Job ID = 6367259 SRX = SRX323680 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:22:16 prefetch.2.10.7: 1) Downloading 'SRR935754'... 2020-06-15T23:22:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:23:18 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:23:19 prefetch.2.10.7: 'SRR935754' is valid 2020-06-15T23:23:19 prefetch.2.10.7: 1) 'SRR935754' was downloaded successfully Read 13374012 spots for SRR935754/SRR935754.sra Written 13374012 spots for SRR935754/SRR935754.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: 00:01:19 13374012 reads; of these: 13374012 (100.00%) were unpaired; of these: 7111160 (53.17%) aligned 0 times 5026079 (37.58%) aligned exactly 1 time 1236773 (9.25%) aligned >1 times 46.83% overall alignment rate Time searching: 00:01:19 Overall time: 00:01:19 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] 1499608 / 6262852 = 0.2394 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 08:27:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX323680/SRX323680.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX323680/SRX323680.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX323680/SRX323680.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX323680/SRX323680.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 08:27:08: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:27:08: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:27:14: 1000000 INFO @ Tue, 16 Jun 2020 08:27:19: 2000000 INFO @ Tue, 16 Jun 2020 08:27:24: 3000000 INFO @ Tue, 16 Jun 2020 08:27:30: 4000000 INFO @ Tue, 16 Jun 2020 08:27:34: #1 tag size is determined as 35 bps INFO @ Tue, 16 Jun 2020 08:27:34: #1 tag size = 35 INFO @ Tue, 16 Jun 2020 08:27:34: #1 total tags in treatment: 4763244 INFO @ Tue, 16 Jun 2020 08:27:34: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:27:34: #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 08:27:34: #1 tags after filtering in treatment: 4763244 INFO @ Tue, 16 Jun 2020 08:27:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:27:34: #1 finished! INFO @ Tue, 16 Jun 2020 08:27:34: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:27:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:27:34: #2 number of paired peaks: 339 WARNING @ Tue, 16 Jun 2020 08:27:34: Fewer paired peaks (339) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 339 pairs to build model! INFO @ Tue, 16 Jun 2020 08:27:34: start model_add_line... INFO @ Tue, 16 Jun 2020 08:27:34: start X-correlation... INFO @ Tue, 16 Jun 2020 08:27:34: end of X-cor INFO @ Tue, 16 Jun 2020 08:27:34: #2 finished! INFO @ Tue, 16 Jun 2020 08:27:34: #2 predicted fragment length is 116 bps INFO @ Tue, 16 Jun 2020 08:27:34: #2 alternative fragment length(s) may be 96,101,116 bps INFO @ Tue, 16 Jun 2020 08:27:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX323680/SRX323680.05_model.r INFO @ Tue, 16 Jun 2020 08:27:34: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:27:34: #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 08:27:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX323680/SRX323680.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX323680/SRX323680.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX323680/SRX323680.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX323680/SRX323680.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 08:27:39: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:27:39: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:27:45: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:27:46: 1000000 INFO @ Tue, 16 Jun 2020 08:27:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX323680/SRX323680.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:27:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX323680/SRX323680.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:27:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX323680/SRX323680.05_summits.bed INFO @ Tue, 16 Jun 2020 08:27:50: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (488 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:27:52: 2000000 INFO @ Tue, 16 Jun 2020 08:27:59: 3000000 INFO @ Tue, 16 Jun 2020 08:28:05: 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 08:28:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX323680/SRX323680.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX323680/SRX323680.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX323680/SRX323680.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX323680/SRX323680.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 08:28:08: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:28:08: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:28:10: #1 tag size is determined as 35 bps INFO @ Tue, 16 Jun 2020 08:28:10: #1 tag size = 35 INFO @ Tue, 16 Jun 2020 08:28:10: #1 total tags in treatment: 4763244 INFO @ Tue, 16 Jun 2020 08:28:10: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:28:10: #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 08:28:10: #1 tags after filtering in treatment: 4763244 INFO @ Tue, 16 Jun 2020 08:28:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:28:10: #1 finished! INFO @ Tue, 16 Jun 2020 08:28:10: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:28:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:28:10: #2 number of paired peaks: 339 WARNING @ Tue, 16 Jun 2020 08:28:10: Fewer paired peaks (339) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 339 pairs to build model! INFO @ Tue, 16 Jun 2020 08:28:10: start model_add_line... INFO @ Tue, 16 Jun 2020 08:28:10: start X-correlation... INFO @ Tue, 16 Jun 2020 08:28:10: end of X-cor INFO @ Tue, 16 Jun 2020 08:28:10: #2 finished! INFO @ Tue, 16 Jun 2020 08:28:10: #2 predicted fragment length is 116 bps INFO @ Tue, 16 Jun 2020 08:28:10: #2 alternative fragment length(s) may be 96,101,116 bps INFO @ Tue, 16 Jun 2020 08:28:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX323680/SRX323680.10_model.r INFO @ Tue, 16 Jun 2020 08:28:10: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:28:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:28:15: 1000000 INFO @ Tue, 16 Jun 2020 08:28:21: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:28:21: 2000000 INFO @ Tue, 16 Jun 2020 08:28:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX323680/SRX323680.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:28:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX323680/SRX323680.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:28:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX323680/SRX323680.10_summits.bed INFO @ Tue, 16 Jun 2020 08:28:26: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (287 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:28:27: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:28:34: 4000000 INFO @ Tue, 16 Jun 2020 08:28:39: #1 tag size is determined as 35 bps INFO @ Tue, 16 Jun 2020 08:28:39: #1 tag size = 35 INFO @ Tue, 16 Jun 2020 08:28:39: #1 total tags in treatment: 4763244 INFO @ Tue, 16 Jun 2020 08:28:39: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:28:39: #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 08:28:39: #1 tags after filtering in treatment: 4763244 INFO @ Tue, 16 Jun 2020 08:28:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:28:39: #1 finished! INFO @ Tue, 16 Jun 2020 08:28:39: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:28:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:28:39: #2 number of paired peaks: 339 WARNING @ Tue, 16 Jun 2020 08:28:39: Fewer paired peaks (339) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 339 pairs to build model! INFO @ Tue, 16 Jun 2020 08:28:39: start model_add_line... INFO @ Tue, 16 Jun 2020 08:28:39: start X-correlation... INFO @ Tue, 16 Jun 2020 08:28:39: end of X-cor INFO @ Tue, 16 Jun 2020 08:28:39: #2 finished! INFO @ Tue, 16 Jun 2020 08:28:39: #2 predicted fragment length is 116 bps INFO @ Tue, 16 Jun 2020 08:28:39: #2 alternative fragment length(s) may be 96,101,116 bps INFO @ Tue, 16 Jun 2020 08:28:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX323680/SRX323680.20_model.r INFO @ Tue, 16 Jun 2020 08:28:39: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:28:39: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:28:49: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:28:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX323680/SRX323680.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:28:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX323680/SRX323680.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:28:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX323680/SRX323680.20_summits.bed INFO @ Tue, 16 Jun 2020 08:28:55: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (148 records, 4 fields): 1 millis CompletedMACS2peakCalling