Job ID = 6365906 SRX = SRX027097 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:35:21 prefetch.2.10.7: 1) Downloading 'SRR066369'... 2020-06-15T22:35:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:40:00 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:40:00 prefetch.2.10.7: 1) 'SRR066369' was downloaded successfully Read 4371299 spots for SRR066369/SRR066369.sra Written 4371299 spots for SRR066369/SRR066369.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: 00:00:40 4371299 reads; of these: 4371299 (100.00%) were unpaired; of these: 1058260 (24.21%) aligned 0 times 2614455 (59.81%) aligned exactly 1 time 698584 (15.98%) aligned >1 times 75.79% overall alignment rate Time searching: 00:00:40 Overall time: 00:00:40 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] 884501 / 3313039 = 0.2670 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 07:42:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX027097/SRX027097.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX027097/SRX027097.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX027097/SRX027097.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX027097/SRX027097.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 07:42:08: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:42:08: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:42:13: 1000000 INFO @ Tue, 16 Jun 2020 07:42:19: 2000000 INFO @ Tue, 16 Jun 2020 07:42:21: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:42:21: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:42:21: #1 total tags in treatment: 2428538 INFO @ Tue, 16 Jun 2020 07:42:21: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:42:21: #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 07:42:21: #1 tags after filtering in treatment: 2428538 INFO @ Tue, 16 Jun 2020 07:42:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:42:21: #1 finished! INFO @ Tue, 16 Jun 2020 07:42:21: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:42:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:42:21: #2 number of paired peaks: 695 WARNING @ Tue, 16 Jun 2020 07:42:21: Fewer paired peaks (695) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 695 pairs to build model! INFO @ Tue, 16 Jun 2020 07:42:21: start model_add_line... INFO @ Tue, 16 Jun 2020 07:42:21: start X-correlation... INFO @ Tue, 16 Jun 2020 07:42:21: end of X-cor INFO @ Tue, 16 Jun 2020 07:42:21: #2 finished! INFO @ Tue, 16 Jun 2020 07:42:21: #2 predicted fragment length is 194 bps INFO @ Tue, 16 Jun 2020 07:42:21: #2 alternative fragment length(s) may be 194 bps INFO @ Tue, 16 Jun 2020 07:42:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX027097/SRX027097.05_model.r INFO @ Tue, 16 Jun 2020 07:42:21: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:42:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:42:27: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:42:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX027097/SRX027097.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:42:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX027097/SRX027097.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:42:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX027097/SRX027097.05_summits.bed INFO @ Tue, 16 Jun 2020 07:42:30: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2038 records, 4 fields): 3 millis CompletedMACS2peakCalling 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 07:42:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX027097/SRX027097.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX027097/SRX027097.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX027097/SRX027097.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX027097/SRX027097.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 07:42:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:42:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:42:44: 1000000 INFO @ Tue, 16 Jun 2020 07:42:49: 2000000 INFO @ Tue, 16 Jun 2020 07:42:51: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:42:51: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:42:51: #1 total tags in treatment: 2428538 INFO @ Tue, 16 Jun 2020 07:42:51: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:42:51: #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 07:42:51: #1 tags after filtering in treatment: 2428538 INFO @ Tue, 16 Jun 2020 07:42:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:42:51: #1 finished! INFO @ Tue, 16 Jun 2020 07:42:51: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:42:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:42:51: #2 number of paired peaks: 695 WARNING @ Tue, 16 Jun 2020 07:42:51: Fewer paired peaks (695) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 695 pairs to build model! INFO @ Tue, 16 Jun 2020 07:42:51: start model_add_line... INFO @ Tue, 16 Jun 2020 07:42:51: start X-correlation... INFO @ Tue, 16 Jun 2020 07:42:51: end of X-cor INFO @ Tue, 16 Jun 2020 07:42:51: #2 finished! INFO @ Tue, 16 Jun 2020 07:42:51: #2 predicted fragment length is 194 bps INFO @ Tue, 16 Jun 2020 07:42:51: #2 alternative fragment length(s) may be 194 bps INFO @ Tue, 16 Jun 2020 07:42:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX027097/SRX027097.10_model.r INFO @ Tue, 16 Jun 2020 07:42:51: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:42:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:42:57: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:43:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX027097/SRX027097.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:43:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX027097/SRX027097.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:43:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX027097/SRX027097.10_summits.bed INFO @ Tue, 16 Jun 2020 07:43:00: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (307 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 07:43:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX027097/SRX027097.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX027097/SRX027097.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX027097/SRX027097.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX027097/SRX027097.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 07:43:09: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:43:09: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:43:14: 1000000 INFO @ Tue, 16 Jun 2020 07:43:19: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:43:21: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:43:21: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:43:21: #1 total tags in treatment: 2428538 INFO @ Tue, 16 Jun 2020 07:43:21: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:43:21: #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 07:43:21: #1 tags after filtering in treatment: 2428538 INFO @ Tue, 16 Jun 2020 07:43:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:43:21: #1 finished! INFO @ Tue, 16 Jun 2020 07:43:21: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:43:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:43:22: #2 number of paired peaks: 695 WARNING @ Tue, 16 Jun 2020 07:43:22: Fewer paired peaks (695) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 695 pairs to build model! INFO @ Tue, 16 Jun 2020 07:43:22: start model_add_line... INFO @ Tue, 16 Jun 2020 07:43:22: start X-correlation... INFO @ Tue, 16 Jun 2020 07:43:22: end of X-cor INFO @ Tue, 16 Jun 2020 07:43:22: #2 finished! INFO @ Tue, 16 Jun 2020 07:43:22: #2 predicted fragment length is 194 bps INFO @ Tue, 16 Jun 2020 07:43:22: #2 alternative fragment length(s) may be 194 bps INFO @ Tue, 16 Jun 2020 07:43:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX027097/SRX027097.20_model.r INFO @ Tue, 16 Jun 2020 07:43:22: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:43:22: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:43:28: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:43:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX027097/SRX027097.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:43:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX027097/SRX027097.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:43:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX027097/SRX027097.20_summits.bed INFO @ Tue, 16 Jun 2020 07:43:31: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (90 records, 4 fields): 1 millis CompletedMACS2peakCalling