Job ID = 6366990 SRX = SRX257689 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:13:46 prefetch.2.10.7: 1) Downloading 'SRR800705'... 2020-06-15T23:13:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:14:38 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:14:38 prefetch.2.10.7: 'SRR800705' is valid 2020-06-15T23:14:38 prefetch.2.10.7: 1) 'SRR800705' was downloaded successfully Read 9567130 spots for SRR800705/SRR800705.sra Written 9567130 spots for SRR800705/SRR800705.sra 2020-06-15T23:15:19 prefetch.2.10.7: 1) Downloading 'SRR800706'... 2020-06-15T23:15:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:16:57 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:16:58 prefetch.2.10.7: 'SRR800706' is valid 2020-06-15T23:16:58 prefetch.2.10.7: 1) 'SRR800706' was downloaded successfully Read 11761129 spots for SRR800706/SRR800706.sra Written 11761129 spots for SRR800706/SRR800706.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: 00:04:06 21328259 reads; of these: 21328259 (100.00%) were unpaired; of these: 5938733 (27.84%) aligned 0 times 12790024 (59.97%) aligned exactly 1 time 2599502 (12.19%) aligned >1 times 72.16% overall alignment rate Time searching: 00:04:06 Overall time: 00:04:06 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] 10372697 / 15389526 = 0.6740 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 08:25:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257689/SRX257689.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257689/SRX257689.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257689/SRX257689.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257689/SRX257689.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 08:25:17: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:25:17: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:25:24: 1000000 INFO @ Tue, 16 Jun 2020 08:25:31: 2000000 INFO @ Tue, 16 Jun 2020 08:25:38: 3000000 INFO @ Tue, 16 Jun 2020 08:25:45: 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 08:25:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257689/SRX257689.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257689/SRX257689.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257689/SRX257689.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257689/SRX257689.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 08:25:47: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:25:47: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:25:52: 5000000 INFO @ Tue, 16 Jun 2020 08:25:53: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:25:53: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:25:53: #1 total tags in treatment: 5016829 INFO @ Tue, 16 Jun 2020 08:25:53: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:25:53: #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 08:25:53: #1 tags after filtering in treatment: 5016829 INFO @ Tue, 16 Jun 2020 08:25:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:25:53: #1 finished! INFO @ Tue, 16 Jun 2020 08:25:53: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:25:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:25:53: #2 number of paired peaks: 656 WARNING @ Tue, 16 Jun 2020 08:25:53: Fewer paired peaks (656) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 656 pairs to build model! INFO @ Tue, 16 Jun 2020 08:25:53: start model_add_line... INFO @ Tue, 16 Jun 2020 08:25:53: start X-correlation... INFO @ Tue, 16 Jun 2020 08:25:53: end of X-cor INFO @ Tue, 16 Jun 2020 08:25:53: #2 finished! INFO @ Tue, 16 Jun 2020 08:25:53: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 08:25:53: #2 alternative fragment length(s) may be 4,49,567,569 bps INFO @ Tue, 16 Jun 2020 08:25:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257689/SRX257689.05_model.r WARNING @ Tue, 16 Jun 2020 08:25:53: #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 08:25:53: #2 You may need to consider one of the other alternative d(s): 4,49,567,569 WARNING @ Tue, 16 Jun 2020 08:25:53: #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 08:25:53: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:25:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:25:54: 1000000 INFO @ Tue, 16 Jun 2020 08:26:00: 2000000 INFO @ Tue, 16 Jun 2020 08:26:04: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:26:06: 3000000 INFO @ Tue, 16 Jun 2020 08:26:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257689/SRX257689.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:26:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257689/SRX257689.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:26:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257689/SRX257689.05_summits.bed INFO @ Tue, 16 Jun 2020 08:26:10: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (773 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:26:13: 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 08:26:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257689/SRX257689.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257689/SRX257689.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257689/SRX257689.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257689/SRX257689.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 08:26:17: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:26:17: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:26:19: 5000000 INFO @ Tue, 16 Jun 2020 08:26:19: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:26:19: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:26:19: #1 total tags in treatment: 5016829 INFO @ Tue, 16 Jun 2020 08:26:19: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:26:19: #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 08:26:19: #1 tags after filtering in treatment: 5016829 INFO @ Tue, 16 Jun 2020 08:26:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:26:19: #1 finished! INFO @ Tue, 16 Jun 2020 08:26:19: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:26:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:26:19: #2 number of paired peaks: 656 WARNING @ Tue, 16 Jun 2020 08:26:19: Fewer paired peaks (656) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 656 pairs to build model! INFO @ Tue, 16 Jun 2020 08:26:19: start model_add_line... INFO @ Tue, 16 Jun 2020 08:26:20: start X-correlation... INFO @ Tue, 16 Jun 2020 08:26:20: end of X-cor INFO @ Tue, 16 Jun 2020 08:26:20: #2 finished! INFO @ Tue, 16 Jun 2020 08:26:20: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 08:26:20: #2 alternative fragment length(s) may be 4,49,567,569 bps INFO @ Tue, 16 Jun 2020 08:26:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257689/SRX257689.10_model.r WARNING @ Tue, 16 Jun 2020 08:26:20: #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 08:26:20: #2 You may need to consider one of the other alternative d(s): 4,49,567,569 WARNING @ Tue, 16 Jun 2020 08:26:20: #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 08:26:20: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:26:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:26:23: 1000000 INFO @ Tue, 16 Jun 2020 08:26:29: 2000000 INFO @ Tue, 16 Jun 2020 08:26:31: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:26:35: 3000000 INFO @ Tue, 16 Jun 2020 08:26:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257689/SRX257689.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:26:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257689/SRX257689.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:26:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257689/SRX257689.10_summits.bed INFO @ Tue, 16 Jun 2020 08:26:36: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (550 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:26:41: 4000000 INFO @ Tue, 16 Jun 2020 08:26:47: 5000000 INFO @ Tue, 16 Jun 2020 08:26:47: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:26:47: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:26:47: #1 total tags in treatment: 5016829 INFO @ Tue, 16 Jun 2020 08:26:47: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:26:47: #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 08:26:47: #1 tags after filtering in treatment: 5016829 INFO @ Tue, 16 Jun 2020 08:26:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:26:47: #1 finished! INFO @ Tue, 16 Jun 2020 08:26:47: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:26:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:26:48: #2 number of paired peaks: 656 WARNING @ Tue, 16 Jun 2020 08:26:48: Fewer paired peaks (656) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 656 pairs to build model! INFO @ Tue, 16 Jun 2020 08:26:48: start model_add_line... INFO @ Tue, 16 Jun 2020 08:26:48: start X-correlation... INFO @ Tue, 16 Jun 2020 08:26:48: end of X-cor INFO @ Tue, 16 Jun 2020 08:26:48: #2 finished! INFO @ Tue, 16 Jun 2020 08:26:48: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 08:26:48: #2 alternative fragment length(s) may be 4,49,567,569 bps INFO @ Tue, 16 Jun 2020 08:26:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257689/SRX257689.20_model.r WARNING @ Tue, 16 Jun 2020 08:26:48: #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 08:26:48: #2 You may need to consider one of the other alternative d(s): 4,49,567,569 WARNING @ Tue, 16 Jun 2020 08:26:48: #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 08:26:48: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:26:48: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:26:59: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:27:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257689/SRX257689.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:27:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257689/SRX257689.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:27:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257689/SRX257689.20_summits.bed INFO @ Tue, 16 Jun 2020 08:27:04: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (232 records, 4 fields): 1 millis CompletedMACS2peakCalling