Job ID = 6369014 SRX = SRX982080 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:44:42 prefetch.2.10.7: 1) Downloading 'SRR1956563'... 2020-06-16T00:44:42 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:46:22 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:46:22 prefetch.2.10.7: 'SRR1956563' is valid 2020-06-16T00:46:22 prefetch.2.10.7: 1) 'SRR1956563' was downloaded successfully Read 6150585 spots for SRR1956563/SRR1956563.sra Written 6150585 spots for SRR1956563/SRR1956563.sra 2020-06-16T00:46:51 prefetch.2.10.7: 1) Downloading 'SRR1956564'... 2020-06-16T00:46:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:48:10 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:48:10 prefetch.2.10.7: 'SRR1956564' is valid 2020-06-16T00:48:10 prefetch.2.10.7: 1) 'SRR1956564' was downloaded successfully Read 7881938 spots for SRR1956564/SRR1956564.sra Written 7881938 spots for SRR1956564/SRR1956564.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: 00:02:39 14032523 reads; of these: 14032523 (100.00%) were unpaired; of these: 4828964 (34.41%) aligned 0 times 7544252 (53.76%) aligned exactly 1 time 1659307 (11.82%) aligned >1 times 65.59% overall alignment rate Time searching: 00:02:39 Overall time: 00:02:39 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] 635746 / 9203559 = 0.0691 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 09:54:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982080/SRX982080.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982080/SRX982080.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982080/SRX982080.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982080/SRX982080.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 09:54:24: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:54:24: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:54:29: 1000000 INFO @ Tue, 16 Jun 2020 09:54:36: 2000000 INFO @ Tue, 16 Jun 2020 09:54:42: 3000000 INFO @ Tue, 16 Jun 2020 09:54:48: 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 09:54:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982080/SRX982080.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982080/SRX982080.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982080/SRX982080.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982080/SRX982080.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 09:54:54: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:54:54: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:54:54: 5000000 INFO @ Tue, 16 Jun 2020 09:55:00: 1000000 INFO @ Tue, 16 Jun 2020 09:55:01: 6000000 INFO @ Tue, 16 Jun 2020 09:55:06: 2000000 INFO @ Tue, 16 Jun 2020 09:55:07: 7000000 INFO @ Tue, 16 Jun 2020 09:55:13: 3000000 INFO @ Tue, 16 Jun 2020 09:55:14: 8000000 INFO @ Tue, 16 Jun 2020 09:55:18: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:55:18: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:55:18: #1 total tags in treatment: 8567813 INFO @ Tue, 16 Jun 2020 09:55:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:55:18: #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 09:55:18: #1 tags after filtering in treatment: 8567813 INFO @ Tue, 16 Jun 2020 09:55:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:55:18: #1 finished! INFO @ Tue, 16 Jun 2020 09:55:18: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:55:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:55:18: #2 number of paired peaks: 356 WARNING @ Tue, 16 Jun 2020 09:55:18: Fewer paired peaks (356) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 356 pairs to build model! INFO @ Tue, 16 Jun 2020 09:55:18: start model_add_line... INFO @ Tue, 16 Jun 2020 09:55:18: start X-correlation... INFO @ Tue, 16 Jun 2020 09:55:19: end of X-cor INFO @ Tue, 16 Jun 2020 09:55:19: #2 finished! INFO @ Tue, 16 Jun 2020 09:55:19: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 09:55:19: #2 alternative fragment length(s) may be 4,49 bps INFO @ Tue, 16 Jun 2020 09:55:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982080/SRX982080.05_model.r WARNING @ Tue, 16 Jun 2020 09:55:19: #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 09:55:19: #2 You may need to consider one of the other alternative d(s): 4,49 WARNING @ Tue, 16 Jun 2020 09:55:19: #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 09:55:19: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:55:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:55:19: 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 09:55:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982080/SRX982080.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982080/SRX982080.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982080/SRX982080.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982080/SRX982080.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 09:55:24: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:55:24: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:55:26: 5000000 INFO @ Tue, 16 Jun 2020 09:55:30: 1000000 INFO @ Tue, 16 Jun 2020 09:55:32: 6000000 INFO @ Tue, 16 Jun 2020 09:55:35: 2000000 INFO @ Tue, 16 Jun 2020 09:55:35: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:55:39: 7000000 INFO @ Tue, 16 Jun 2020 09:55:41: 3000000 INFO @ Tue, 16 Jun 2020 09:55:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982080/SRX982080.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:55:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982080/SRX982080.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:55:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982080/SRX982080.05_summits.bed INFO @ Tue, 16 Jun 2020 09:55:44: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (621 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:55:46: 8000000 INFO @ Tue, 16 Jun 2020 09:55:47: 4000000 INFO @ Tue, 16 Jun 2020 09:55:49: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:55:49: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:55:49: #1 total tags in treatment: 8567813 INFO @ Tue, 16 Jun 2020 09:55:49: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:55:49: #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 09:55:49: #1 tags after filtering in treatment: 8567813 INFO @ Tue, 16 Jun 2020 09:55:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:55:49: #1 finished! INFO @ Tue, 16 Jun 2020 09:55:49: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:55:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:55:50: #2 number of paired peaks: 356 WARNING @ Tue, 16 Jun 2020 09:55:50: Fewer paired peaks (356) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 356 pairs to build model! INFO @ Tue, 16 Jun 2020 09:55:50: start model_add_line... INFO @ Tue, 16 Jun 2020 09:55:50: start X-correlation... INFO @ Tue, 16 Jun 2020 09:55:50: end of X-cor INFO @ Tue, 16 Jun 2020 09:55:50: #2 finished! INFO @ Tue, 16 Jun 2020 09:55:50: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 09:55:50: #2 alternative fragment length(s) may be 4,49 bps INFO @ Tue, 16 Jun 2020 09:55:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982080/SRX982080.10_model.r WARNING @ Tue, 16 Jun 2020 09:55:50: #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 09:55:50: #2 You may need to consider one of the other alternative d(s): 4,49 WARNING @ Tue, 16 Jun 2020 09:55:50: #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 09:55:50: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:55:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:55:53: 5000000 INFO @ Tue, 16 Jun 2020 09:55:58: 6000000 INFO @ Tue, 16 Jun 2020 09:56:04: 7000000 INFO @ Tue, 16 Jun 2020 09:56:07: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:56:09: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:56:12: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:56:12: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:56:12: #1 total tags in treatment: 8567813 INFO @ Tue, 16 Jun 2020 09:56:12: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:56:12: #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 09:56:12: #1 tags after filtering in treatment: 8567813 INFO @ Tue, 16 Jun 2020 09:56:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:56:12: #1 finished! INFO @ Tue, 16 Jun 2020 09:56:12: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:56:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:56:13: #2 number of paired peaks: 356 WARNING @ Tue, 16 Jun 2020 09:56:13: Fewer paired peaks (356) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 356 pairs to build model! INFO @ Tue, 16 Jun 2020 09:56:13: start model_add_line... INFO @ Tue, 16 Jun 2020 09:56:13: start X-correlation... INFO @ Tue, 16 Jun 2020 09:56:13: end of X-cor INFO @ Tue, 16 Jun 2020 09:56:13: #2 finished! INFO @ Tue, 16 Jun 2020 09:56:13: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 09:56:13: #2 alternative fragment length(s) may be 4,49 bps INFO @ Tue, 16 Jun 2020 09:56:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982080/SRX982080.20_model.r WARNING @ Tue, 16 Jun 2020 09:56:13: #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 09:56:13: #2 You may need to consider one of the other alternative d(s): 4,49 WARNING @ Tue, 16 Jun 2020 09:56:13: #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 09:56:13: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:56:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:56:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982080/SRX982080.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:56:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982080/SRX982080.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:56:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982080/SRX982080.10_summits.bed INFO @ Tue, 16 Jun 2020 09:56:15: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (376 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:56:29: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:56:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982080/SRX982080.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:56:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982080/SRX982080.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:56:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982080/SRX982080.20_summits.bed INFO @ Tue, 16 Jun 2020 09:56:38: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (163 records, 4 fields): 1 millis CompletedMACS2peakCalling