Job ID = 6367989 SRX = SRX463081 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:04:45 prefetch.2.10.7: 1) Downloading 'SRR1159143'... 2020-06-16T00:04:45 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:07:15 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:07:16 prefetch.2.10.7: 'SRR1159143' is valid 2020-06-16T00:07:16 prefetch.2.10.7: 1) 'SRR1159143' was downloaded successfully Read 19555555 spots for SRR1159143/SRR1159143.sra Written 19555555 spots for SRR1159143/SRR1159143.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: 00:02:26 19555555 reads; of these: 19555555 (100.00%) were unpaired; of these: 8711943 (44.55%) aligned 0 times 9074750 (46.40%) aligned exactly 1 time 1768862 (9.05%) aligned >1 times 55.45% overall alignment rate Time searching: 00:02:26 Overall time: 00:02:26 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] 648341 / 10843612 = 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 09:13:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX463081/SRX463081.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX463081/SRX463081.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX463081/SRX463081.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX463081/SRX463081.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 09:13:24: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:13:24: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:13:30: 1000000 INFO @ Tue, 16 Jun 2020 09:13:35: 2000000 INFO @ Tue, 16 Jun 2020 09:13:41: 3000000 INFO @ Tue, 16 Jun 2020 09:13:46: 4000000 INFO @ Tue, 16 Jun 2020 09:13:52: 5000000 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 09:13:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX463081/SRX463081.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX463081/SRX463081.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX463081/SRX463081.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX463081/SRX463081.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 09:13:54: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:13:54: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:13:58: 6000000 INFO @ Tue, 16 Jun 2020 09:14:00: 1000000 INFO @ Tue, 16 Jun 2020 09:14:04: 7000000 INFO @ Tue, 16 Jun 2020 09:14:06: 2000000 INFO @ Tue, 16 Jun 2020 09:14:10: 8000000 INFO @ Tue, 16 Jun 2020 09:14:12: 3000000 INFO @ Tue, 16 Jun 2020 09:14:16: 9000000 INFO @ Tue, 16 Jun 2020 09:14:18: 4000000 INFO @ Tue, 16 Jun 2020 09:14:22: 10000000 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 09:14:23: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:14:23: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:14:23: #1 total tags in treatment: 10195271 INFO @ Tue, 16 Jun 2020 09:14:23: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:14:23: #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 09:14:23: #1 tags after filtering in treatment: 10195271 INFO @ Tue, 16 Jun 2020 09:14:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:14:23: #1 finished! INFO @ Tue, 16 Jun 2020 09:14:23: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:14:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:14:24: 5000000 INFO @ Tue, 16 Jun 2020 09:14:24: #2 number of paired peaks: 253 WARNING @ Tue, 16 Jun 2020 09:14:24: 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 09:14:24: start model_add_line... INFO @ Tue, 16 Jun 2020 09:14:24: start X-correlation... INFO @ Tue, 16 Jun 2020 09:14:24: end of X-cor INFO @ Tue, 16 Jun 2020 09:14:24: #2 finished! INFO @ Tue, 16 Jun 2020 09:14:24: #2 predicted fragment length is 31 bps INFO @ Tue, 16 Jun 2020 09:14:24: #2 alternative fragment length(s) may be 0,31 bps INFO @ Tue, 16 Jun 2020 09:14:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX463081/SRX463081.05_model.r INFO @ Tue, 16 Jun 2020 09:14:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX463081/SRX463081.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX463081/SRX463081.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX463081/SRX463081.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX463081/SRX463081.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 09:14:24: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:14:24: #1 read treatment tags... WARNING @ Tue, 16 Jun 2020 09:14:24: #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 09:14:24: #2 You may need to consider one of the other alternative d(s): 0,31 WARNING @ Tue, 16 Jun 2020 09:14:24: #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 09:14:24: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:14:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:14:30: 6000000 INFO @ Tue, 16 Jun 2020 09:14:30: 1000000 INFO @ Tue, 16 Jun 2020 09:14:36: 7000000 INFO @ Tue, 16 Jun 2020 09:14:36: 2000000 INFO @ Tue, 16 Jun 2020 09:14:42: 8000000 INFO @ Tue, 16 Jun 2020 09:14:42: 3000000 INFO @ Tue, 16 Jun 2020 09:14:45: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:14:48: 9000000 INFO @ Tue, 16 Jun 2020 09:14:48: 4000000 INFO @ Tue, 16 Jun 2020 09:14:54: 10000000 INFO @ Tue, 16 Jun 2020 09:14:54: 5000000 INFO @ Tue, 16 Jun 2020 09:14:55: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:14:55: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:14:55: #1 total tags in treatment: 10195271 INFO @ Tue, 16 Jun 2020 09:14:55: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:14:55: #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 09:14:55: #1 tags after filtering in treatment: 10195271 INFO @ Tue, 16 Jun 2020 09:14:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:14:55: #1 finished! INFO @ Tue, 16 Jun 2020 09:14:55: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:14:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:14:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX463081/SRX463081.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:14:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX463081/SRX463081.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:14:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX463081/SRX463081.05_summits.bed INFO @ Tue, 16 Jun 2020 09:14:55: Done! INFO @ Tue, 16 Jun 2020 09:14:56: #2 number of paired peaks: 253 WARNING @ Tue, 16 Jun 2020 09:14:56: 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 09:14:56: start model_add_line... INFO @ Tue, 16 Jun 2020 09:14:56: start X-correlation... INFO @ Tue, 16 Jun 2020 09:14:56: end of X-cor INFO @ Tue, 16 Jun 2020 09:14:56: #2 finished! INFO @ Tue, 16 Jun 2020 09:14:56: #2 predicted fragment length is 31 bps INFO @ Tue, 16 Jun 2020 09:14:56: #2 alternative fragment length(s) may be 0,31 bps INFO @ Tue, 16 Jun 2020 09:14:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX463081/SRX463081.10_model.r WARNING @ Tue, 16 Jun 2020 09:14:56: #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 09:14:56: #2 You may need to consider one of the other alternative d(s): 0,31 WARNING @ Tue, 16 Jun 2020 09:14:56: #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 09:14:56: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:14:56: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (568 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:15:00: 6000000 INFO @ Tue, 16 Jun 2020 09:15:05: 7000000 INFO @ Tue, 16 Jun 2020 09:15:11: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:15:17: 9000000 INFO @ Tue, 16 Jun 2020 09:15:17: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:15:22: 10000000 INFO @ Tue, 16 Jun 2020 09:15:24: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:15:24: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:15:24: #1 total tags in treatment: 10195271 INFO @ Tue, 16 Jun 2020 09:15:24: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:15:24: #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 09:15:24: #1 tags after filtering in treatment: 10195271 INFO @ Tue, 16 Jun 2020 09:15:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:15:24: #1 finished! INFO @ Tue, 16 Jun 2020 09:15:24: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:15:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:15:24: #2 number of paired peaks: 253 WARNING @ Tue, 16 Jun 2020 09:15:24: 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 09:15:24: start model_add_line... INFO @ Tue, 16 Jun 2020 09:15:25: start X-correlation... INFO @ Tue, 16 Jun 2020 09:15:25: end of X-cor INFO @ Tue, 16 Jun 2020 09:15:25: #2 finished! INFO @ Tue, 16 Jun 2020 09:15:25: #2 predicted fragment length is 31 bps INFO @ Tue, 16 Jun 2020 09:15:25: #2 alternative fragment length(s) may be 0,31 bps INFO @ Tue, 16 Jun 2020 09:15:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX463081/SRX463081.20_model.r WARNING @ Tue, 16 Jun 2020 09:15:25: #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 09:15:25: #2 You may need to consider one of the other alternative d(s): 0,31 WARNING @ Tue, 16 Jun 2020 09:15:25: #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 09:15:25: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:15:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:15:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX463081/SRX463081.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:15:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX463081/SRX463081.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:15:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX463081/SRX463081.10_summits.bed INFO @ Tue, 16 Jun 2020 09:15:28: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (259 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:15:45: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:15:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX463081/SRX463081.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:15:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX463081/SRX463081.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:15:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX463081/SRX463081.20_summits.bed INFO @ Tue, 16 Jun 2020 09:15:56: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (59 records, 4 fields): 0 millis CompletedMACS2peakCalling