Job ID = 6368568 SRX = SRX5020794 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:23:18 prefetch.2.10.7: 1) Downloading 'SRR8201417'... 2020-06-16T00:23:18 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:24:51 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:24:51 prefetch.2.10.7: 'SRR8201417' is valid 2020-06-16T00:24:51 prefetch.2.10.7: 1) 'SRR8201417' was downloaded successfully 2020-06-16T00:24:51 prefetch.2.10.7: 'SRR8201417' has 0 unresolved dependencies Read 11496496 spots for SRR8201417/SRR8201417.sra Written 11496496 spots for SRR8201417/SRR8201417.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: 00:02:32 11496496 reads; of these: 11496496 (100.00%) were unpaired; of these: 226307 (1.97%) aligned 0 times 9484996 (82.50%) aligned exactly 1 time 1785193 (15.53%) aligned >1 times 98.03% overall alignment rate Time searching: 00:02:32 Overall time: 00:02:32 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] 796457 / 11270189 = 0.0707 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 09:31:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020794/SRX5020794.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020794/SRX5020794.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020794/SRX5020794.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020794/SRX5020794.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 09:31:01: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:31:01: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:31:07: 1000000 INFO @ Tue, 16 Jun 2020 09:31:12: 2000000 INFO @ Tue, 16 Jun 2020 09:31:18: 3000000 INFO @ Tue, 16 Jun 2020 09:31:23: 4000000 INFO @ Tue, 16 Jun 2020 09:31:29: 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 09:31:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020794/SRX5020794.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020794/SRX5020794.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020794/SRX5020794.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020794/SRX5020794.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 09:31:33: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:31:33: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:31:35: 6000000 INFO @ Tue, 16 Jun 2020 09:31:40: 1000000 INFO @ Tue, 16 Jun 2020 09:31:41: 7000000 INFO @ Tue, 16 Jun 2020 09:31:47: 2000000 INFO @ Tue, 16 Jun 2020 09:31:48: 8000000 INFO @ Tue, 16 Jun 2020 09:31:53: 3000000 INFO @ Tue, 16 Jun 2020 09:31:54: 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 09:32:00: 4000000 INFO @ Tue, 16 Jun 2020 09:32:01: 10000000 INFO @ Tue, 16 Jun 2020 09:32:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020794/SRX5020794.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020794/SRX5020794.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020794/SRX5020794.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020794/SRX5020794.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 09:32:01: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:32:01: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:32:04: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:32:04: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:32:04: #1 total tags in treatment: 10473732 INFO @ Tue, 16 Jun 2020 09:32:04: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:32:04: #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 09:32:04: #1 tags after filtering in treatment: 10473732 INFO @ Tue, 16 Jun 2020 09:32:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:32:04: #1 finished! INFO @ Tue, 16 Jun 2020 09:32:04: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:32:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:32:04: #2 number of paired peaks: 278 WARNING @ Tue, 16 Jun 2020 09:32:04: Fewer paired peaks (278) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 278 pairs to build model! INFO @ Tue, 16 Jun 2020 09:32:04: start model_add_line... INFO @ Tue, 16 Jun 2020 09:32:05: start X-correlation... INFO @ Tue, 16 Jun 2020 09:32:05: end of X-cor INFO @ Tue, 16 Jun 2020 09:32:05: #2 finished! INFO @ Tue, 16 Jun 2020 09:32:05: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 09:32:05: #2 alternative fragment length(s) may be 2,49,551 bps INFO @ Tue, 16 Jun 2020 09:32:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020794/SRX5020794.05_model.r WARNING @ Tue, 16 Jun 2020 09:32:05: #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 09:32:05: #2 You may need to consider one of the other alternative d(s): 2,49,551 WARNING @ Tue, 16 Jun 2020 09:32:05: #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 09:32:05: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:32:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:32:07: 5000000 INFO @ Tue, 16 Jun 2020 09:32:08: 1000000 INFO @ Tue, 16 Jun 2020 09:32:13: 6000000 INFO @ Tue, 16 Jun 2020 09:32:15: 2000000 INFO @ Tue, 16 Jun 2020 09:32:20: 7000000 INFO @ Tue, 16 Jun 2020 09:32:21: 3000000 INFO @ Tue, 16 Jun 2020 09:32:23: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:32:27: 8000000 INFO @ Tue, 16 Jun 2020 09:32:28: 4000000 INFO @ Tue, 16 Jun 2020 09:32:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020794/SRX5020794.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:32:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020794/SRX5020794.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:32:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020794/SRX5020794.05_summits.bed INFO @ Tue, 16 Jun 2020 09:32:33: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (637 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:32:33: 9000000 INFO @ Tue, 16 Jun 2020 09:32:34: 5000000 INFO @ Tue, 16 Jun 2020 09:32:40: 10000000 INFO @ Tue, 16 Jun 2020 09:32:41: 6000000 INFO @ Tue, 16 Jun 2020 09:32:43: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:32:43: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:32:43: #1 total tags in treatment: 10473732 INFO @ Tue, 16 Jun 2020 09:32:43: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:32:43: #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 09:32:43: #1 tags after filtering in treatment: 10473732 INFO @ Tue, 16 Jun 2020 09:32:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:32:43: #1 finished! INFO @ Tue, 16 Jun 2020 09:32:43: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:32:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:32:44: #2 number of paired peaks: 278 WARNING @ Tue, 16 Jun 2020 09:32:44: Fewer paired peaks (278) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 278 pairs to build model! INFO @ Tue, 16 Jun 2020 09:32:44: start model_add_line... INFO @ Tue, 16 Jun 2020 09:32:44: start X-correlation... INFO @ Tue, 16 Jun 2020 09:32:44: end of X-cor INFO @ Tue, 16 Jun 2020 09:32:44: #2 finished! INFO @ Tue, 16 Jun 2020 09:32:44: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 09:32:44: #2 alternative fragment length(s) may be 2,49,551 bps INFO @ Tue, 16 Jun 2020 09:32:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020794/SRX5020794.10_model.r WARNING @ Tue, 16 Jun 2020 09:32:44: #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 09:32:44: #2 You may need to consider one of the other alternative d(s): 2,49,551 WARNING @ Tue, 16 Jun 2020 09:32:44: #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 09:32:44: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:32:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:32:47: 7000000 INFO @ Tue, 16 Jun 2020 09:32:53: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:32:59: 9000000 INFO @ Tue, 16 Jun 2020 09:33:03: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:33:04: 10000000 INFO @ Tue, 16 Jun 2020 09:33:07: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:33:07: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:33:07: #1 total tags in treatment: 10473732 INFO @ Tue, 16 Jun 2020 09:33:07: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:33:07: #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 09:33:07: #1 tags after filtering in treatment: 10473732 INFO @ Tue, 16 Jun 2020 09:33:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:33:07: #1 finished! INFO @ Tue, 16 Jun 2020 09:33:07: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:33:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:33:07: #2 number of paired peaks: 278 WARNING @ Tue, 16 Jun 2020 09:33:07: Fewer paired peaks (278) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 278 pairs to build model! INFO @ Tue, 16 Jun 2020 09:33:07: start model_add_line... INFO @ Tue, 16 Jun 2020 09:33:07: start X-correlation... INFO @ Tue, 16 Jun 2020 09:33:07: end of X-cor INFO @ Tue, 16 Jun 2020 09:33:07: #2 finished! INFO @ Tue, 16 Jun 2020 09:33:07: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 09:33:07: #2 alternative fragment length(s) may be 2,49,551 bps INFO @ Tue, 16 Jun 2020 09:33:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020794/SRX5020794.20_model.r WARNING @ Tue, 16 Jun 2020 09:33:07: #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 09:33:07: #2 You may need to consider one of the other alternative d(s): 2,49,551 WARNING @ Tue, 16 Jun 2020 09:33:07: #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 09:33:07: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:33:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:33:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020794/SRX5020794.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:33:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020794/SRX5020794.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:33:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020794/SRX5020794.10_summits.bed INFO @ Tue, 16 Jun 2020 09:33:13: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (347 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:33:27: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:33:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020794/SRX5020794.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:33:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020794/SRX5020794.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:33:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020794/SRX5020794.20_summits.bed INFO @ Tue, 16 Jun 2020 09:33:37: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (145 records, 4 fields): 1 millis CompletedMACS2peakCalling