Job ID = 6368807 SRX = SRX5729149 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:29:19 prefetch.2.10.7: 1) Downloading 'SRR8949161'... 2020-06-16T00:29:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:30:34 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:30:35 prefetch.2.10.7: 'SRR8949161' is valid 2020-06-16T00:30:35 prefetch.2.10.7: 1) 'SRR8949161' was downloaded successfully 2020-06-16T00:30:35 prefetch.2.10.7: 'SRR8949161' has 0 unresolved dependencies Read 10378315 spots for SRR8949161/SRR8949161.sra Written 10378315 spots for SRR8949161/SRR8949161.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: 00:03:09 10378315 reads; of these: 10378315 (100.00%) were unpaired; of these: 856673 (8.25%) aligned 0 times 7817553 (75.33%) aligned exactly 1 time 1704089 (16.42%) aligned >1 times 91.75% overall alignment rate Time searching: 00:03:09 Overall time: 00:03:09 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] 808554 / 9521642 = 0.0849 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 09:37:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5729149/SRX5729149.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5729149/SRX5729149.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5729149/SRX5729149.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5729149/SRX5729149.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 09:37:10: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:37:10: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:37:16: 1000000 INFO @ Tue, 16 Jun 2020 09:37:22: 2000000 INFO @ Tue, 16 Jun 2020 09:37:28: 3000000 INFO @ Tue, 16 Jun 2020 09:37:33: 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 09:37:39: 5000000 INFO @ Tue, 16 Jun 2020 09:37:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5729149/SRX5729149.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5729149/SRX5729149.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5729149/SRX5729149.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5729149/SRX5729149.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 09:37:41: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:37:41: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:37:46: 6000000 INFO @ Tue, 16 Jun 2020 09:37:48: 1000000 INFO @ Tue, 16 Jun 2020 09:37:52: 7000000 INFO @ Tue, 16 Jun 2020 09:37:54: 2000000 INFO @ Tue, 16 Jun 2020 09:37:59: 8000000 INFO @ Tue, 16 Jun 2020 09:38:01: 3000000 INFO @ Tue, 16 Jun 2020 09:38:03: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:38:03: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:38:03: #1 total tags in treatment: 8713088 INFO @ Tue, 16 Jun 2020 09:38:03: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:38:03: #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 09:38:04: #1 tags after filtering in treatment: 8713088 INFO @ Tue, 16 Jun 2020 09:38:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:38:04: #1 finished! INFO @ Tue, 16 Jun 2020 09:38:04: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:38:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:38:04: #2 number of paired peaks: 336 WARNING @ Tue, 16 Jun 2020 09:38:04: Fewer paired peaks (336) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 336 pairs to build model! INFO @ Tue, 16 Jun 2020 09:38:04: start model_add_line... INFO @ Tue, 16 Jun 2020 09:38:04: start X-correlation... INFO @ Tue, 16 Jun 2020 09:38:04: end of X-cor INFO @ Tue, 16 Jun 2020 09:38:04: #2 finished! INFO @ Tue, 16 Jun 2020 09:38:04: #2 predicted fragment length is 74 bps INFO @ Tue, 16 Jun 2020 09:38:04: #2 alternative fragment length(s) may be 4,74 bps INFO @ Tue, 16 Jun 2020 09:38:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5729149/SRX5729149.05_model.r WARNING @ Tue, 16 Jun 2020 09:38:04: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:38:04: #2 You may need to consider one of the other alternative d(s): 4,74 WARNING @ Tue, 16 Jun 2020 09:38:04: #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 09:38:04: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:38:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:38:07: 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 09:38:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5729149/SRX5729149.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5729149/SRX5729149.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5729149/SRX5729149.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5729149/SRX5729149.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 09:38:10: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:38:10: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:38:14: 5000000 INFO @ Tue, 16 Jun 2020 09:38:17: 1000000 INFO @ Tue, 16 Jun 2020 09:38:20: 6000000 INFO @ Tue, 16 Jun 2020 09:38:22: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:38:23: 2000000 INFO @ Tue, 16 Jun 2020 09:38:27: 7000000 INFO @ Tue, 16 Jun 2020 09:38:30: 3000000 INFO @ Tue, 16 Jun 2020 09:38:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5729149/SRX5729149.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:38:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5729149/SRX5729149.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:38:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5729149/SRX5729149.05_summits.bed INFO @ Tue, 16 Jun 2020 09:38:31: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1188 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:38:34: 8000000 INFO @ Tue, 16 Jun 2020 09:38:37: 4000000 INFO @ Tue, 16 Jun 2020 09:38:38: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:38:38: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:38:38: #1 total tags in treatment: 8713088 INFO @ Tue, 16 Jun 2020 09:38:38: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:38:38: #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 09:38:39: #1 tags after filtering in treatment: 8713088 INFO @ Tue, 16 Jun 2020 09:38:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:38:39: #1 finished! INFO @ Tue, 16 Jun 2020 09:38:39: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:38:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:38:39: #2 number of paired peaks: 336 WARNING @ Tue, 16 Jun 2020 09:38:39: Fewer paired peaks (336) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 336 pairs to build model! INFO @ Tue, 16 Jun 2020 09:38:39: start model_add_line... INFO @ Tue, 16 Jun 2020 09:38:39: start X-correlation... INFO @ Tue, 16 Jun 2020 09:38:39: end of X-cor INFO @ Tue, 16 Jun 2020 09:38:39: #2 finished! INFO @ Tue, 16 Jun 2020 09:38:39: #2 predicted fragment length is 74 bps INFO @ Tue, 16 Jun 2020 09:38:39: #2 alternative fragment length(s) may be 4,74 bps INFO @ Tue, 16 Jun 2020 09:38:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5729149/SRX5729149.10_model.r WARNING @ Tue, 16 Jun 2020 09:38:39: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:38:39: #2 You may need to consider one of the other alternative d(s): 4,74 WARNING @ Tue, 16 Jun 2020 09:38:39: #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 09:38:39: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:38:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:38:43: 5000000 INFO @ Tue, 16 Jun 2020 09:38:49: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:38:55: 7000000 INFO @ Tue, 16 Jun 2020 09:38:56: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:39:01: 8000000 INFO @ Tue, 16 Jun 2020 09:39:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5729149/SRX5729149.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:39:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5729149/SRX5729149.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:39:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5729149/SRX5729149.10_summits.bed INFO @ Tue, 16 Jun 2020 09:39:05: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (477 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:39:05: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:39:05: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:39:05: #1 total tags in treatment: 8713088 INFO @ Tue, 16 Jun 2020 09:39:05: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:39:05: #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 09:39:06: #1 tags after filtering in treatment: 8713088 INFO @ Tue, 16 Jun 2020 09:39:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:39:06: #1 finished! INFO @ Tue, 16 Jun 2020 09:39:06: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:39:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:39:06: #2 number of paired peaks: 336 WARNING @ Tue, 16 Jun 2020 09:39:06: Fewer paired peaks (336) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 336 pairs to build model! INFO @ Tue, 16 Jun 2020 09:39:06: start model_add_line... INFO @ Tue, 16 Jun 2020 09:39:06: start X-correlation... INFO @ Tue, 16 Jun 2020 09:39:06: end of X-cor INFO @ Tue, 16 Jun 2020 09:39:06: #2 finished! INFO @ Tue, 16 Jun 2020 09:39:06: #2 predicted fragment length is 74 bps INFO @ Tue, 16 Jun 2020 09:39:06: #2 alternative fragment length(s) may be 4,74 bps INFO @ Tue, 16 Jun 2020 09:39:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5729149/SRX5729149.20_model.r WARNING @ Tue, 16 Jun 2020 09:39:06: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:39:06: #2 You may need to consider one of the other alternative d(s): 4,74 WARNING @ Tue, 16 Jun 2020 09:39:06: #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 09:39:06: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:39:06: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:39:23: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:39:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5729149/SRX5729149.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:39:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5729149/SRX5729149.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:39:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5729149/SRX5729149.20_summits.bed INFO @ Tue, 16 Jun 2020 09:39:31: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (218 records, 4 fields): 2 millis CompletedMACS2peakCalling