56 prefetch.2.10.7: 'SRR298919' is valid 2020-06-15T22:56:56 prefetch.2.10.7: 1) 'SRR298919' was downloaded successfully Read 4021791 spots for SRR298919/SRR298919.sra Written 4021791 spots for SRR298919/SRR298919.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: 00:00:37 4021791 reads; of these: 4021791 (100.00%) were unpaired; of these: 202500 (5.04%) aligned 0 times 3228237 (80.27%) aligned exactly 1 time 591054 (14.70%) aligned >1 times 94.96% overall alignment rate Time searching: 00:00:37 Overall time: 00:00:37 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] 207793 / 3819291 = 0.0544 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 07:59:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX080099/SRX080099.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX080099/SRX080099.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX080099/SRX080099.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX080099/SRX080099.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 07:59:01: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:59:01: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:59:08: 1000000 INFO @ Tue, 16 Jun 2020 07:59:15: 2000000 INFO @ Tue, 16 Jun 2020 07:59:22: 3000000 INFO @ Tue, 16 Jun 2020 07:59:26: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:59:26: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:59:26: #1 total tags in treatment: 3611498 INFO @ Tue, 16 Jun 2020 07:59:26: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:59:26: #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 07:59:26: #1 tags after filtering in treatment: 3611498 INFO @ Tue, 16 Jun 2020 07:59:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:59:26: #1 finished! INFO @ Tue, 16 Jun 2020 07:59:26: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:59:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:59:26: #2 number of paired peaks: 438 WARNING @ Tue, 16 Jun 2020 07:59:26: Fewer paired peaks (438) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 438 pairs to build model! INFO @ Tue, 16 Jun 2020 07:59:26: start model_add_line... INFO @ Tue, 16 Jun 2020 07:59:26: start X-correlation... INFO @ Tue, 16 Jun 2020 07:59:26: end of X-cor INFO @ Tue, 16 Jun 2020 07:59:26: #2 finished! INFO @ Tue, 16 Jun 2020 07:59:26: #2 predicted fragment length is 34 bps INFO @ Tue, 16 Jun 2020 07:59:26: #2 alternative fragment length(s) may be 4,34,593 bps INFO @ Tue, 16 Jun 2020 07:59:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX080099/SRX080099.05_model.r WARNING @ Tue, 16 Jun 2020 07:59:26: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:59:26: #2 You may need to consider one of the other alternative d(s): 4,34,593 WARNING @ Tue, 16 Jun 2020 07:59:26: #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 07:59:26: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:59:26: #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 07:59:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX080099/SRX080099.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX080099/SRX080099.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX080099/SRX080099.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX080099/SRX080099.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 07:59:31: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:59:31: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:59:34: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:59:37: 1000000 INFO @ Tue, 16 Jun 2020 07:59:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX080099/SRX080099.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:59:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX080099/SRX080099.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:59:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX080099/SRX080099.05_summits.bed INFO @ Tue, 16 Jun 2020 07:59:39: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (413 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:59:43: 2000000 INFO @ Tue, 16 Jun 2020 07:59:49: 3000000 INFO @ Tue, 16 Jun 2020 07:59:52: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:59:52: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:59:52: #1 total tags in treatment: 3611498 INFO @ Tue, 16 Jun 2020 07:59:52: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:59:52: #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 07:59:53: #1 tags after filtering in treatment: 3611498 INFO @ Tue, 16 Jun 2020 07:59:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:59:53: #1 finished! INFO @ Tue, 16 Jun 2020 07:59:53: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:59:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:59:53: #2 number of paired peaks: 438 WARNING @ Tue, 16 Jun 2020 07:59:53: Fewer paired peaks (438) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 438 pairs to build model! INFO @ Tue, 16 Jun 2020 07:59:53: start model_add_line... INFO @ Tue, 16 Jun 2020 07:59:53: start X-correlation... INFO @ Tue, 16 Jun 2020 07:59:53: end of X-cor INFO @ Tue, 16 Jun 2020 07:59:53: #2 finished! INFO @ Tue, 16 Jun 2020 07:59:53: #2 predicted fragment length is 34 bps INFO @ Tue, 16 Jun 2020 07:59:53: #2 alternative fragment length(s) may be 4,34,593 bps INFO @ Tue, 16 Jun 2020 07:59:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX080099/SRX080099.10_model.r WARNING @ Tue, 16 Jun 2020 07:59:53: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:59:53: #2 You may need to consider one of the other alternative d(s): 4,34,593 WARNING @ Tue, 16 Jun 2020 07:59:53: #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 07:59:53: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:59:53: #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 08:00:01: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:00:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX080099/SRX080099.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX080099/SRX080099.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX080099/SRX080099.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX080099/SRX080099.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 08:00:02: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:00:02: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:00:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX080099/SRX080099.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:00:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX080099/SRX080099.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:00:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX080099/SRX080099.10_summits.bed INFO @ Tue, 16 Jun 2020 08:00:06: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (191 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:00:08: 1000000 INFO @ Tue, 16 Jun 2020 08:00:14: 2000000 INFO @ Tue, 16 Jun 2020 08:00:19: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:00:23: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:00:23: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:00:23: #1 total tags in treatment: 3611498 INFO @ Tue, 16 Jun 2020 08:00:23: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:00:23: #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 08:00:23: #1 tags after filtering in treatment: 3611498 INFO @ Tue, 16 Jun 2020 08:00:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:00:23: #1 finished! INFO @ Tue, 16 Jun 2020 08:00:23: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:00:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:00:23: #2 number of paired peaks: 438 WARNING @ Tue, 16 Jun 2020 08:00:23: Fewer paired peaks (438) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 438 pairs to build model! INFO @ Tue, 16 Jun 2020 08:00:23: start model_add_line... INFO @ Tue, 16 Jun 2020 08:00:23: start X-correlation... INFO @ Tue, 16 Jun 2020 08:00:23: end of X-cor INFO @ Tue, 16 Jun 2020 08:00:23: #2 finished! INFO @ Tue, 16 Jun 2020 08:00:23: #2 predicted fragment length is 34 bps INFO @ Tue, 16 Jun 2020 08:00:23: #2 alternative fragment length(s) may be 4,34,593 bps INFO @ Tue, 16 Jun 2020 08:00:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX080099/SRX080099.20_model.r WARNING @ Tue, 16 Jun 2020 08:00:24: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:00:24: #2 You may need to consider one of the other alternative d(s): 4,34,593 WARNING @ Tue, 16 Jun 2020 08:00:24: #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 08:00:24: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:00:24: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:00:32: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:00:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX080099/SRX080099.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:00:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX080099/SRX080099.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:00:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX080099/SRX080099.20_summits.bed INFO @ Tue, 16 Jun 2020 08:00:36: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (43 records, 4 fields): 1 millis CompletedMACS2peakCalling