Job ID = 6366889 SRX = SRX2543057 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:21:01 prefetch.2.10.7: 1) Downloading 'SRR5235993'... 2020-06-15T23:21:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:21:55 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:21:56 prefetch.2.10.7: 'SRR5235993' is valid 2020-06-15T23:21:56 prefetch.2.10.7: 1) 'SRR5235993' was downloaded successfully 2020-06-15T23:21:56 prefetch.2.10.7: 'SRR5235993' has 0 unresolved dependencies Read 15742744 spots for SRR5235993/SRR5235993.sra Written 15742744 spots for SRR5235993/SRR5235993.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: 00:06:53 15742744 reads; of these: 15742744 (100.00%) were unpaired; of these: 263780 (1.68%) aligned 0 times 12708430 (80.73%) aligned exactly 1 time 2770534 (17.60%) aligned >1 times 98.32% overall alignment rate Time searching: 00:06:53 Overall time: 00:06:53 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_sort_core] merging from 8 files... [bam_rmdupse_core] 2008961 / 15478964 = 0.1298 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 08:34:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2543057/SRX2543057.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2543057/SRX2543057.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2543057/SRX2543057.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2543057/SRX2543057.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 08:34:49: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:34:49: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:34:55: 1000000 INFO @ Tue, 16 Jun 2020 08:35:01: 2000000 INFO @ Tue, 16 Jun 2020 08:35:06: 3000000 INFO @ Tue, 16 Jun 2020 08:35:12: 4000000 INFO @ Tue, 16 Jun 2020 08:35:17: 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 08:35:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2543057/SRX2543057.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2543057/SRX2543057.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2543057/SRX2543057.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2543057/SRX2543057.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 08:35:19: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:35:19: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:35:23: 6000000 INFO @ Tue, 16 Jun 2020 08:35:26: 1000000 INFO @ Tue, 16 Jun 2020 08:35:29: 7000000 INFO @ Tue, 16 Jun 2020 08:35:32: 2000000 INFO @ Tue, 16 Jun 2020 08:35:35: 8000000 INFO @ Tue, 16 Jun 2020 08:35:38: 3000000 INFO @ Tue, 16 Jun 2020 08:35:42: 9000000 INFO @ Tue, 16 Jun 2020 08:35:44: 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 08:35:48: 10000000 INFO @ Tue, 16 Jun 2020 08:35:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2543057/SRX2543057.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2543057/SRX2543057.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2543057/SRX2543057.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2543057/SRX2543057.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 08:35:50: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:35:50: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:35:50: 5000000 INFO @ Tue, 16 Jun 2020 08:35:54: 11000000 INFO @ Tue, 16 Jun 2020 08:35:56: 1000000 INFO @ Tue, 16 Jun 2020 08:35:57: 6000000 INFO @ Tue, 16 Jun 2020 08:36:01: 12000000 INFO @ Tue, 16 Jun 2020 08:36:03: 2000000 INFO @ Tue, 16 Jun 2020 08:36:04: 7000000 INFO @ Tue, 16 Jun 2020 08:36:07: 13000000 INFO @ Tue, 16 Jun 2020 08:36:10: 3000000 INFO @ Tue, 16 Jun 2020 08:36:10: 8000000 INFO @ Tue, 16 Jun 2020 08:36:11: #1 tag size is determined as 75 bps INFO @ Tue, 16 Jun 2020 08:36:11: #1 tag size = 75 INFO @ Tue, 16 Jun 2020 08:36:11: #1 total tags in treatment: 13470003 INFO @ Tue, 16 Jun 2020 08:36:11: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:36:11: #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 08:36:11: #1 tags after filtering in treatment: 13470003 INFO @ Tue, 16 Jun 2020 08:36:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:36:11: #1 finished! INFO @ Tue, 16 Jun 2020 08:36:11: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:36:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:36:12: #2 number of paired peaks: 273 WARNING @ Tue, 16 Jun 2020 08:36:12: Fewer paired peaks (273) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 273 pairs to build model! INFO @ Tue, 16 Jun 2020 08:36:12: start model_add_line... INFO @ Tue, 16 Jun 2020 08:36:12: start X-correlation... INFO @ Tue, 16 Jun 2020 08:36:12: end of X-cor INFO @ Tue, 16 Jun 2020 08:36:12: #2 finished! INFO @ Tue, 16 Jun 2020 08:36:12: #2 predicted fragment length is 72 bps INFO @ Tue, 16 Jun 2020 08:36:12: #2 alternative fragment length(s) may be 3,59,72,572 bps INFO @ Tue, 16 Jun 2020 08:36:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2543057/SRX2543057.05_model.r WARNING @ Tue, 16 Jun 2020 08:36:12: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:36:12: #2 You may need to consider one of the other alternative d(s): 3,59,72,572 WARNING @ Tue, 16 Jun 2020 08:36:12: #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 08:36:12: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:36:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:36:16: 4000000 INFO @ Tue, 16 Jun 2020 08:36:16: 9000000 INFO @ Tue, 16 Jun 2020 08:36:22: 5000000 INFO @ Tue, 16 Jun 2020 08:36:22: 10000000 INFO @ Tue, 16 Jun 2020 08:36:28: 11000000 INFO @ Tue, 16 Jun 2020 08:36:28: 6000000 INFO @ Tue, 16 Jun 2020 08:36:35: 12000000 INFO @ Tue, 16 Jun 2020 08:36:35: 7000000 INFO @ Tue, 16 Jun 2020 08:36:36: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:36:41: 13000000 INFO @ Tue, 16 Jun 2020 08:36:41: 8000000 INFO @ Tue, 16 Jun 2020 08:36:44: #1 tag size is determined as 75 bps INFO @ Tue, 16 Jun 2020 08:36:44: #1 tag size = 75 INFO @ Tue, 16 Jun 2020 08:36:44: #1 total tags in treatment: 13470003 INFO @ Tue, 16 Jun 2020 08:36:44: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:36:44: #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 08:36:44: #1 tags after filtering in treatment: 13470003 INFO @ Tue, 16 Jun 2020 08:36:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:36:44: #1 finished! INFO @ Tue, 16 Jun 2020 08:36:44: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:36:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:36:45: #2 number of paired peaks: 273 WARNING @ Tue, 16 Jun 2020 08:36:45: Fewer paired peaks (273) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 273 pairs to build model! INFO @ Tue, 16 Jun 2020 08:36:45: start model_add_line... INFO @ Tue, 16 Jun 2020 08:36:45: start X-correlation... INFO @ Tue, 16 Jun 2020 08:36:45: end of X-cor INFO @ Tue, 16 Jun 2020 08:36:45: #2 finished! INFO @ Tue, 16 Jun 2020 08:36:45: #2 predicted fragment length is 72 bps INFO @ Tue, 16 Jun 2020 08:36:45: #2 alternative fragment length(s) may be 3,59,72,572 bps INFO @ Tue, 16 Jun 2020 08:36:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2543057/SRX2543057.10_model.r WARNING @ Tue, 16 Jun 2020 08:36:45: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:36:45: #2 You may need to consider one of the other alternative d(s): 3,59,72,572 WARNING @ Tue, 16 Jun 2020 08:36:45: #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 08:36:45: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:36:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:36:47: 9000000 INFO @ Tue, 16 Jun 2020 08:36:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2543057/SRX2543057.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:36:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2543057/SRX2543057.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:36:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2543057/SRX2543057.05_summits.bed INFO @ Tue, 16 Jun 2020 08:36:48: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (647 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:36:52: 10000000 INFO @ Tue, 16 Jun 2020 08:36:58: 11000000 INFO @ Tue, 16 Jun 2020 08:37:03: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:37:09: 13000000 INFO @ Tue, 16 Jun 2020 08:37:09: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:37:11: #1 tag size is determined as 75 bps INFO @ Tue, 16 Jun 2020 08:37:11: #1 tag size = 75 INFO @ Tue, 16 Jun 2020 08:37:11: #1 total tags in treatment: 13470003 INFO @ Tue, 16 Jun 2020 08:37:11: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:37:11: #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 08:37:12: #1 tags after filtering in treatment: 13470003 INFO @ Tue, 16 Jun 2020 08:37:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:37:12: #1 finished! INFO @ Tue, 16 Jun 2020 08:37:12: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:37:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:37:13: #2 number of paired peaks: 273 WARNING @ Tue, 16 Jun 2020 08:37:13: Fewer paired peaks (273) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 273 pairs to build model! INFO @ Tue, 16 Jun 2020 08:37:13: start model_add_line... INFO @ Tue, 16 Jun 2020 08:37:13: start X-correlation... INFO @ Tue, 16 Jun 2020 08:37:13: end of X-cor INFO @ Tue, 16 Jun 2020 08:37:13: #2 finished! INFO @ Tue, 16 Jun 2020 08:37:13: #2 predicted fragment length is 72 bps INFO @ Tue, 16 Jun 2020 08:37:13: #2 alternative fragment length(s) may be 3,59,72,572 bps INFO @ Tue, 16 Jun 2020 08:37:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2543057/SRX2543057.20_model.r WARNING @ Tue, 16 Jun 2020 08:37:13: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:37:13: #2 You may need to consider one of the other alternative d(s): 3,59,72,572 WARNING @ Tue, 16 Jun 2020 08:37:13: #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 08:37:13: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:37:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:37:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2543057/SRX2543057.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:37:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2543057/SRX2543057.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:37:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2543057/SRX2543057.10_summits.bed INFO @ Tue, 16 Jun 2020 08:37:21: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (427 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:37:37: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:37:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2543057/SRX2543057.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:37:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2543057/SRX2543057.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:37:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2543057/SRX2543057.20_summits.bed INFO @ Tue, 16 Jun 2020 08:37:48: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (218 records, 4 fields): 1 millis CompletedMACS2peakCalling