Job ID = 6368996 SRX = SRX982062 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:34:10 prefetch.2.10.7: 1) Downloading 'SRR1956538'... 2020-06-16T00:34:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:35:26 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:35:27 prefetch.2.10.7: 'SRR1956538' is valid 2020-06-16T00:35:27 prefetch.2.10.7: 1) 'SRR1956538' was downloaded successfully Read 7648332 spots for SRR1956538/SRR1956538.sra Written 7648332 spots for SRR1956538/SRR1956538.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: 00:01:48 7648332 reads; of these: 7648332 (100.00%) were unpaired; of these: 1029014 (13.45%) aligned 0 times 5532777 (72.34%) aligned exactly 1 time 1086541 (14.21%) aligned >1 times 86.55% overall alignment rate Time searching: 00:01:48 Overall time: 00:01:48 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] 957649 / 6619318 = 0.1447 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 09:39:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982062/SRX982062.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982062/SRX982062.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982062/SRX982062.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982062/SRX982062.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 09:39:57: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:39:57: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:40:03: 1000000 INFO @ Tue, 16 Jun 2020 09:40:09: 2000000 INFO @ Tue, 16 Jun 2020 09:40:15: 3000000 INFO @ Tue, 16 Jun 2020 09:40:21: 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 09:40:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982062/SRX982062.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982062/SRX982062.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982062/SRX982062.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982062/SRX982062.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 09:40:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:40:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:40:28: 5000000 INFO @ Tue, 16 Jun 2020 09:40:32: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:40:32: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:40:32: #1 total tags in treatment: 5661669 INFO @ Tue, 16 Jun 2020 09:40:32: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:40:32: #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 09:40:32: #1 tags after filtering in treatment: 5661669 INFO @ Tue, 16 Jun 2020 09:40:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:40:32: #1 finished! INFO @ Tue, 16 Jun 2020 09:40:32: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:40:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:40:33: #2 number of paired peaks: 513 WARNING @ Tue, 16 Jun 2020 09:40:33: Fewer paired peaks (513) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 513 pairs to build model! INFO @ Tue, 16 Jun 2020 09:40:33: start model_add_line... INFO @ Tue, 16 Jun 2020 09:40:33: start X-correlation... INFO @ Tue, 16 Jun 2020 09:40:33: end of X-cor INFO @ Tue, 16 Jun 2020 09:40:33: #2 finished! INFO @ Tue, 16 Jun 2020 09:40:33: #2 predicted fragment length is 127 bps INFO @ Tue, 16 Jun 2020 09:40:33: #2 alternative fragment length(s) may be 127 bps INFO @ Tue, 16 Jun 2020 09:40:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982062/SRX982062.05_model.r INFO @ Tue, 16 Jun 2020 09:40:33: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:40:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:40:34: 1000000 INFO @ Tue, 16 Jun 2020 09:40:41: 2000000 INFO @ Tue, 16 Jun 2020 09:40:46: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:40:47: 3000000 INFO @ Tue, 16 Jun 2020 09:40:53: 4000000 INFO @ Tue, 16 Jun 2020 09:40:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982062/SRX982062.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:40:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982062/SRX982062.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:40:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982062/SRX982062.05_summits.bed INFO @ Tue, 16 Jun 2020 09:40:54: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (876 records, 4 fields): 3 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 09:40:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982062/SRX982062.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982062/SRX982062.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982062/SRX982062.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982062/SRX982062.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 09:40:57: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:40:57: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:41:00: 5000000 INFO @ Tue, 16 Jun 2020 09:41:04: 1000000 INFO @ Tue, 16 Jun 2020 09:41:04: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:41:04: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:41:04: #1 total tags in treatment: 5661669 INFO @ Tue, 16 Jun 2020 09:41:04: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:41:04: #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 09:41:04: #1 tags after filtering in treatment: 5661669 INFO @ Tue, 16 Jun 2020 09:41:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:41:04: #1 finished! INFO @ Tue, 16 Jun 2020 09:41:04: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:41:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:41:05: #2 number of paired peaks: 513 WARNING @ Tue, 16 Jun 2020 09:41:05: Fewer paired peaks (513) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 513 pairs to build model! INFO @ Tue, 16 Jun 2020 09:41:05: start model_add_line... INFO @ Tue, 16 Jun 2020 09:41:05: start X-correlation... INFO @ Tue, 16 Jun 2020 09:41:05: end of X-cor INFO @ Tue, 16 Jun 2020 09:41:05: #2 finished! INFO @ Tue, 16 Jun 2020 09:41:05: #2 predicted fragment length is 127 bps INFO @ Tue, 16 Jun 2020 09:41:05: #2 alternative fragment length(s) may be 127 bps INFO @ Tue, 16 Jun 2020 09:41:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982062/SRX982062.10_model.r INFO @ Tue, 16 Jun 2020 09:41:05: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:41:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:41:10: 2000000 INFO @ Tue, 16 Jun 2020 09:41:16: 3000000 INFO @ Tue, 16 Jun 2020 09:41:18: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:41:23: 4000000 INFO @ Tue, 16 Jun 2020 09:41:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982062/SRX982062.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:41:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982062/SRX982062.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:41:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982062/SRX982062.10_summits.bed INFO @ Tue, 16 Jun 2020 09:41:25: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (548 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:41:29: 5000000 INFO @ Tue, 16 Jun 2020 09:41:33: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:41:33: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:41:33: #1 total tags in treatment: 5661669 INFO @ Tue, 16 Jun 2020 09:41:33: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:41:33: #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 09:41:33: #1 tags after filtering in treatment: 5661669 INFO @ Tue, 16 Jun 2020 09:41:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:41:33: #1 finished! INFO @ Tue, 16 Jun 2020 09:41:33: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:41:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:41:33: #2 number of paired peaks: 513 WARNING @ Tue, 16 Jun 2020 09:41:33: Fewer paired peaks (513) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 513 pairs to build model! INFO @ Tue, 16 Jun 2020 09:41:33: start model_add_line... INFO @ Tue, 16 Jun 2020 09:41:33: start X-correlation... INFO @ Tue, 16 Jun 2020 09:41:34: end of X-cor INFO @ Tue, 16 Jun 2020 09:41:34: #2 finished! INFO @ Tue, 16 Jun 2020 09:41:34: #2 predicted fragment length is 127 bps INFO @ Tue, 16 Jun 2020 09:41:34: #2 alternative fragment length(s) may be 127 bps INFO @ Tue, 16 Jun 2020 09:41:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982062/SRX982062.20_model.r INFO @ Tue, 16 Jun 2020 09:41:34: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:41:34: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:41:47: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:41:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982062/SRX982062.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:41:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982062/SRX982062.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:41:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982062/SRX982062.20_summits.bed INFO @ Tue, 16 Jun 2020 09:41:54: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (253 records, 4 fields): 1 millis CompletedMACS2peakCalling