Job ID = 6368371 SRX = SRX495051 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:14:51 prefetch.2.10.7: 1) Downloading 'SRR1198583'... 2020-06-16T00:14:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:16:31 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:16:32 prefetch.2.10.7: 'SRR1198583' is valid 2020-06-16T00:16:32 prefetch.2.10.7: 1) 'SRR1198583' was downloaded successfully Read 13687242 spots for SRR1198583/SRR1198583.sra Written 13687242 spots for SRR1198583/SRR1198583.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: 00:02:27 13687242 reads; of these: 13687242 (100.00%) were unpaired; of these: 1769295 (12.93%) aligned 0 times 10029961 (73.28%) aligned exactly 1 time 1887986 (13.79%) aligned >1 times 87.07% overall alignment rate Time searching: 00:02:27 Overall time: 00:02:27 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] 6528341 / 11917947 = 0.5478 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 09:22:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495051/SRX495051.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495051/SRX495051.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495051/SRX495051.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495051/SRX495051.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 09:22:10: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:22:10: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:22:15: 1000000 INFO @ Tue, 16 Jun 2020 09:22:20: 2000000 INFO @ Tue, 16 Jun 2020 09:22:25: 3000000 INFO @ Tue, 16 Jun 2020 09:22:30: 4000000 INFO @ Tue, 16 Jun 2020 09:22:35: 5000000 INFO @ Tue, 16 Jun 2020 09:22:37: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:22:37: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:22:37: #1 total tags in treatment: 5389606 INFO @ Tue, 16 Jun 2020 09:22:37: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:22:37: #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 09:22:37: #1 tags after filtering in treatment: 5389606 INFO @ Tue, 16 Jun 2020 09:22:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:22:37: #1 finished! INFO @ Tue, 16 Jun 2020 09:22:37: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:22:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:22:37: #2 number of paired peaks: 731 WARNING @ Tue, 16 Jun 2020 09:22:37: Fewer paired peaks (731) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 731 pairs to build model! INFO @ Tue, 16 Jun 2020 09:22:37: start model_add_line... INFO @ Tue, 16 Jun 2020 09:22:37: start X-correlation... INFO @ Tue, 16 Jun 2020 09:22:37: end of X-cor INFO @ Tue, 16 Jun 2020 09:22:37: #2 finished! INFO @ Tue, 16 Jun 2020 09:22:37: #2 predicted fragment length is 106 bps INFO @ Tue, 16 Jun 2020 09:22:37: #2 alternative fragment length(s) may be 106 bps INFO @ Tue, 16 Jun 2020 09:22:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495051/SRX495051.05_model.r INFO @ Tue, 16 Jun 2020 09:22:37: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:22:37: #3 Pre-compute pvalue-qvalue table... 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 09:22:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495051/SRX495051.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495051/SRX495051.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495051/SRX495051.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495051/SRX495051.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 09:22:40: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:22:40: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:22:46: 1000000 INFO @ Tue, 16 Jun 2020 09:22:50: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:22:52: 2000000 INFO @ Tue, 16 Jun 2020 09:22:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495051/SRX495051.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:22:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495051/SRX495051.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:22:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495051/SRX495051.05_summits.bed INFO @ Tue, 16 Jun 2020 09:22:56: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1465 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:22:58: 3000000 INFO @ Tue, 16 Jun 2020 09:23:04: 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 09:23:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495051/SRX495051.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495051/SRX495051.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495051/SRX495051.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495051/SRX495051.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 09:23:10: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:23:10: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:23:10: 5000000 INFO @ Tue, 16 Jun 2020 09:23:13: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:23:13: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:23:13: #1 total tags in treatment: 5389606 INFO @ Tue, 16 Jun 2020 09:23:13: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:23:13: #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 09:23:13: #1 tags after filtering in treatment: 5389606 INFO @ Tue, 16 Jun 2020 09:23:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:23:13: #1 finished! INFO @ Tue, 16 Jun 2020 09:23:13: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:23:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:23:13: #2 number of paired peaks: 731 WARNING @ Tue, 16 Jun 2020 09:23:13: Fewer paired peaks (731) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 731 pairs to build model! INFO @ Tue, 16 Jun 2020 09:23:13: start model_add_line... INFO @ Tue, 16 Jun 2020 09:23:13: start X-correlation... INFO @ Tue, 16 Jun 2020 09:23:13: end of X-cor INFO @ Tue, 16 Jun 2020 09:23:13: #2 finished! INFO @ Tue, 16 Jun 2020 09:23:13: #2 predicted fragment length is 106 bps INFO @ Tue, 16 Jun 2020 09:23:13: #2 alternative fragment length(s) may be 106 bps INFO @ Tue, 16 Jun 2020 09:23:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495051/SRX495051.10_model.r INFO @ Tue, 16 Jun 2020 09:23:13: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:23:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:23:17: 1000000 INFO @ Tue, 16 Jun 2020 09:23:23: 2000000 INFO @ Tue, 16 Jun 2020 09:23:26: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:23:29: 3000000 INFO @ Tue, 16 Jun 2020 09:23:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495051/SRX495051.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:23:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495051/SRX495051.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:23:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495051/SRX495051.10_summits.bed INFO @ Tue, 16 Jun 2020 09:23:32: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (726 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:23:35: 4000000 INFO @ Tue, 16 Jun 2020 09:23:41: 5000000 INFO @ Tue, 16 Jun 2020 09:23:43: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:23:43: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:23:43: #1 total tags in treatment: 5389606 INFO @ Tue, 16 Jun 2020 09:23:43: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:23:43: #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 09:23:43: #1 tags after filtering in treatment: 5389606 INFO @ Tue, 16 Jun 2020 09:23:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:23:43: #1 finished! INFO @ Tue, 16 Jun 2020 09:23:43: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:23:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:23:44: #2 number of paired peaks: 731 WARNING @ Tue, 16 Jun 2020 09:23:44: Fewer paired peaks (731) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 731 pairs to build model! INFO @ Tue, 16 Jun 2020 09:23:44: start model_add_line... INFO @ Tue, 16 Jun 2020 09:23:44: start X-correlation... INFO @ Tue, 16 Jun 2020 09:23:44: end of X-cor INFO @ Tue, 16 Jun 2020 09:23:44: #2 finished! INFO @ Tue, 16 Jun 2020 09:23:44: #2 predicted fragment length is 106 bps INFO @ Tue, 16 Jun 2020 09:23:44: #2 alternative fragment length(s) may be 106 bps INFO @ Tue, 16 Jun 2020 09:23:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495051/SRX495051.20_model.r INFO @ Tue, 16 Jun 2020 09:23:44: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:23:44: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:23:56: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:24:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495051/SRX495051.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:24:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495051/SRX495051.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:24:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495051/SRX495051.20_summits.bed INFO @ Tue, 16 Jun 2020 09:24:02: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (299 records, 4 fields): 2 millis CompletedMACS2peakCalling