Job ID = 6367134 SRX = SRX277092 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:18:01 prefetch.2.10.7: 1) Downloading 'SRR849768'... 2020-06-15T23:18:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:18:35 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:18:35 prefetch.2.10.7: 'SRR849768' is valid 2020-06-15T23:18:35 prefetch.2.10.7: 1) 'SRR849768' was downloaded successfully Read 6184224 spots for SRR849768/SRR849768.sra Written 6184224 spots for SRR849768/SRR849768.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: 00:00:51 6184224 reads; of these: 6184224 (100.00%) were unpaired; of these: 831203 (13.44%) aligned 0 times 4565474 (73.82%) aligned exactly 1 time 787547 (12.73%) aligned >1 times 86.56% overall alignment rate Time searching: 00:00:51 Overall time: 00:00:51 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] 748073 / 5353021 = 0.1397 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 08:21:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX277092/SRX277092.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX277092/SRX277092.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX277092/SRX277092.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX277092/SRX277092.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 08:21:14: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:21:14: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:21:18: 1000000 INFO @ Tue, 16 Jun 2020 08:21:23: 2000000 INFO @ Tue, 16 Jun 2020 08:21:27: 3000000 INFO @ Tue, 16 Jun 2020 08:21:32: 4000000 INFO @ Tue, 16 Jun 2020 08:21:35: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:21:35: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:21:35: #1 total tags in treatment: 4604948 INFO @ Tue, 16 Jun 2020 08:21:35: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:21:35: #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 08:21:35: #1 tags after filtering in treatment: 4604948 INFO @ Tue, 16 Jun 2020 08:21:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:21:35: #1 finished! INFO @ Tue, 16 Jun 2020 08:21:35: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:21:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:21:35: #2 number of paired peaks: 805 WARNING @ Tue, 16 Jun 2020 08:21:35: Fewer paired peaks (805) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 805 pairs to build model! INFO @ Tue, 16 Jun 2020 08:21:35: start model_add_line... INFO @ Tue, 16 Jun 2020 08:21:36: start X-correlation... INFO @ Tue, 16 Jun 2020 08:21:36: end of X-cor INFO @ Tue, 16 Jun 2020 08:21:36: #2 finished! INFO @ Tue, 16 Jun 2020 08:21:36: #2 predicted fragment length is 131 bps INFO @ Tue, 16 Jun 2020 08:21:36: #2 alternative fragment length(s) may be 131 bps INFO @ Tue, 16 Jun 2020 08:21:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX277092/SRX277092.05_model.r INFO @ Tue, 16 Jun 2020 08:21:36: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:21:36: #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 08:21:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX277092/SRX277092.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX277092/SRX277092.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX277092/SRX277092.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX277092/SRX277092.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 08:21:44: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:21:44: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:21:46: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:21:48: 1000000 INFO @ Tue, 16 Jun 2020 08:21:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX277092/SRX277092.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:21:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX277092/SRX277092.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:21:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX277092/SRX277092.05_summits.bed INFO @ Tue, 16 Jun 2020 08:21:52: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3042 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:21:53: 2000000 INFO @ Tue, 16 Jun 2020 08:21:57: 3000000 INFO @ Tue, 16 Jun 2020 08:22:02: 4000000 INFO @ Tue, 16 Jun 2020 08:22:05: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:22:05: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:22:05: #1 total tags in treatment: 4604948 INFO @ Tue, 16 Jun 2020 08:22:05: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:22:05: #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 08:22:05: #1 tags after filtering in treatment: 4604948 INFO @ Tue, 16 Jun 2020 08:22:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:22:05: #1 finished! INFO @ Tue, 16 Jun 2020 08:22:05: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:22:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:22:05: #2 number of paired peaks: 805 WARNING @ Tue, 16 Jun 2020 08:22:05: Fewer paired peaks (805) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 805 pairs to build model! INFO @ Tue, 16 Jun 2020 08:22:05: start model_add_line... INFO @ Tue, 16 Jun 2020 08:22:05: start X-correlation... INFO @ Tue, 16 Jun 2020 08:22:05: end of X-cor INFO @ Tue, 16 Jun 2020 08:22:05: #2 finished! INFO @ Tue, 16 Jun 2020 08:22:05: #2 predicted fragment length is 131 bps INFO @ Tue, 16 Jun 2020 08:22:05: #2 alternative fragment length(s) may be 131 bps INFO @ Tue, 16 Jun 2020 08:22:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX277092/SRX277092.10_model.r INFO @ Tue, 16 Jun 2020 08:22:05: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:22:05: #3 Pre-compute pvalue-qvalue table... 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 08:22:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX277092/SRX277092.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX277092/SRX277092.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX277092/SRX277092.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX277092/SRX277092.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 08:22:14: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:22:14: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:22:16: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:22:18: 1000000 INFO @ Tue, 16 Jun 2020 08:22:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX277092/SRX277092.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:22:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX277092/SRX277092.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:22:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX277092/SRX277092.10_summits.bed INFO @ Tue, 16 Jun 2020 08:22:21: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1700 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:22:23: 2000000 INFO @ Tue, 16 Jun 2020 08:22:28: 3000000 INFO @ Tue, 16 Jun 2020 08:22:32: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:22:35: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:22:35: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:22:35: #1 total tags in treatment: 4604948 INFO @ Tue, 16 Jun 2020 08:22:35: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:22:35: #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 08:22:35: #1 tags after filtering in treatment: 4604948 INFO @ Tue, 16 Jun 2020 08:22:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:22:35: #1 finished! INFO @ Tue, 16 Jun 2020 08:22:35: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:22:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:22:36: #2 number of paired peaks: 805 WARNING @ Tue, 16 Jun 2020 08:22:36: Fewer paired peaks (805) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 805 pairs to build model! INFO @ Tue, 16 Jun 2020 08:22:36: start model_add_line... INFO @ Tue, 16 Jun 2020 08:22:36: start X-correlation... INFO @ Tue, 16 Jun 2020 08:22:36: end of X-cor INFO @ Tue, 16 Jun 2020 08:22:36: #2 finished! INFO @ Tue, 16 Jun 2020 08:22:36: #2 predicted fragment length is 131 bps INFO @ Tue, 16 Jun 2020 08:22:36: #2 alternative fragment length(s) may be 131 bps INFO @ Tue, 16 Jun 2020 08:22:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX277092/SRX277092.20_model.r INFO @ Tue, 16 Jun 2020 08:22:36: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:22:36: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:22:47: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:22:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX277092/SRX277092.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:22:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX277092/SRX277092.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:22:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX277092/SRX277092.20_summits.bed INFO @ Tue, 16 Jun 2020 08:22:52: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (683 records, 4 fields): 1 millis CompletedMACS2peakCalling