Job ID = 6366064 SRX = SRX059236 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:30:59 prefetch.2.10.7: 1) Downloading 'SRR190676'... 2020-06-15T22:30:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:32:19 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:32:20 prefetch.2.10.7: 'SRR190676' is valid 2020-06-15T22:32:20 prefetch.2.10.7: 1) 'SRR190676' was downloaded successfully Read 19555555 spots for SRR190676/SRR190676.sra Written 19555555 spots for SRR190676/SRR190676.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: 00:02:30 19555555 reads; of these: 19555555 (100.00%) were unpaired; of these: 8711931 (44.55%) aligned 0 times 9074734 (46.40%) aligned exactly 1 time 1768890 (9.05%) aligned >1 times 55.45% overall alignment rate Time searching: 00:02:30 Overall time: 00:02:30 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] 648795 / 10843624 = 0.0598 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 07:38:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059236/SRX059236.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059236/SRX059236.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059236/SRX059236.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059236/SRX059236.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 07:38:25: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:38:25: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:38:31: 1000000 INFO @ Tue, 16 Jun 2020 07:38:37: 2000000 INFO @ Tue, 16 Jun 2020 07:38:43: 3000000 INFO @ Tue, 16 Jun 2020 07:38:50: 4000000 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 07:38:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059236/SRX059236.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059236/SRX059236.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059236/SRX059236.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059236/SRX059236.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 07:38:55: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:38:55: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:38:56: 5000000 INFO @ Tue, 16 Jun 2020 07:39:02: 1000000 INFO @ Tue, 16 Jun 2020 07:39:02: 6000000 INFO @ Tue, 16 Jun 2020 07:39:09: 2000000 INFO @ Tue, 16 Jun 2020 07:39:09: 7000000 INFO @ Tue, 16 Jun 2020 07:39:15: 3000000 INFO @ Tue, 16 Jun 2020 07:39:16: 8000000 INFO @ Tue, 16 Jun 2020 07:39:22: 4000000 INFO @ Tue, 16 Jun 2020 07:39:22: 9000000 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 07:39:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059236/SRX059236.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059236/SRX059236.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059236/SRX059236.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059236/SRX059236.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 07:39:25: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:39:25: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:39:28: 5000000 INFO @ Tue, 16 Jun 2020 07:39:29: 10000000 INFO @ Tue, 16 Jun 2020 07:39:30: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:39:30: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:39:30: #1 total tags in treatment: 10194829 INFO @ Tue, 16 Jun 2020 07:39:30: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:39:30: #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 07:39:30: #1 tags after filtering in treatment: 10194829 INFO @ Tue, 16 Jun 2020 07:39:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:39:30: #1 finished! INFO @ Tue, 16 Jun 2020 07:39:30: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:39:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:39:31: #2 number of paired peaks: 253 WARNING @ Tue, 16 Jun 2020 07:39:31: Fewer paired peaks (253) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 253 pairs to build model! INFO @ Tue, 16 Jun 2020 07:39:31: start model_add_line... INFO @ Tue, 16 Jun 2020 07:39:31: start X-correlation... INFO @ Tue, 16 Jun 2020 07:39:31: end of X-cor INFO @ Tue, 16 Jun 2020 07:39:31: #2 finished! INFO @ Tue, 16 Jun 2020 07:39:31: #2 predicted fragment length is 31 bps INFO @ Tue, 16 Jun 2020 07:39:31: #2 alternative fragment length(s) may be 1,31,527,552,592 bps INFO @ Tue, 16 Jun 2020 07:39:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059236/SRX059236.05_model.r WARNING @ Tue, 16 Jun 2020 07:39:31: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:39:31: #2 You may need to consider one of the other alternative d(s): 1,31,527,552,592 WARNING @ Tue, 16 Jun 2020 07:39:31: #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 07:39:31: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:39:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:39:32: 1000000 INFO @ Tue, 16 Jun 2020 07:39:35: 6000000 INFO @ Tue, 16 Jun 2020 07:39:38: 2000000 INFO @ Tue, 16 Jun 2020 07:39:41: 7000000 INFO @ Tue, 16 Jun 2020 07:39:44: 3000000 INFO @ Tue, 16 Jun 2020 07:39:47: 8000000 INFO @ Tue, 16 Jun 2020 07:39:50: 4000000 INFO @ Tue, 16 Jun 2020 07:39:50: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:39:53: 9000000 INFO @ Tue, 16 Jun 2020 07:39:56: 5000000 INFO @ Tue, 16 Jun 2020 07:40:00: 10000000 INFO @ Tue, 16 Jun 2020 07:40:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059236/SRX059236.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:40:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059236/SRX059236.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:40:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059236/SRX059236.05_summits.bed INFO @ Tue, 16 Jun 2020 07:40:00: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (575 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:40:01: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:40:01: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:40:01: #1 total tags in treatment: 10194829 INFO @ Tue, 16 Jun 2020 07:40:01: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:40:01: #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 07:40:01: #1 tags after filtering in treatment: 10194829 INFO @ Tue, 16 Jun 2020 07:40:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:40:01: #1 finished! INFO @ Tue, 16 Jun 2020 07:40:01: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:40:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:40:02: #2 number of paired peaks: 253 WARNING @ Tue, 16 Jun 2020 07:40:02: Fewer paired peaks (253) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 253 pairs to build model! INFO @ Tue, 16 Jun 2020 07:40:02: start model_add_line... INFO @ Tue, 16 Jun 2020 07:40:02: start X-correlation... INFO @ Tue, 16 Jun 2020 07:40:02: end of X-cor INFO @ Tue, 16 Jun 2020 07:40:02: #2 finished! INFO @ Tue, 16 Jun 2020 07:40:02: #2 predicted fragment length is 31 bps INFO @ Tue, 16 Jun 2020 07:40:02: #2 alternative fragment length(s) may be 1,31,527,552,592 bps INFO @ Tue, 16 Jun 2020 07:40:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059236/SRX059236.10_model.r WARNING @ Tue, 16 Jun 2020 07:40:02: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:40:02: #2 You may need to consider one of the other alternative d(s): 1,31,527,552,592 WARNING @ Tue, 16 Jun 2020 07:40:02: #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 07:40:02: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:40:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:40:02: 6000000 INFO @ Tue, 16 Jun 2020 07:40:08: 7000000 INFO @ Tue, 16 Jun 2020 07:40:14: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:40:20: 9000000 INFO @ Tue, 16 Jun 2020 07:40:22: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:40:26: 10000000 INFO @ Tue, 16 Jun 2020 07:40:27: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:40:27: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:40:27: #1 total tags in treatment: 10194829 INFO @ Tue, 16 Jun 2020 07:40:27: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:40:27: #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 07:40:27: #1 tags after filtering in treatment: 10194829 INFO @ Tue, 16 Jun 2020 07:40:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:40:27: #1 finished! INFO @ Tue, 16 Jun 2020 07:40:27: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:40:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:40:28: #2 number of paired peaks: 253 WARNING @ Tue, 16 Jun 2020 07:40:28: Fewer paired peaks (253) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 253 pairs to build model! INFO @ Tue, 16 Jun 2020 07:40:28: start model_add_line... INFO @ Tue, 16 Jun 2020 07:40:28: start X-correlation... INFO @ Tue, 16 Jun 2020 07:40:28: end of X-cor INFO @ Tue, 16 Jun 2020 07:40:28: #2 finished! INFO @ Tue, 16 Jun 2020 07:40:28: #2 predicted fragment length is 31 bps INFO @ Tue, 16 Jun 2020 07:40:28: #2 alternative fragment length(s) may be 1,31,527,552,592 bps INFO @ Tue, 16 Jun 2020 07:40:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059236/SRX059236.20_model.r WARNING @ Tue, 16 Jun 2020 07:40:28: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:40:28: #2 You may need to consider one of the other alternative d(s): 1,31,527,552,592 WARNING @ Tue, 16 Jun 2020 07:40:28: #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 07:40:28: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:40:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:40:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059236/SRX059236.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:40:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059236/SRX059236.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:40:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059236/SRX059236.10_summits.bed INFO @ Tue, 16 Jun 2020 07:40:32: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (251 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:40:48: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:40:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059236/SRX059236.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:40:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059236/SRX059236.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:40:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059236/SRX059236.20_summits.bed INFO @ Tue, 16 Jun 2020 07:40:58: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (52 records, 4 fields): 1 millis CompletedMACS2peakCalling