Job ID = 6368998 SRX = SRX982064 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:33:55 prefetch.2.10.7: 1) Downloading 'SRR1956540'... 2020-06-16T00:33:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:34:56 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:34:57 prefetch.2.10.7: 'SRR1956540' is valid 2020-06-16T00:34:57 prefetch.2.10.7: 1) 'SRR1956540' was downloaded successfully Read 7887410 spots for SRR1956540/SRR1956540.sra Written 7887410 spots for SRR1956540/SRR1956540.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: 00:01:39 7887410 reads; of these: 7887410 (100.00%) were unpaired; of these: 962881 (12.21%) aligned 0 times 5740466 (72.78%) aligned exactly 1 time 1184063 (15.01%) aligned >1 times 87.79% overall alignment rate Time searching: 00:01:39 Overall time: 00:01:39 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] 626061 / 6924529 = 0.0904 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 09:39:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982064/SRX982064.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982064/SRX982064.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982064/SRX982064.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982064/SRX982064.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 09:39:48: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:39:48: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:39:56: 1000000 INFO @ Tue, 16 Jun 2020 09:40:03: 2000000 INFO @ Tue, 16 Jun 2020 09:40:09: 3000000 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 09:40:16: 4000000 INFO @ Tue, 16 Jun 2020 09:40:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982064/SRX982064.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982064/SRX982064.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982064/SRX982064.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982064/SRX982064.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 09:40:18: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:40:18: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:40:23: 5000000 INFO @ Tue, 16 Jun 2020 09:40:25: 1000000 INFO @ Tue, 16 Jun 2020 09:40:29: 6000000 INFO @ Tue, 16 Jun 2020 09:40:31: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:40:31: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:40:31: #1 total tags in treatment: 6298468 INFO @ Tue, 16 Jun 2020 09:40:31: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:40:31: #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 09:40:31: #1 tags after filtering in treatment: 6298468 INFO @ Tue, 16 Jun 2020 09:40:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:40:31: #1 finished! INFO @ Tue, 16 Jun 2020 09:40:31: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:40:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:40:32: 2000000 INFO @ Tue, 16 Jun 2020 09:40:32: #2 number of paired peaks: 661 WARNING @ Tue, 16 Jun 2020 09:40:32: Fewer paired peaks (661) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 661 pairs to build model! INFO @ Tue, 16 Jun 2020 09:40:32: start model_add_line... INFO @ Tue, 16 Jun 2020 09:40:32: start X-correlation... INFO @ Tue, 16 Jun 2020 09:40:32: end of X-cor INFO @ Tue, 16 Jun 2020 09:40:32: #2 finished! INFO @ Tue, 16 Jun 2020 09:40:32: #2 predicted fragment length is 133 bps INFO @ Tue, 16 Jun 2020 09:40:32: #2 alternative fragment length(s) may be 133 bps INFO @ Tue, 16 Jun 2020 09:40:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982064/SRX982064.05_model.r INFO @ Tue, 16 Jun 2020 09:40:32: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:40:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:40:38: 3000000 INFO @ Tue, 16 Jun 2020 09:40:44: 4000000 INFO @ Tue, 16 Jun 2020 09:40:46: #3 Call peaks for each chromosome... 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 09:40:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982064/SRX982064.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982064/SRX982064.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982064/SRX982064.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982064/SRX982064.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 09:40:48: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:40:48: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:40:51: 5000000 INFO @ Tue, 16 Jun 2020 09:40:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982064/SRX982064.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:40:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982064/SRX982064.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:40:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982064/SRX982064.05_summits.bed INFO @ Tue, 16 Jun 2020 09:40:52: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1353 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:40:55: 1000000 INFO @ Tue, 16 Jun 2020 09:40:57: 6000000 INFO @ Tue, 16 Jun 2020 09:40:59: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:40:59: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:40:59: #1 total tags in treatment: 6298468 INFO @ Tue, 16 Jun 2020 09:40:59: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:40:59: #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 09:40:59: #1 tags after filtering in treatment: 6298468 INFO @ Tue, 16 Jun 2020 09:40:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:40:59: #1 finished! INFO @ Tue, 16 Jun 2020 09:40:59: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:40:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:41:00: #2 number of paired peaks: 661 WARNING @ Tue, 16 Jun 2020 09:41:00: Fewer paired peaks (661) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 661 pairs to build model! INFO @ Tue, 16 Jun 2020 09:41:00: start model_add_line... INFO @ Tue, 16 Jun 2020 09:41:00: start X-correlation... INFO @ Tue, 16 Jun 2020 09:41:00: end of X-cor INFO @ Tue, 16 Jun 2020 09:41:00: #2 finished! INFO @ Tue, 16 Jun 2020 09:41:00: #2 predicted fragment length is 133 bps INFO @ Tue, 16 Jun 2020 09:41:00: #2 alternative fragment length(s) may be 133 bps INFO @ Tue, 16 Jun 2020 09:41:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982064/SRX982064.10_model.r INFO @ Tue, 16 Jun 2020 09:41:00: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:41:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:41:02: 2000000 INFO @ Tue, 16 Jun 2020 09:41:08: 3000000 INFO @ Tue, 16 Jun 2020 09:41:14: 4000000 INFO @ Tue, 16 Jun 2020 09:41:14: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:41:20: 5000000 INFO @ Tue, 16 Jun 2020 09:41:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982064/SRX982064.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:41:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982064/SRX982064.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:41:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982064/SRX982064.10_summits.bed INFO @ Tue, 16 Jun 2020 09:41:20: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (885 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:41:26: 6000000 INFO @ Tue, 16 Jun 2020 09:41:28: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:41:28: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:41:28: #1 total tags in treatment: 6298468 INFO @ Tue, 16 Jun 2020 09:41:28: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:41:28: #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 09:41:28: #1 tags after filtering in treatment: 6298468 INFO @ Tue, 16 Jun 2020 09:41:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:41:28: #1 finished! INFO @ Tue, 16 Jun 2020 09:41:28: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:41:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:41:28: #2 number of paired peaks: 661 WARNING @ Tue, 16 Jun 2020 09:41:28: Fewer paired peaks (661) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 661 pairs to build model! INFO @ Tue, 16 Jun 2020 09:41:28: start model_add_line... INFO @ Tue, 16 Jun 2020 09:41:28: start X-correlation... INFO @ Tue, 16 Jun 2020 09:41:28: end of X-cor INFO @ Tue, 16 Jun 2020 09:41:28: #2 finished! INFO @ Tue, 16 Jun 2020 09:41:28: #2 predicted fragment length is 133 bps INFO @ Tue, 16 Jun 2020 09:41:28: #2 alternative fragment length(s) may be 133 bps INFO @ Tue, 16 Jun 2020 09:41:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982064/SRX982064.20_model.r INFO @ Tue, 16 Jun 2020 09:41:28: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:41:28: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:41:42: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:41:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982064/SRX982064.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:41:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982064/SRX982064.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:41:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982064/SRX982064.20_summits.bed INFO @ Tue, 16 Jun 2020 09:41:48: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (506 records, 4 fields): 2 millis CompletedMACS2peakCalling