Job ID = 6367705 SRX = SRX395529 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:34:50 prefetch.2.10.7: 1) Downloading 'SRR1054258'... 2020-06-15T23:34:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:35:35 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:35:35 prefetch.2.10.7: 'SRR1054258' is valid 2020-06-15T23:35:35 prefetch.2.10.7: 1) 'SRR1054258' was downloaded successfully Read 3927501 spots for SRR1054258/SRR1054258.sra Written 3927501 spots for SRR1054258/SRR1054258.sra 2020-06-15T23:35:55 prefetch.2.10.7: 1) Downloading 'SRR1054259'... 2020-06-15T23:35:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:37:04 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:37:05 prefetch.2.10.7: 'SRR1054259' is valid 2020-06-15T23:37:05 prefetch.2.10.7: 1) 'SRR1054259' was downloaded successfully Read 5036258 spots for SRR1054259/SRR1054259.sra Written 5036258 spots for SRR1054259/SRR1054259.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: 00:01:12 8963759 reads; of these: 8963759 (100.00%) were unpaired; of these: 2049518 (22.86%) aligned 0 times 5489410 (61.24%) aligned exactly 1 time 1424831 (15.90%) aligned >1 times 77.14% overall alignment rate Time searching: 00:01:12 Overall time: 00:01:12 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] 4090554 / 6914241 = 0.5916 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 08:40:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX395529/SRX395529.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX395529/SRX395529.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX395529/SRX395529.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX395529/SRX395529.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 08:40:03: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:40:03: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:40:08: 1000000 INFO @ Tue, 16 Jun 2020 08:40:12: 2000000 INFO @ Tue, 16 Jun 2020 08:40:15: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:40:15: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:40:15: #1 total tags in treatment: 2823687 INFO @ Tue, 16 Jun 2020 08:40:15: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:40:15: #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 08:40:16: #1 tags after filtering in treatment: 2823687 INFO @ Tue, 16 Jun 2020 08:40:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:40:16: #1 finished! INFO @ Tue, 16 Jun 2020 08:40:16: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:40:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:40:16: #2 number of paired peaks: 865 WARNING @ Tue, 16 Jun 2020 08:40:16: Fewer paired peaks (865) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 865 pairs to build model! INFO @ Tue, 16 Jun 2020 08:40:16: start model_add_line... INFO @ Tue, 16 Jun 2020 08:40:16: start X-correlation... INFO @ Tue, 16 Jun 2020 08:40:16: end of X-cor INFO @ Tue, 16 Jun 2020 08:40:16: #2 finished! INFO @ Tue, 16 Jun 2020 08:40:16: #2 predicted fragment length is 164 bps INFO @ Tue, 16 Jun 2020 08:40:16: #2 alternative fragment length(s) may be 164 bps INFO @ Tue, 16 Jun 2020 08:40:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX395529/SRX395529.05_model.r INFO @ Tue, 16 Jun 2020 08:40:16: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:40:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:40:23: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:40:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX395529/SRX395529.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:40:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX395529/SRX395529.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:40:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX395529/SRX395529.05_summits.bed INFO @ Tue, 16 Jun 2020 08:40:26: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2083 records, 4 fields): 3 millis CompletedMACS2peakCalling 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 08:40:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX395529/SRX395529.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX395529/SRX395529.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX395529/SRX395529.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX395529/SRX395529.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 08:40:33: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:40:33: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:40:38: 1000000 INFO @ Tue, 16 Jun 2020 08:40:43: 2000000 INFO @ Tue, 16 Jun 2020 08:40:47: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:40:47: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:40:47: #1 total tags in treatment: 2823687 INFO @ Tue, 16 Jun 2020 08:40:47: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:40:47: #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 08:40:47: #1 tags after filtering in treatment: 2823687 INFO @ Tue, 16 Jun 2020 08:40:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:40:47: #1 finished! INFO @ Tue, 16 Jun 2020 08:40:47: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:40:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:40:47: #2 number of paired peaks: 865 WARNING @ Tue, 16 Jun 2020 08:40:47: Fewer paired peaks (865) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 865 pairs to build model! INFO @ Tue, 16 Jun 2020 08:40:47: start model_add_line... INFO @ Tue, 16 Jun 2020 08:40:47: start X-correlation... INFO @ Tue, 16 Jun 2020 08:40:47: end of X-cor INFO @ Tue, 16 Jun 2020 08:40:47: #2 finished! INFO @ Tue, 16 Jun 2020 08:40:47: #2 predicted fragment length is 164 bps INFO @ Tue, 16 Jun 2020 08:40:47: #2 alternative fragment length(s) may be 164 bps INFO @ Tue, 16 Jun 2020 08:40:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX395529/SRX395529.10_model.r INFO @ Tue, 16 Jun 2020 08:40:47: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:40:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:40:54: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:40:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX395529/SRX395529.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:40:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX395529/SRX395529.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:40:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX395529/SRX395529.10_summits.bed INFO @ Tue, 16 Jun 2020 08:40:57: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1024 records, 4 fields): 2 millis CompletedMACS2peakCalling 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 08:41:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX395529/SRX395529.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX395529/SRX395529.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX395529/SRX395529.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX395529/SRX395529.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 08:41:03: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:41:03: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:41:08: 1000000 INFO @ Tue, 16 Jun 2020 08:41:12: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:41:15: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:41:15: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:41:15: #1 total tags in treatment: 2823687 INFO @ Tue, 16 Jun 2020 08:41:15: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:41:15: #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 08:41:15: #1 tags after filtering in treatment: 2823687 INFO @ Tue, 16 Jun 2020 08:41:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:41:15: #1 finished! INFO @ Tue, 16 Jun 2020 08:41:15: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:41:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:41:16: #2 number of paired peaks: 865 WARNING @ Tue, 16 Jun 2020 08:41:16: Fewer paired peaks (865) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 865 pairs to build model! INFO @ Tue, 16 Jun 2020 08:41:16: start model_add_line... INFO @ Tue, 16 Jun 2020 08:41:16: start X-correlation... INFO @ Tue, 16 Jun 2020 08:41:16: end of X-cor INFO @ Tue, 16 Jun 2020 08:41:16: #2 finished! INFO @ Tue, 16 Jun 2020 08:41:16: #2 predicted fragment length is 164 bps INFO @ Tue, 16 Jun 2020 08:41:16: #2 alternative fragment length(s) may be 164 bps INFO @ Tue, 16 Jun 2020 08:41:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX395529/SRX395529.20_model.r INFO @ Tue, 16 Jun 2020 08:41:16: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:41:16: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:41:22: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:41:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX395529/SRX395529.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:41:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX395529/SRX395529.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:41:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX395529/SRX395529.20_summits.bed INFO @ Tue, 16 Jun 2020 08:41:25: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (414 records, 4 fields): 2 millis CompletedMACS2peakCalling