Job ID = 6367037 SRX = SRX2761382 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:18:31 prefetch.2.10.7: 1) Downloading 'SRR5476956'... 2020-06-15T23:18:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:19:26 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:19:26 prefetch.2.10.7: 'SRR5476956' is valid 2020-06-15T23:19:26 prefetch.2.10.7: 1) 'SRR5476956' was downloaded successfully Read 8215578 spots for SRR5476956/SRR5476956.sra Written 8215578 spots for SRR5476956/SRR5476956.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: 00:00:01 Multiseed full-index search: 00:01:54 8215578 reads; of these: 8215578 (100.00%) were unpaired; of these: 627056 (7.63%) aligned 0 times 5827879 (70.94%) aligned exactly 1 time 1760643 (21.43%) aligned >1 times 92.37% overall alignment rate Time searching: 00:01:55 Overall time: 00:01:55 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] 1680744 / 7588522 = 0.2215 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 08:24:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2761382/SRX2761382.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2761382/SRX2761382.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2761382/SRX2761382.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2761382/SRX2761382.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 08:24:00: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:24:00: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:24:06: 1000000 INFO @ Tue, 16 Jun 2020 08:24:11: 2000000 INFO @ Tue, 16 Jun 2020 08:24:17: 3000000 INFO @ Tue, 16 Jun 2020 08:24:23: 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 08:24:28: 5000000 INFO @ Tue, 16 Jun 2020 08:24:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2761382/SRX2761382.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2761382/SRX2761382.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2761382/SRX2761382.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2761382/SRX2761382.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 08:24:29: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:24:29: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:24:34: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:24:34: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:24:34: #1 total tags in treatment: 5907778 INFO @ Tue, 16 Jun 2020 08:24:34: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:24:34: #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 08:24:34: #1 tags after filtering in treatment: 5907778 INFO @ Tue, 16 Jun 2020 08:24:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:24:34: #1 finished! INFO @ Tue, 16 Jun 2020 08:24:34: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:24:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:24:34: #2 number of paired peaks: 634 WARNING @ Tue, 16 Jun 2020 08:24:34: Fewer paired peaks (634) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 634 pairs to build model! INFO @ Tue, 16 Jun 2020 08:24:34: start model_add_line... INFO @ Tue, 16 Jun 2020 08:24:34: start X-correlation... INFO @ Tue, 16 Jun 2020 08:24:34: end of X-cor INFO @ Tue, 16 Jun 2020 08:24:34: #2 finished! INFO @ Tue, 16 Jun 2020 08:24:34: #2 predicted fragment length is 53 bps INFO @ Tue, 16 Jun 2020 08:24:34: #2 alternative fragment length(s) may be 4,53 bps INFO @ Tue, 16 Jun 2020 08:24:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2761382/SRX2761382.05_model.r WARNING @ Tue, 16 Jun 2020 08:24:34: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:24:34: #2 You may need to consider one of the other alternative d(s): 4,53 WARNING @ Tue, 16 Jun 2020 08:24:34: #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 08:24:34: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:24:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:24:36: 1000000 INFO @ Tue, 16 Jun 2020 08:24:42: 2000000 INFO @ Tue, 16 Jun 2020 08:24:46: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:24:48: 3000000 INFO @ Tue, 16 Jun 2020 08:24:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2761382/SRX2761382.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:24:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2761382/SRX2761382.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:24:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2761382/SRX2761382.05_summits.bed INFO @ Tue, 16 Jun 2020 08:24:53: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (668 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:24:54: 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 08:24:59: 5000000 INFO @ Tue, 16 Jun 2020 08:24:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2761382/SRX2761382.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2761382/SRX2761382.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2761382/SRX2761382.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2761382/SRX2761382.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 08:24:59: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:24:59: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:25:05: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:25:05: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:25:05: #1 total tags in treatment: 5907778 INFO @ Tue, 16 Jun 2020 08:25:05: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:25:05: #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 08:25:05: #1 tags after filtering in treatment: 5907778 INFO @ Tue, 16 Jun 2020 08:25:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:25:05: #1 finished! INFO @ Tue, 16 Jun 2020 08:25:05: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:25:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:25:06: 1000000 INFO @ Tue, 16 Jun 2020 08:25:06: #2 number of paired peaks: 634 WARNING @ Tue, 16 Jun 2020 08:25:06: Fewer paired peaks (634) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 634 pairs to build model! INFO @ Tue, 16 Jun 2020 08:25:06: start model_add_line... INFO @ Tue, 16 Jun 2020 08:25:06: start X-correlation... INFO @ Tue, 16 Jun 2020 08:25:06: end of X-cor INFO @ Tue, 16 Jun 2020 08:25:06: #2 finished! INFO @ Tue, 16 Jun 2020 08:25:06: #2 predicted fragment length is 53 bps INFO @ Tue, 16 Jun 2020 08:25:06: #2 alternative fragment length(s) may be 4,53 bps INFO @ Tue, 16 Jun 2020 08:25:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2761382/SRX2761382.10_model.r WARNING @ Tue, 16 Jun 2020 08:25:06: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:25:06: #2 You may need to consider one of the other alternative d(s): 4,53 WARNING @ Tue, 16 Jun 2020 08:25:06: #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 08:25:06: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:25:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:25:12: 2000000 INFO @ Tue, 16 Jun 2020 08:25:18: 3000000 INFO @ Tue, 16 Jun 2020 08:25:18: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:25:24: 4000000 INFO @ Tue, 16 Jun 2020 08:25:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2761382/SRX2761382.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:25:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2761382/SRX2761382.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:25:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2761382/SRX2761382.10_summits.bed INFO @ Tue, 16 Jun 2020 08:25:25: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (393 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:25:30: 5000000 INFO @ Tue, 16 Jun 2020 08:25:35: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:25:35: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:25:35: #1 total tags in treatment: 5907778 INFO @ Tue, 16 Jun 2020 08:25:35: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:25:35: #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 08:25:35: #1 tags after filtering in treatment: 5907778 INFO @ Tue, 16 Jun 2020 08:25:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:25:35: #1 finished! INFO @ Tue, 16 Jun 2020 08:25:35: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:25:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:25:36: #2 number of paired peaks: 634 WARNING @ Tue, 16 Jun 2020 08:25:36: Fewer paired peaks (634) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 634 pairs to build model! INFO @ Tue, 16 Jun 2020 08:25:36: start model_add_line... INFO @ Tue, 16 Jun 2020 08:25:36: start X-correlation... INFO @ Tue, 16 Jun 2020 08:25:36: end of X-cor INFO @ Tue, 16 Jun 2020 08:25:36: #2 finished! INFO @ Tue, 16 Jun 2020 08:25:36: #2 predicted fragment length is 53 bps INFO @ Tue, 16 Jun 2020 08:25:36: #2 alternative fragment length(s) may be 4,53 bps INFO @ Tue, 16 Jun 2020 08:25:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2761382/SRX2761382.20_model.r WARNING @ Tue, 16 Jun 2020 08:25:36: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:25:36: #2 You may need to consider one of the other alternative d(s): 4,53 WARNING @ Tue, 16 Jun 2020 08:25:36: #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 08:25:36: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:25:36: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:25:48: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:25:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2761382/SRX2761382.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:25:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2761382/SRX2761382.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:25:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2761382/SRX2761382.20_summits.bed INFO @ Tue, 16 Jun 2020 08:25:54: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (167 records, 4 fields): 1 millis CompletedMACS2peakCalling