Job ID = 6366975 SRX = SRX257674 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:15:46 prefetch.2.10.7: 1) Downloading 'SRR800685'... 2020-06-15T23:15:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:17:18 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:17:19 prefetch.2.10.7: 'SRR800685' is valid 2020-06-15T23:17:19 prefetch.2.10.7: 1) 'SRR800685' was downloaded successfully Read 16729386 spots for SRR800685/SRR800685.sra Written 16729386 spots for SRR800685/SRR800685.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: 00:03:06 16729386 reads; of these: 16729386 (100.00%) were unpaired; of these: 2428302 (14.52%) aligned 0 times 11754921 (70.27%) aligned exactly 1 time 2546163 (15.22%) aligned >1 times 85.48% overall alignment rate Time searching: 00:03:06 Overall time: 00:03:06 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] 9688567 / 14301084 = 0.6775 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 08:24:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257674/SRX257674.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257674/SRX257674.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257674/SRX257674.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257674/SRX257674.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 08:24:02: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:24:02: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:24:08: 1000000 INFO @ Tue, 16 Jun 2020 08:24:13: 2000000 INFO @ Tue, 16 Jun 2020 08:24:19: 3000000 INFO @ Tue, 16 Jun 2020 08:24:24: 4000000 INFO @ Tue, 16 Jun 2020 08:24:28: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 08:24:28: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 08:24:28: #1 total tags in treatment: 4612517 INFO @ Tue, 16 Jun 2020 08:24:28: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:24:28: #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 08:24:28: #1 tags after filtering in treatment: 4612517 INFO @ Tue, 16 Jun 2020 08:24:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:24:28: #1 finished! INFO @ Tue, 16 Jun 2020 08:24:28: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:24:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:24:28: #2 number of paired peaks: 923 WARNING @ Tue, 16 Jun 2020 08:24:28: Fewer paired peaks (923) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 923 pairs to build model! INFO @ Tue, 16 Jun 2020 08:24:28: start model_add_line... INFO @ Tue, 16 Jun 2020 08:24:28: start X-correlation... INFO @ Tue, 16 Jun 2020 08:24:28: end of X-cor INFO @ Tue, 16 Jun 2020 08:24:28: #2 finished! INFO @ Tue, 16 Jun 2020 08:24:28: #2 predicted fragment length is 143 bps INFO @ Tue, 16 Jun 2020 08:24:28: #2 alternative fragment length(s) may be 143 bps INFO @ Tue, 16 Jun 2020 08:24:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257674/SRX257674.05_model.r INFO @ Tue, 16 Jun 2020 08:24:28: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:24:28: #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 08:24:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257674/SRX257674.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257674/SRX257674.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257674/SRX257674.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257674/SRX257674.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 08:24:32: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:24:32: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:24:39: 1000000 INFO @ Tue, 16 Jun 2020 08:24:40: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:24:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257674/SRX257674.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:24:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257674/SRX257674.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:24:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257674/SRX257674.05_summits.bed INFO @ Tue, 16 Jun 2020 08:24:46: Done! INFO @ Tue, 16 Jun 2020 08:24:46: 2000000 pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2577 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:24:53: 3000000 INFO @ Tue, 16 Jun 2020 08:24:59: 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 08:25:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257674/SRX257674.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257674/SRX257674.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257674/SRX257674.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257674/SRX257674.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 08:25:02: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:25:02: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:25:03: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 08:25:03: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 08:25:03: #1 total tags in treatment: 4612517 INFO @ Tue, 16 Jun 2020 08:25:03: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:25:03: #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 08:25:03: #1 tags after filtering in treatment: 4612517 INFO @ Tue, 16 Jun 2020 08:25:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:25:03: #1 finished! INFO @ Tue, 16 Jun 2020 08:25:03: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:25:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:25:03: #2 number of paired peaks: 923 WARNING @ Tue, 16 Jun 2020 08:25:03: Fewer paired peaks (923) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 923 pairs to build model! INFO @ Tue, 16 Jun 2020 08:25:03: start model_add_line... INFO @ Tue, 16 Jun 2020 08:25:04: start X-correlation... INFO @ Tue, 16 Jun 2020 08:25:04: end of X-cor INFO @ Tue, 16 Jun 2020 08:25:04: #2 finished! INFO @ Tue, 16 Jun 2020 08:25:04: #2 predicted fragment length is 143 bps INFO @ Tue, 16 Jun 2020 08:25:04: #2 alternative fragment length(s) may be 143 bps INFO @ Tue, 16 Jun 2020 08:25:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257674/SRX257674.10_model.r INFO @ Tue, 16 Jun 2020 08:25:04: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:25:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:25:08: 1000000 INFO @ Tue, 16 Jun 2020 08:25:15: 2000000 INFO @ Tue, 16 Jun 2020 08:25:15: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:25:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257674/SRX257674.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:25:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257674/SRX257674.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:25:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257674/SRX257674.10_summits.bed INFO @ Tue, 16 Jun 2020 08:25:21: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1279 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:25:21: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:25:28: 4000000 INFO @ Tue, 16 Jun 2020 08:25:31: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 08:25:31: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 08:25:31: #1 total tags in treatment: 4612517 INFO @ Tue, 16 Jun 2020 08:25:31: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:25:31: #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 08:25:32: #1 tags after filtering in treatment: 4612517 INFO @ Tue, 16 Jun 2020 08:25:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:25:32: #1 finished! INFO @ Tue, 16 Jun 2020 08:25:32: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:25:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:25:32: #2 number of paired peaks: 923 WARNING @ Tue, 16 Jun 2020 08:25:32: Fewer paired peaks (923) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 923 pairs to build model! INFO @ Tue, 16 Jun 2020 08:25:32: start model_add_line... INFO @ Tue, 16 Jun 2020 08:25:32: start X-correlation... INFO @ Tue, 16 Jun 2020 08:25:32: end of X-cor INFO @ Tue, 16 Jun 2020 08:25:32: #2 finished! INFO @ Tue, 16 Jun 2020 08:25:32: #2 predicted fragment length is 143 bps INFO @ Tue, 16 Jun 2020 08:25:32: #2 alternative fragment length(s) may be 143 bps INFO @ Tue, 16 Jun 2020 08:25:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257674/SRX257674.20_model.r INFO @ Tue, 16 Jun 2020 08:25:32: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:25:32: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:25:44: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:25:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257674/SRX257674.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:25:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257674/SRX257674.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:25:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257674/SRX257674.20_summits.bed INFO @ Tue, 16 Jun 2020 08:25:49: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (516 records, 4 fields): 2 millis CompletedMACS2peakCalling