Job ID = 6367040 SRX = SRX2761385 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:16:01 prefetch.2.10.7: 1) Downloading 'SRR5476959'... 2020-06-15T23:16:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:17:41 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:17:42 prefetch.2.10.7: 'SRR5476959' is valid 2020-06-15T23:17:42 prefetch.2.10.7: 1) 'SRR5476959' was downloaded successfully Read 9606069 spots for SRR5476959/SRR5476959.sra Written 9606069 spots for SRR5476959/SRR5476959.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: 00:02:19 9606069 reads; of these: 9606069 (100.00%) were unpaired; of these: 1226570 (12.77%) aligned 0 times 6506782 (67.74%) aligned exactly 1 time 1872717 (19.50%) aligned >1 times 87.23% overall alignment rate Time searching: 00:02:19 Overall time: 00:02:19 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] 837348 / 8379499 = 0.0999 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 08:23:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2761385/SRX2761385.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2761385/SRX2761385.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2761385/SRX2761385.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2761385/SRX2761385.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 08:23:10: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:23:10: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:23:16: 1000000 INFO @ Tue, 16 Jun 2020 08:23:23: 2000000 INFO @ Tue, 16 Jun 2020 08:23:29: 3000000 INFO @ Tue, 16 Jun 2020 08:23:35: 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 08:23:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2761385/SRX2761385.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2761385/SRX2761385.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2761385/SRX2761385.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2761385/SRX2761385.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 08:23:40: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:23:40: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:23:42: 5000000 INFO @ Tue, 16 Jun 2020 08:23:46: 1000000 INFO @ Tue, 16 Jun 2020 08:23:48: 6000000 INFO @ Tue, 16 Jun 2020 08:23:52: 2000000 INFO @ Tue, 16 Jun 2020 08:23:55: 7000000 INFO @ Tue, 16 Jun 2020 08:23:58: 3000000 INFO @ Tue, 16 Jun 2020 08:23:58: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:23:58: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:23:58: #1 total tags in treatment: 7542151 INFO @ Tue, 16 Jun 2020 08:23:58: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:23:58: #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 08:23:59: #1 tags after filtering in treatment: 7542151 INFO @ Tue, 16 Jun 2020 08:23:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:23:59: #1 finished! INFO @ Tue, 16 Jun 2020 08:23:59: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:23:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:23:59: #2 number of paired peaks: 544 WARNING @ Tue, 16 Jun 2020 08:23:59: Fewer paired peaks (544) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 544 pairs to build model! INFO @ Tue, 16 Jun 2020 08:23:59: start model_add_line... INFO @ Tue, 16 Jun 2020 08:23:59: start X-correlation... INFO @ Tue, 16 Jun 2020 08:23:59: end of X-cor INFO @ Tue, 16 Jun 2020 08:23:59: #2 finished! INFO @ Tue, 16 Jun 2020 08:23:59: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 08:23:59: #2 alternative fragment length(s) may be 3,49 bps INFO @ Tue, 16 Jun 2020 08:23:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2761385/SRX2761385.05_model.r WARNING @ Tue, 16 Jun 2020 08:23:59: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:23:59: #2 You may need to consider one of the other alternative d(s): 3,49 WARNING @ Tue, 16 Jun 2020 08:23:59: #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 08:23:59: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:23:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:24:04: 4000000 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 08:24:09: 5000000 INFO @ Tue, 16 Jun 2020 08:24:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2761385/SRX2761385.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2761385/SRX2761385.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2761385/SRX2761385.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2761385/SRX2761385.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 08:24:10: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:24:10: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:24:16: 6000000 INFO @ Tue, 16 Jun 2020 08:24:16: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:24:17: 1000000 INFO @ Tue, 16 Jun 2020 08:24:22: 7000000 INFO @ Tue, 16 Jun 2020 08:24:24: 2000000 INFO @ Tue, 16 Jun 2020 08:24:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2761385/SRX2761385.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:24:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2761385/SRX2761385.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:24:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2761385/SRX2761385.05_summits.bed INFO @ Tue, 16 Jun 2020 08:24:25: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (669 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:24:25: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:24:25: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:24:25: #1 total tags in treatment: 7542151 INFO @ Tue, 16 Jun 2020 08:24:25: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:24:25: #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 08:24:25: #1 tags after filtering in treatment: 7542151 INFO @ Tue, 16 Jun 2020 08:24:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:24:25: #1 finished! INFO @ Tue, 16 Jun 2020 08:24:25: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:24:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:24:26: #2 number of paired peaks: 544 WARNING @ Tue, 16 Jun 2020 08:24:26: Fewer paired peaks (544) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 544 pairs to build model! INFO @ Tue, 16 Jun 2020 08:24:26: start model_add_line... INFO @ Tue, 16 Jun 2020 08:24:26: start X-correlation... INFO @ Tue, 16 Jun 2020 08:24:26: end of X-cor INFO @ Tue, 16 Jun 2020 08:24:26: #2 finished! INFO @ Tue, 16 Jun 2020 08:24:26: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 08:24:26: #2 alternative fragment length(s) may be 3,49 bps INFO @ Tue, 16 Jun 2020 08:24:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2761385/SRX2761385.10_model.r WARNING @ Tue, 16 Jun 2020 08:24:26: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:24:26: #2 You may need to consider one of the other alternative d(s): 3,49 WARNING @ Tue, 16 Jun 2020 08:24:26: #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 08:24:26: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:24:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:24:30: 3000000 INFO @ Tue, 16 Jun 2020 08:24:37: 4000000 INFO @ Tue, 16 Jun 2020 08:24:43: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:24:44: 5000000 INFO @ Tue, 16 Jun 2020 08:24:51: 6000000 INFO @ Tue, 16 Jun 2020 08:24:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2761385/SRX2761385.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:24:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2761385/SRX2761385.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:24:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2761385/SRX2761385.10_summits.bed INFO @ Tue, 16 Jun 2020 08:24:52: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (458 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:24:58: 7000000 INFO @ Tue, 16 Jun 2020 08:25:02: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:25:02: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:25:02: #1 total tags in treatment: 7542151 INFO @ Tue, 16 Jun 2020 08:25:02: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:25:02: #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 08:25:02: #1 tags after filtering in treatment: 7542151 INFO @ Tue, 16 Jun 2020 08:25:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:25:02: #1 finished! INFO @ Tue, 16 Jun 2020 08:25:02: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:25:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:25:02: #2 number of paired peaks: 544 WARNING @ Tue, 16 Jun 2020 08:25:02: Fewer paired peaks (544) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 544 pairs to build model! INFO @ Tue, 16 Jun 2020 08:25:02: start model_add_line... INFO @ Tue, 16 Jun 2020 08:25:02: start X-correlation... INFO @ Tue, 16 Jun 2020 08:25:02: end of X-cor INFO @ Tue, 16 Jun 2020 08:25:02: #2 finished! INFO @ Tue, 16 Jun 2020 08:25:02: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 08:25:02: #2 alternative fragment length(s) may be 3,49 bps INFO @ Tue, 16 Jun 2020 08:25:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2761385/SRX2761385.20_model.r WARNING @ Tue, 16 Jun 2020 08:25:02: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:25:02: #2 You may need to consider one of the other alternative d(s): 3,49 WARNING @ Tue, 16 Jun 2020 08:25:02: #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 08:25:02: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:25:02: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:25:20: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:25:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2761385/SRX2761385.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:25:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2761385/SRX2761385.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:25:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2761385/SRX2761385.20_summits.bed INFO @ Tue, 16 Jun 2020 08:25:29: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (184 records, 4 fields): 1 millis CompletedMACS2peakCalling