Job ID = 6369015 SRX = SRX982081 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:41:29 prefetch.2.10.7: 1) Downloading 'SRR1956565'... 2020-06-16T00:41:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:42:47 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:42:47 prefetch.2.10.7: 'SRR1956565' is valid 2020-06-16T00:42:47 prefetch.2.10.7: 1) 'SRR1956565' was downloaded successfully Read 5330567 spots for SRR1956565/SRR1956565.sra Written 5330567 spots for SRR1956565/SRR1956565.sra 2020-06-16T00:43:14 prefetch.2.10.7: 1) Downloading 'SRR1956566'... 2020-06-16T00:43:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:44:42 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:44:42 prefetch.2.10.7: 'SRR1956566' is valid 2020-06-16T00:44:42 prefetch.2.10.7: 1) 'SRR1956566' was downloaded successfully Read 6203332 spots for SRR1956566/SRR1956566.sra Written 6203332 spots for SRR1956566/SRR1956566.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: 00:02:11 11533899 reads; of these: 11533899 (100.00%) were unpaired; of these: 3836774 (33.27%) aligned 0 times 6277705 (54.43%) aligned exactly 1 time 1419420 (12.31%) aligned >1 times 66.73% overall alignment rate Time searching: 00:02:11 Overall time: 00:02:11 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] 554812 / 7697125 = 0.0721 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 09:50:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982081/SRX982081.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982081/SRX982081.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982081/SRX982081.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982081/SRX982081.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 09:50:02: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:50:02: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:50:09: 1000000 INFO @ Tue, 16 Jun 2020 09:50:15: 2000000 INFO @ Tue, 16 Jun 2020 09:50:22: 3000000 INFO @ Tue, 16 Jun 2020 09:50:29: 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 09:50:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982081/SRX982081.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982081/SRX982081.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982081/SRX982081.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982081/SRX982081.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 09:50:32: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:50:32: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:50:36: 5000000 INFO @ Tue, 16 Jun 2020 09:50:39: 1000000 INFO @ Tue, 16 Jun 2020 09:50:44: 6000000 INFO @ Tue, 16 Jun 2020 09:50:46: 2000000 INFO @ Tue, 16 Jun 2020 09:50:51: 7000000 INFO @ Tue, 16 Jun 2020 09:50:52: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:50:52: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:50:52: #1 total tags in treatment: 7142313 INFO @ Tue, 16 Jun 2020 09:50:52: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:50:52: #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 09:50:52: #1 tags after filtering in treatment: 7142313 INFO @ Tue, 16 Jun 2020 09:50:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:50:52: #1 finished! INFO @ Tue, 16 Jun 2020 09:50:52: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:50:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:50:53: #2 number of paired peaks: 372 WARNING @ Tue, 16 Jun 2020 09:50:53: Fewer paired peaks (372) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 372 pairs to build model! INFO @ Tue, 16 Jun 2020 09:50:53: start model_add_line... INFO @ Tue, 16 Jun 2020 09:50:53: start X-correlation... INFO @ Tue, 16 Jun 2020 09:50:53: end of X-cor INFO @ Tue, 16 Jun 2020 09:50:53: #2 finished! INFO @ Tue, 16 Jun 2020 09:50:53: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 09:50:53: #2 alternative fragment length(s) may be 4,50,542,573 bps INFO @ Tue, 16 Jun 2020 09:50:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982081/SRX982081.05_model.r WARNING @ Tue, 16 Jun 2020 09:50:53: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:50:53: #2 You may need to consider one of the other alternative d(s): 4,50,542,573 WARNING @ Tue, 16 Jun 2020 09:50:53: #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 09:50:53: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:50:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:50:53: 3000000 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 09:51:00: 4000000 INFO @ Tue, 16 Jun 2020 09:51:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982081/SRX982081.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982081/SRX982081.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982081/SRX982081.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982081/SRX982081.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 09:51:02: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:51:02: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:51:08: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:51:08: 5000000 INFO @ Tue, 16 Jun 2020 09:51:09: 1000000 INFO @ Tue, 16 Jun 2020 09:51:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982081/SRX982081.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:51:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982081/SRX982081.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:51:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982081/SRX982081.05_summits.bed INFO @ Tue, 16 Jun 2020 09:51:15: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (615 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:51:15: 6000000 INFO @ Tue, 16 Jun 2020 09:51:16: 2000000 INFO @ Tue, 16 Jun 2020 09:51:22: 7000000 INFO @ Tue, 16 Jun 2020 09:51:23: 3000000 INFO @ Tue, 16 Jun 2020 09:51:23: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:51:23: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:51:23: #1 total tags in treatment: 7142313 INFO @ Tue, 16 Jun 2020 09:51:23: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:51:23: #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 09:51:23: #1 tags after filtering in treatment: 7142313 INFO @ Tue, 16 Jun 2020 09:51:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:51:23: #1 finished! INFO @ Tue, 16 Jun 2020 09:51:23: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:51:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:51:24: #2 number of paired peaks: 372 WARNING @ Tue, 16 Jun 2020 09:51:24: Fewer paired peaks (372) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 372 pairs to build model! INFO @ Tue, 16 Jun 2020 09:51:24: start model_add_line... INFO @ Tue, 16 Jun 2020 09:51:24: start X-correlation... INFO @ Tue, 16 Jun 2020 09:51:24: end of X-cor INFO @ Tue, 16 Jun 2020 09:51:24: #2 finished! INFO @ Tue, 16 Jun 2020 09:51:24: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 09:51:24: #2 alternative fragment length(s) may be 4,50,542,573 bps INFO @ Tue, 16 Jun 2020 09:51:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982081/SRX982081.10_model.r WARNING @ Tue, 16 Jun 2020 09:51:24: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:51:24: #2 You may need to consider one of the other alternative d(s): 4,50,542,573 WARNING @ Tue, 16 Jun 2020 09:51:24: #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 09:51:24: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:51:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:51:28: 4000000 INFO @ Tue, 16 Jun 2020 09:51:34: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:51:38: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:51:40: 6000000 INFO @ Tue, 16 Jun 2020 09:51:45: 7000000 INFO @ Tue, 16 Jun 2020 09:51:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982081/SRX982081.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:51:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982081/SRX982081.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:51:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982081/SRX982081.10_summits.bed INFO @ Tue, 16 Jun 2020 09:51:45: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (371 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:51:46: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:51:46: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:51:46: #1 total tags in treatment: 7142313 INFO @ Tue, 16 Jun 2020 09:51:46: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:51:46: #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 09:51:46: #1 tags after filtering in treatment: 7142313 INFO @ Tue, 16 Jun 2020 09:51:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:51:46: #1 finished! INFO @ Tue, 16 Jun 2020 09:51:46: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:51:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:51:47: #2 number of paired peaks: 372 WARNING @ Tue, 16 Jun 2020 09:51:47: Fewer paired peaks (372) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 372 pairs to build model! INFO @ Tue, 16 Jun 2020 09:51:47: start model_add_line... INFO @ Tue, 16 Jun 2020 09:51:47: start X-correlation... INFO @ Tue, 16 Jun 2020 09:51:47: end of X-cor INFO @ Tue, 16 Jun 2020 09:51:47: #2 finished! INFO @ Tue, 16 Jun 2020 09:51:47: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 09:51:47: #2 alternative fragment length(s) may be 4,50,542,573 bps INFO @ Tue, 16 Jun 2020 09:51:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982081/SRX982081.20_model.r WARNING @ Tue, 16 Jun 2020 09:51:47: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:51:47: #2 You may need to consider one of the other alternative d(s): 4,50,542,573 WARNING @ Tue, 16 Jun 2020 09:51:47: #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 09:51:47: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:51:47: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:52:01: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:52:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982081/SRX982081.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:52:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982081/SRX982081.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:52:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982081/SRX982081.20_summits.bed INFO @ Tue, 16 Jun 2020 09:52:09: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (163 records, 4 fields): 1 millis CompletedMACS2peakCalling