Job ID = 6366886 SRX = SRX2543054 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:07:08 prefetch.2.10.7: 1) Downloading 'SRR5235990'... 2020-06-15T23:07:08 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:08:24 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:08:25 prefetch.2.10.7: 'SRR5235990' is valid 2020-06-15T23:08:25 prefetch.2.10.7: 1) 'SRR5235990' was downloaded successfully 2020-06-15T23:08:25 prefetch.2.10.7: 'SRR5235990' has 0 unresolved dependencies Read 17807102 spots for SRR5235990/SRR5235990.sra Written 17807102 spots for SRR5235990/SRR5235990.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: 00:06:28 17807102 reads; of these: 17807102 (100.00%) were unpaired; of these: 1007817 (5.66%) aligned 0 times 14568477 (81.81%) aligned exactly 1 time 2230808 (12.53%) aligned >1 times 94.34% overall alignment rate Time searching: 00:06:28 Overall time: 00:06:28 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] 3116367 / 16799285 = 0.1855 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 08:20:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2543054/SRX2543054.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2543054/SRX2543054.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2543054/SRX2543054.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2543054/SRX2543054.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 08:20:51: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:20:51: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:20:58: 1000000 INFO @ Tue, 16 Jun 2020 08:21:06: 2000000 INFO @ Tue, 16 Jun 2020 08:21:14: 3000000 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 08:21:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2543054/SRX2543054.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2543054/SRX2543054.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2543054/SRX2543054.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2543054/SRX2543054.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 08:21:19: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:21:19: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:21:21: 4000000 INFO @ Tue, 16 Jun 2020 08:21:26: 1000000 INFO @ Tue, 16 Jun 2020 08:21:29: 5000000 INFO @ Tue, 16 Jun 2020 08:21:33: 2000000 INFO @ Tue, 16 Jun 2020 08:21:36: 6000000 INFO @ Tue, 16 Jun 2020 08:21:40: 3000000 INFO @ Tue, 16 Jun 2020 08:21:44: 7000000 INFO @ Tue, 16 Jun 2020 08:21:47: 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 08:21:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2543054/SRX2543054.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2543054/SRX2543054.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2543054/SRX2543054.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2543054/SRX2543054.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 08:21:49: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:21:49: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:21:52: 8000000 INFO @ Tue, 16 Jun 2020 08:21:53: 5000000 INFO @ Tue, 16 Jun 2020 08:21:57: 1000000 INFO @ Tue, 16 Jun 2020 08:22:00: 6000000 INFO @ Tue, 16 Jun 2020 08:22:00: 9000000 INFO @ Tue, 16 Jun 2020 08:22:05: 2000000 INFO @ Tue, 16 Jun 2020 08:22:07: 7000000 INFO @ Tue, 16 Jun 2020 08:22:08: 10000000 INFO @ Tue, 16 Jun 2020 08:22:13: 3000000 INFO @ Tue, 16 Jun 2020 08:22:14: 8000000 INFO @ Tue, 16 Jun 2020 08:22:16: 11000000 INFO @ Tue, 16 Jun 2020 08:22:20: 4000000 INFO @ Tue, 16 Jun 2020 08:22:20: 9000000 INFO @ Tue, 16 Jun 2020 08:22:24: 12000000 INFO @ Tue, 16 Jun 2020 08:22:27: 10000000 INFO @ Tue, 16 Jun 2020 08:22:28: 5000000 INFO @ Tue, 16 Jun 2020 08:22:31: 13000000 INFO @ Tue, 16 Jun 2020 08:22:34: 11000000 INFO @ Tue, 16 Jun 2020 08:22:35: 6000000 INFO @ Tue, 16 Jun 2020 08:22:36: #1 tag size is determined as 75 bps INFO @ Tue, 16 Jun 2020 08:22:36: #1 tag size = 75 INFO @ Tue, 16 Jun 2020 08:22:36: #1 total tags in treatment: 13682918 INFO @ Tue, 16 Jun 2020 08:22:36: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:22:36: #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 08:22:37: #1 tags after filtering in treatment: 13682918 INFO @ Tue, 16 Jun 2020 08:22:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:22:37: #1 finished! INFO @ Tue, 16 Jun 2020 08:22:37: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:22:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:22:37: #2 number of paired peaks: 297 WARNING @ Tue, 16 Jun 2020 08:22:37: Fewer paired peaks (297) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 297 pairs to build model! INFO @ Tue, 16 Jun 2020 08:22:37: start model_add_line... INFO @ Tue, 16 Jun 2020 08:22:38: start X-correlation... INFO @ Tue, 16 Jun 2020 08:22:38: end of X-cor INFO @ Tue, 16 Jun 2020 08:22:38: #2 finished! INFO @ Tue, 16 Jun 2020 08:22:38: #2 predicted fragment length is 140 bps INFO @ Tue, 16 Jun 2020 08:22:38: #2 alternative fragment length(s) may be 4,140,150 bps INFO @ Tue, 16 Jun 2020 08:22:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2543054/SRX2543054.05_model.r WARNING @ Tue, 16 Jun 2020 08:22:38: #2 Since the d (140) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:22:38: #2 You may need to consider one of the other alternative d(s): 4,140,150 WARNING @ Tue, 16 Jun 2020 08:22:38: #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 08:22:38: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:22:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:22:41: 12000000 INFO @ Tue, 16 Jun 2020 08:22:43: 7000000 INFO @ Tue, 16 Jun 2020 08:22:47: 13000000 INFO @ Tue, 16 Jun 2020 08:22:50: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:22:52: #1 tag size is determined as 75 bps INFO @ Tue, 16 Jun 2020 08:22:52: #1 tag size = 75 INFO @ Tue, 16 Jun 2020 08:22:52: #1 total tags in treatment: 13682918 INFO @ Tue, 16 Jun 2020 08:22:52: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:22:52: #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 08:22:52: #1 tags after filtering in treatment: 13682918 INFO @ Tue, 16 Jun 2020 08:22:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:22:52: #1 finished! INFO @ Tue, 16 Jun 2020 08:22:52: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:22:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:22:53: #2 number of paired peaks: 297 WARNING @ Tue, 16 Jun 2020 08:22:53: Fewer paired peaks (297) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 297 pairs to build model! INFO @ Tue, 16 Jun 2020 08:22:53: start model_add_line... INFO @ Tue, 16 Jun 2020 08:22:53: start X-correlation... INFO @ Tue, 16 Jun 2020 08:22:53: end of X-cor INFO @ Tue, 16 Jun 2020 08:22:53: #2 finished! INFO @ Tue, 16 Jun 2020 08:22:53: #2 predicted fragment length is 140 bps INFO @ Tue, 16 Jun 2020 08:22:53: #2 alternative fragment length(s) may be 4,140,150 bps INFO @ Tue, 16 Jun 2020 08:22:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2543054/SRX2543054.10_model.r WARNING @ Tue, 16 Jun 2020 08:22:53: #2 Since the d (140) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:22:53: #2 You may need to consider one of the other alternative d(s): 4,140,150 WARNING @ Tue, 16 Jun 2020 08:22:53: #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 08:22:53: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:22:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:22:58: 9000000 INFO @ Tue, 16 Jun 2020 08:23:05: 10000000 INFO @ Tue, 16 Jun 2020 08:23:06: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:23:12: 11000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:23:19: 12000000 INFO @ Tue, 16 Jun 2020 08:23:21: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:23:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2543054/SRX2543054.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:23:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2543054/SRX2543054.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:23:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2543054/SRX2543054.05_summits.bed INFO @ Tue, 16 Jun 2020 08:23:21: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (5740 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:23:26: 13000000 INFO @ Tue, 16 Jun 2020 08:23:30: #1 tag size is determined as 75 bps INFO @ Tue, 16 Jun 2020 08:23:30: #1 tag size = 75 INFO @ Tue, 16 Jun 2020 08:23:30: #1 total tags in treatment: 13682918 INFO @ Tue, 16 Jun 2020 08:23:30: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:23:30: #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 08:23:30: #1 tags after filtering in treatment: 13682918 INFO @ Tue, 16 Jun 2020 08:23:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:23:30: #1 finished! INFO @ Tue, 16 Jun 2020 08:23:30: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:23:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:23:31: #2 number of paired peaks: 297 WARNING @ Tue, 16 Jun 2020 08:23:31: Fewer paired peaks (297) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 297 pairs to build model! INFO @ Tue, 16 Jun 2020 08:23:31: start model_add_line... INFO @ Tue, 16 Jun 2020 08:23:31: start X-correlation... INFO @ Tue, 16 Jun 2020 08:23:31: end of X-cor INFO @ Tue, 16 Jun 2020 08:23:31: #2 finished! INFO @ Tue, 16 Jun 2020 08:23:31: #2 predicted fragment length is 140 bps INFO @ Tue, 16 Jun 2020 08:23:31: #2 alternative fragment length(s) may be 4,140,150 bps INFO @ Tue, 16 Jun 2020 08:23:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2543054/SRX2543054.20_model.r WARNING @ Tue, 16 Jun 2020 08:23:31: #2 Since the d (140) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:23:31: #2 You may need to consider one of the other alternative d(s): 4,140,150 WARNING @ Tue, 16 Jun 2020 08:23:31: #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 08:23:31: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:23:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:23:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2543054/SRX2543054.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:23:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2543054/SRX2543054.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:23:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2543054/SRX2543054.10_summits.bed INFO @ Tue, 16 Jun 2020 08:23:35: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1845 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:24:01: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:24:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2543054/SRX2543054.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:24:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2543054/SRX2543054.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:24:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2543054/SRX2543054.20_summits.bed INFO @ Tue, 16 Jun 2020 08:24:15: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (340 records, 4 fields): 1 millis CompletedMACS2peakCalling