Job ID = 6366983 SRX = SRX257682 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:12:02 prefetch.2.10.7: 1) Downloading 'SRR800698'... 2020-06-15T23:12:02 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:13:31 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:13:32 prefetch.2.10.7: 'SRR800698' is valid 2020-06-15T23:13:32 prefetch.2.10.7: 1) 'SRR800698' was downloaded successfully Read 13687242 spots for SRR800698/SRR800698.sra Written 13687242 spots for SRR800698/SRR800698.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: 00:02:33 13687242 reads; of these: 13687242 (100.00%) were unpaired; of these: 1769303 (12.93%) aligned 0 times 10029939 (73.28%) aligned exactly 1 time 1888000 (13.79%) aligned >1 times 87.07% overall alignment rate Time searching: 00:02:33 Overall time: 00:02:33 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] 6528206 / 11917939 = 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 08:19:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257682/SRX257682.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257682/SRX257682.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257682/SRX257682.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257682/SRX257682.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 08:19:16: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:19:16: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:19:21: 1000000 INFO @ Tue, 16 Jun 2020 08:19:27: 2000000 INFO @ Tue, 16 Jun 2020 08:19:32: 3000000 INFO @ Tue, 16 Jun 2020 08:19:37: 4000000 INFO @ Tue, 16 Jun 2020 08:19:43: 5000000 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 08:19:45: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 08:19:45: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 08:19:45: #1 total tags in treatment: 5389733 INFO @ Tue, 16 Jun 2020 08:19:45: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:19:45: #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 08:19:45: #1 tags after filtering in treatment: 5389733 INFO @ Tue, 16 Jun 2020 08:19:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:19:45: #1 finished! INFO @ Tue, 16 Jun 2020 08:19:45: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:19:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:19:46: #2 number of paired peaks: 713 WARNING @ Tue, 16 Jun 2020 08:19:46: Fewer paired peaks (713) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 713 pairs to build model! INFO @ Tue, 16 Jun 2020 08:19:46: start model_add_line... INFO @ Tue, 16 Jun 2020 08:19:46: start X-correlation... INFO @ Tue, 16 Jun 2020 08:19:46: end of X-cor INFO @ Tue, 16 Jun 2020 08:19:46: #2 finished! INFO @ Tue, 16 Jun 2020 08:19:46: #2 predicted fragment length is 123 bps INFO @ Tue, 16 Jun 2020 08:19:46: #2 alternative fragment length(s) may be 123 bps INFO @ Tue, 16 Jun 2020 08:19:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257682/SRX257682.05_model.r INFO @ Tue, 16 Jun 2020 08:19:46: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:19:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:19:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257682/SRX257682.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257682/SRX257682.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257682/SRX257682.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257682/SRX257682.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 08:19:46: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:19:46: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:19:51: 1000000 INFO @ Tue, 16 Jun 2020 08:19:57: 2000000 INFO @ Tue, 16 Jun 2020 08:19:59: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:20:02: 3000000 INFO @ Tue, 16 Jun 2020 08:20:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257682/SRX257682.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:20:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257682/SRX257682.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:20:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257682/SRX257682.05_summits.bed INFO @ Tue, 16 Jun 2020 08:20:06: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1580 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:20:08: 4000000 INFO @ Tue, 16 Jun 2020 08:20:13: 5000000 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 08:20:15: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 08:20:15: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 08:20:15: #1 total tags in treatment: 5389733 INFO @ Tue, 16 Jun 2020 08:20:15: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:20:15: #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 08:20:15: #1 tags after filtering in treatment: 5389733 INFO @ Tue, 16 Jun 2020 08:20:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:20:15: #1 finished! INFO @ Tue, 16 Jun 2020 08:20:15: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:20:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:20:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257682/SRX257682.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257682/SRX257682.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257682/SRX257682.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257682/SRX257682.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 08:20:16: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:20:16: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:20:16: #2 number of paired peaks: 713 WARNING @ Tue, 16 Jun 2020 08:20:16: Fewer paired peaks (713) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 713 pairs to build model! INFO @ Tue, 16 Jun 2020 08:20:16: start model_add_line... INFO @ Tue, 16 Jun 2020 08:20:16: start X-correlation... INFO @ Tue, 16 Jun 2020 08:20:16: end of X-cor INFO @ Tue, 16 Jun 2020 08:20:16: #2 finished! INFO @ Tue, 16 Jun 2020 08:20:16: #2 predicted fragment length is 123 bps INFO @ Tue, 16 Jun 2020 08:20:16: #2 alternative fragment length(s) may be 123 bps INFO @ Tue, 16 Jun 2020 08:20:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257682/SRX257682.10_model.r INFO @ Tue, 16 Jun 2020 08:20:16: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:20:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:20:22: 1000000 INFO @ Tue, 16 Jun 2020 08:20:28: 2000000 INFO @ Tue, 16 Jun 2020 08:20:30: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:20:33: 3000000 INFO @ Tue, 16 Jun 2020 08:20:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257682/SRX257682.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:20:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257682/SRX257682.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:20:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257682/SRX257682.10_summits.bed INFO @ Tue, 16 Jun 2020 08:20:36: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (807 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:20:38: 4000000 INFO @ Tue, 16 Jun 2020 08:20:44: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:20:46: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 08:20:46: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 08:20:46: #1 total tags in treatment: 5389733 INFO @ Tue, 16 Jun 2020 08:20:46: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:20:46: #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 08:20:46: #1 tags after filtering in treatment: 5389733 INFO @ Tue, 16 Jun 2020 08:20:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:20:46: #1 finished! INFO @ Tue, 16 Jun 2020 08:20:46: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:20:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:20:46: #2 number of paired peaks: 713 WARNING @ Tue, 16 Jun 2020 08:20:46: Fewer paired peaks (713) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 713 pairs to build model! INFO @ Tue, 16 Jun 2020 08:20:46: start model_add_line... INFO @ Tue, 16 Jun 2020 08:20:46: start X-correlation... INFO @ Tue, 16 Jun 2020 08:20:46: end of X-cor INFO @ Tue, 16 Jun 2020 08:20:46: #2 finished! INFO @ Tue, 16 Jun 2020 08:20:46: #2 predicted fragment length is 123 bps INFO @ Tue, 16 Jun 2020 08:20:46: #2 alternative fragment length(s) may be 123 bps INFO @ Tue, 16 Jun 2020 08:20:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257682/SRX257682.20_model.r INFO @ Tue, 16 Jun 2020 08:20:46: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:20:46: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:20:59: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:21:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257682/SRX257682.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:21:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257682/SRX257682.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:21:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257682/SRX257682.20_summits.bed INFO @ Tue, 16 Jun 2020 08:21:05: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (341 records, 4 fields): 2 millis CompletedMACS2peakCalling