Job ID = 6366208 SRX = SRX080062 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:20:59 prefetch.2.10.7: 1) Downloading 'SRR298882'... 2020-06-15T22:20:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:21:28 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:21:28 prefetch.2.10.7: 'SRR298882' is valid 2020-06-15T22:21:28 prefetch.2.10.7: 1) 'SRR298882' was downloaded successfully Read 5307262 spots for SRR298882/SRR298882.sra Written 5307262 spots for SRR298882/SRR298882.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: 00:00:50 5307262 reads; of these: 5307262 (100.00%) were unpaired; of these: 797838 (15.03%) aligned 0 times 3757395 (70.80%) aligned exactly 1 time 752029 (14.17%) aligned >1 times 84.97% overall alignment rate Time searching: 00:00:50 Overall time: 00:00:50 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] 226536 / 4509424 = 0.0502 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 07:24:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX080062/SRX080062.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX080062/SRX080062.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX080062/SRX080062.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX080062/SRX080062.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 07:24:00: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:24:00: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:24:05: 1000000 INFO @ Tue, 16 Jun 2020 07:24:11: 2000000 INFO @ Tue, 16 Jun 2020 07:24:16: 3000000 INFO @ Tue, 16 Jun 2020 07:24:22: 4000000 INFO @ Tue, 16 Jun 2020 07:24:23: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:24:23: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:24:23: #1 total tags in treatment: 4282888 INFO @ Tue, 16 Jun 2020 07:24:23: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:24:23: #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 07:24:23: #1 tags after filtering in treatment: 4282888 INFO @ Tue, 16 Jun 2020 07:24:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:24:23: #1 finished! INFO @ Tue, 16 Jun 2020 07:24:23: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:24:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:24:24: #2 number of paired peaks: 419 WARNING @ Tue, 16 Jun 2020 07:24:24: Fewer paired peaks (419) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 419 pairs to build model! INFO @ Tue, 16 Jun 2020 07:24:24: start model_add_line... INFO @ Tue, 16 Jun 2020 07:24:24: start X-correlation... INFO @ Tue, 16 Jun 2020 07:24:24: end of X-cor INFO @ Tue, 16 Jun 2020 07:24:24: #2 finished! INFO @ Tue, 16 Jun 2020 07:24:24: #2 predicted fragment length is 33 bps INFO @ Tue, 16 Jun 2020 07:24:24: #2 alternative fragment length(s) may be 3,33,585 bps INFO @ Tue, 16 Jun 2020 07:24:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX080062/SRX080062.05_model.r WARNING @ Tue, 16 Jun 2020 07:24:24: #2 Since the d (33) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:24:24: #2 You may need to consider one of the other alternative d(s): 3,33,585 WARNING @ Tue, 16 Jun 2020 07:24:24: #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 07:24:24: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:24:24: #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 07:24:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX080062/SRX080062.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX080062/SRX080062.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX080062/SRX080062.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX080062/SRX080062.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 07:24:30: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:24:30: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:24:32: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:24:35: 1000000 INFO @ Tue, 16 Jun 2020 07:24:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX080062/SRX080062.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:24:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX080062/SRX080062.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:24:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX080062/SRX080062.05_summits.bed INFO @ Tue, 16 Jun 2020 07:24:37: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (409 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:24:41: 2000000 INFO @ Tue, 16 Jun 2020 07:24:46: 3000000 INFO @ Tue, 16 Jun 2020 07:24:52: 4000000 INFO @ Tue, 16 Jun 2020 07:24:53: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:24:53: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:24:53: #1 total tags in treatment: 4282888 INFO @ Tue, 16 Jun 2020 07:24:53: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:24:53: #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 07:24:53: #1 tags after filtering in treatment: 4282888 INFO @ Tue, 16 Jun 2020 07:24:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:24:53: #1 finished! INFO @ Tue, 16 Jun 2020 07:24:53: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:24:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:24:54: #2 number of paired peaks: 419 WARNING @ Tue, 16 Jun 2020 07:24:54: Fewer paired peaks (419) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 419 pairs to build model! INFO @ Tue, 16 Jun 2020 07:24:54: start model_add_line... INFO @ Tue, 16 Jun 2020 07:24:54: start X-correlation... INFO @ Tue, 16 Jun 2020 07:24:54: end of X-cor INFO @ Tue, 16 Jun 2020 07:24:54: #2 finished! INFO @ Tue, 16 Jun 2020 07:24:54: #2 predicted fragment length is 33 bps INFO @ Tue, 16 Jun 2020 07:24:54: #2 alternative fragment length(s) may be 3,33,585 bps INFO @ Tue, 16 Jun 2020 07:24:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX080062/SRX080062.10_model.r WARNING @ Tue, 16 Jun 2020 07:24:54: #2 Since the d (33) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:24:54: #2 You may need to consider one of the other alternative d(s): 3,33,585 WARNING @ Tue, 16 Jun 2020 07:24:54: #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 07:24:54: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:24:54: #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 07:25:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX080062/SRX080062.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX080062/SRX080062.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX080062/SRX080062.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX080062/SRX080062.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 07:25:00: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:25:00: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:25:03: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:25:05: 1000000 INFO @ Tue, 16 Jun 2020 07:25:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX080062/SRX080062.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:25:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX080062/SRX080062.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:25:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX080062/SRX080062.10_summits.bed INFO @ Tue, 16 Jun 2020 07:25:07: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (175 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:25:10: 2000000 INFO @ Tue, 16 Jun 2020 07:25:16: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:25:22: 4000000 INFO @ Tue, 16 Jun 2020 07:25:23: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:25:23: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:25:23: #1 total tags in treatment: 4282888 INFO @ Tue, 16 Jun 2020 07:25:23: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:25:23: #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 07:25:23: #1 tags after filtering in treatment: 4282888 INFO @ Tue, 16 Jun 2020 07:25:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:25:23: #1 finished! INFO @ Tue, 16 Jun 2020 07:25:23: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:25:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:25:24: #2 number of paired peaks: 419 WARNING @ Tue, 16 Jun 2020 07:25:24: Fewer paired peaks (419) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 419 pairs to build model! INFO @ Tue, 16 Jun 2020 07:25:24: start model_add_line... INFO @ Tue, 16 Jun 2020 07:25:24: start X-correlation... INFO @ Tue, 16 Jun 2020 07:25:24: end of X-cor INFO @ Tue, 16 Jun 2020 07:25:24: #2 finished! INFO @ Tue, 16 Jun 2020 07:25:24: #2 predicted fragment length is 33 bps INFO @ Tue, 16 Jun 2020 07:25:24: #2 alternative fragment length(s) may be 3,33,585 bps INFO @ Tue, 16 Jun 2020 07:25:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX080062/SRX080062.20_model.r WARNING @ Tue, 16 Jun 2020 07:25:24: #2 Since the d (33) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:25:24: #2 You may need to consider one of the other alternative d(s): 3,33,585 WARNING @ Tue, 16 Jun 2020 07:25:24: #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 07:25:24: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:25:24: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:25:32: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:25:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX080062/SRX080062.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:25:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX080062/SRX080062.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:25:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX080062/SRX080062.20_summits.bed INFO @ Tue, 16 Jun 2020 07:25:37: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (40 records, 4 fields): 1 millis CompletedMACS2peakCalling