Job ID = 6365976 SRX = SRX043987 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:36:06 prefetch.2.10.7: 1) Downloading 'SRR107562'... 2020-06-15T22:36:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:36:31 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:36:31 prefetch.2.10.7: 'SRR107562' is valid 2020-06-15T22:36:31 prefetch.2.10.7: 1) 'SRR107562' was downloaded successfully Read 4732745 spots for SRR107562/SRR107562.sra Written 4732745 spots for SRR107562/SRR107562.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: 00:00:41 4732745 reads; of these: 4732745 (100.00%) were unpaired; of these: 1380001 (29.16%) aligned 0 times 2698888 (57.03%) aligned exactly 1 time 653856 (13.82%) aligned >1 times 70.84% overall alignment rate Time searching: 00:00:41 Overall time: 00:00:41 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] 234033 / 3352744 = 0.0698 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 07:38:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX043987/SRX043987.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX043987/SRX043987.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX043987/SRX043987.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX043987/SRX043987.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 07:38:44: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:38:44: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:38:49: 1000000 INFO @ Tue, 16 Jun 2020 07:38:55: 2000000 INFO @ Tue, 16 Jun 2020 07:39:01: 3000000 INFO @ Tue, 16 Jun 2020 07:39:01: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:39:01: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:39:01: #1 total tags in treatment: 3118711 INFO @ Tue, 16 Jun 2020 07:39:01: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:39:01: #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 07:39:01: #1 tags after filtering in treatment: 3118711 INFO @ Tue, 16 Jun 2020 07:39:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:39:01: #1 finished! INFO @ Tue, 16 Jun 2020 07:39:01: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:39:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:39:01: #2 number of paired peaks: 460 WARNING @ Tue, 16 Jun 2020 07:39:01: Fewer paired peaks (460) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 460 pairs to build model! INFO @ Tue, 16 Jun 2020 07:39:01: start model_add_line... INFO @ Tue, 16 Jun 2020 07:39:02: start X-correlation... INFO @ Tue, 16 Jun 2020 07:39:02: end of X-cor INFO @ Tue, 16 Jun 2020 07:39:02: #2 finished! INFO @ Tue, 16 Jun 2020 07:39:02: #2 predicted fragment length is 33 bps INFO @ Tue, 16 Jun 2020 07:39:02: #2 alternative fragment length(s) may be 3,33,432,483,542,584 bps INFO @ Tue, 16 Jun 2020 07:39:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX043987/SRX043987.05_model.r WARNING @ Tue, 16 Jun 2020 07:39:02: #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 07:39:02: #2 You may need to consider one of the other alternative d(s): 3,33,432,483,542,584 WARNING @ Tue, 16 Jun 2020 07:39:02: #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 07:39:02: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:39:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:39:09: #3 Call peaks for each chromosome... 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 07:39:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX043987/SRX043987.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:39:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX043987/SRX043987.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:39:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX043987/SRX043987.05_summits.bed INFO @ Tue, 16 Jun 2020 07:39:13: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (445 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:39:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX043987/SRX043987.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX043987/SRX043987.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX043987/SRX043987.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX043987/SRX043987.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 07:39:14: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:39:14: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:39:20: 1000000 INFO @ Tue, 16 Jun 2020 07:39:26: 2000000 INFO @ Tue, 16 Jun 2020 07:39:32: 3000000 INFO @ Tue, 16 Jun 2020 07:39:33: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:39:33: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:39:33: #1 total tags in treatment: 3118711 INFO @ Tue, 16 Jun 2020 07:39:33: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:39:33: #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 07:39:33: #1 tags after filtering in treatment: 3118711 INFO @ Tue, 16 Jun 2020 07:39:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:39:33: #1 finished! INFO @ Tue, 16 Jun 2020 07:39:33: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:39:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:39:33: #2 number of paired peaks: 460 WARNING @ Tue, 16 Jun 2020 07:39:33: Fewer paired peaks (460) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 460 pairs to build model! INFO @ Tue, 16 Jun 2020 07:39:33: start model_add_line... INFO @ Tue, 16 Jun 2020 07:39:33: start X-correlation... INFO @ Tue, 16 Jun 2020 07:39:33: end of X-cor INFO @ Tue, 16 Jun 2020 07:39:33: #2 finished! INFO @ Tue, 16 Jun 2020 07:39:33: #2 predicted fragment length is 33 bps INFO @ Tue, 16 Jun 2020 07:39:33: #2 alternative fragment length(s) may be 3,33,432,483,542,584 bps INFO @ Tue, 16 Jun 2020 07:39:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX043987/SRX043987.10_model.r WARNING @ Tue, 16 Jun 2020 07:39:33: #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 07:39:33: #2 You may need to consider one of the other alternative d(s): 3,33,432,483,542,584 WARNING @ Tue, 16 Jun 2020 07:39:33: #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 07:39:33: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:39:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:39:40: #3 Call peaks for each chromosome... 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 07:39:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX043987/SRX043987.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX043987/SRX043987.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX043987/SRX043987.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX043987/SRX043987.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 07:39:44: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:39:44: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:39:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX043987/SRX043987.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:39:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX043987/SRX043987.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:39:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX043987/SRX043987.10_summits.bed INFO @ Tue, 16 Jun 2020 07:39:44: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (196 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:39:50: 1000000 INFO @ Tue, 16 Jun 2020 07:39:56: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:40:02: 3000000 INFO @ Tue, 16 Jun 2020 07:40:03: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:40:03: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:40:03: #1 total tags in treatment: 3118711 INFO @ Tue, 16 Jun 2020 07:40:03: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:40:03: #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 07:40:03: #1 tags after filtering in treatment: 3118711 INFO @ Tue, 16 Jun 2020 07:40:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:40:03: #1 finished! INFO @ Tue, 16 Jun 2020 07:40:03: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:40:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:40:03: #2 number of paired peaks: 460 WARNING @ Tue, 16 Jun 2020 07:40:03: Fewer paired peaks (460) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 460 pairs to build model! INFO @ Tue, 16 Jun 2020 07:40:03: start model_add_line... INFO @ Tue, 16 Jun 2020 07:40:03: start X-correlation... INFO @ Tue, 16 Jun 2020 07:40:03: end of X-cor INFO @ Tue, 16 Jun 2020 07:40:03: #2 finished! INFO @ Tue, 16 Jun 2020 07:40:03: #2 predicted fragment length is 33 bps INFO @ Tue, 16 Jun 2020 07:40:03: #2 alternative fragment length(s) may be 3,33,432,483,542,584 bps INFO @ Tue, 16 Jun 2020 07:40:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX043987/SRX043987.20_model.r WARNING @ Tue, 16 Jun 2020 07:40:03: #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 07:40:03: #2 You may need to consider one of the other alternative d(s): 3,33,432,483,542,584 WARNING @ Tue, 16 Jun 2020 07:40:03: #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 07:40:03: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:40:03: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:40:11: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:40:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX043987/SRX043987.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:40:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX043987/SRX043987.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:40:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX043987/SRX043987.20_summits.bed INFO @ Tue, 16 Jun 2020 07:40:15: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (45 records, 4 fields): 1 millis CompletedMACS2peakCalling