Job ID = 6497514 SRX = SRX495104 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T22:27:43 prefetch.2.10.7: 1) Downloading 'SRR1198636'... 2020-06-25T22:27:43 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:30:17 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:30:17 prefetch.2.10.7: 1) 'SRR1198636' was downloaded successfully Read 13968794 spots for SRR1198636/SRR1198636.sra Written 13968794 spots for SRR1198636/SRR1198636.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: 00:02:14 13968794 reads; of these: 13968794 (100.00%) were unpaired; of these: 6374301 (45.63%) aligned 0 times 6536980 (46.80%) aligned exactly 1 time 1057513 (7.57%) aligned >1 times 54.37% overall alignment rate Time searching: 00:02:14 Overall time: 00:02:14 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] 3828149 / 7594493 = 0.5041 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 @ Fri, 26 Jun 2020 07:35:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495104/SRX495104.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495104/SRX495104.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495104/SRX495104.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495104/SRX495104.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 @ Fri, 26 Jun 2020 07:35:16: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:35:16: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:35:21: 1000000 INFO @ Fri, 26 Jun 2020 07:35:27: 2000000 INFO @ Fri, 26 Jun 2020 07:35:33: 3000000 INFO @ Fri, 26 Jun 2020 07:35:37: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 07:35:37: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 07:35:37: #1 total tags in treatment: 3766344 INFO @ Fri, 26 Jun 2020 07:35:37: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:35:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:35:38: #1 tags after filtering in treatment: 3766344 INFO @ Fri, 26 Jun 2020 07:35:38: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:35:38: #1 finished! INFO @ Fri, 26 Jun 2020 07:35:38: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:35:38: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:35:38: #2 number of paired peaks: 701 WARNING @ Fri, 26 Jun 2020 07:35:38: Fewer paired peaks (701) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 701 pairs to build model! INFO @ Fri, 26 Jun 2020 07:35:38: start model_add_line... INFO @ Fri, 26 Jun 2020 07:35:38: start X-correlation... INFO @ Fri, 26 Jun 2020 07:35:38: end of X-cor INFO @ Fri, 26 Jun 2020 07:35:38: #2 finished! INFO @ Fri, 26 Jun 2020 07:35:38: #2 predicted fragment length is 104 bps INFO @ Fri, 26 Jun 2020 07:35:38: #2 alternative fragment length(s) may be 4,104 bps INFO @ Fri, 26 Jun 2020 07:35:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495104/SRX495104.05_model.r INFO @ Fri, 26 Jun 2020 07:35:38: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:35:38: #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 @ Fri, 26 Jun 2020 07:35:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495104/SRX495104.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495104/SRX495104.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495104/SRX495104.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495104/SRX495104.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 @ Fri, 26 Jun 2020 07:35:46: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:35:46: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:35:48: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:35:52: 1000000 INFO @ Fri, 26 Jun 2020 07:35:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495104/SRX495104.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:35:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495104/SRX495104.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:35:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495104/SRX495104.05_summits.bed INFO @ Fri, 26 Jun 2020 07:35:53: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (570 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:35:58: 2000000 INFO @ Fri, 26 Jun 2020 07:36:04: 3000000 INFO @ Fri, 26 Jun 2020 07:36:08: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 07:36:08: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 07:36:08: #1 total tags in treatment: 3766344 INFO @ Fri, 26 Jun 2020 07:36:08: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:36:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:36:08: #1 tags after filtering in treatment: 3766344 INFO @ Fri, 26 Jun 2020 07:36:08: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:36:08: #1 finished! INFO @ Fri, 26 Jun 2020 07:36:08: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:36:08: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:36:08: #2 number of paired peaks: 701 WARNING @ Fri, 26 Jun 2020 07:36:08: Fewer paired peaks (701) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 701 pairs to build model! INFO @ Fri, 26 Jun 2020 07:36:08: start model_add_line... INFO @ Fri, 26 Jun 2020 07:36:08: start X-correlation... INFO @ Fri, 26 Jun 2020 07:36:08: end of X-cor INFO @ Fri, 26 Jun 2020 07:36:08: #2 finished! INFO @ Fri, 26 Jun 2020 07:36:08: #2 predicted fragment length is 104 bps INFO @ Fri, 26 Jun 2020 07:36:08: #2 alternative fragment length(s) may be 4,104 bps INFO @ Fri, 26 Jun 2020 07:36:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495104/SRX495104.10_model.r INFO @ Fri, 26 Jun 2020 07:36:08: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:36:08: #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 @ Fri, 26 Jun 2020 07:36:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495104/SRX495104.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495104/SRX495104.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495104/SRX495104.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495104/SRX495104.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 @ Fri, 26 Jun 2020 07:36:16: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:36:16: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:36:18: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:36:22: 1000000 INFO @ Fri, 26 Jun 2020 07:36:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495104/SRX495104.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:36:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495104/SRX495104.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:36:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495104/SRX495104.10_summits.bed INFO @ Fri, 26 Jun 2020 07:36:23: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (329 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:36:28: 2000000 INFO @ Fri, 26 Jun 2020 07:36:34: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:36:38: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 07:36:38: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 07:36:38: #1 total tags in treatment: 3766344 INFO @ Fri, 26 Jun 2020 07:36:38: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:36:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:36:38: #1 tags after filtering in treatment: 3766344 INFO @ Fri, 26 Jun 2020 07:36:38: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:36:38: #1 finished! INFO @ Fri, 26 Jun 2020 07:36:38: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:36:38: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:36:39: #2 number of paired peaks: 701 WARNING @ Fri, 26 Jun 2020 07:36:39: Fewer paired peaks (701) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 701 pairs to build model! INFO @ Fri, 26 Jun 2020 07:36:39: start model_add_line... INFO @ Fri, 26 Jun 2020 07:36:39: start X-correlation... INFO @ Fri, 26 Jun 2020 07:36:39: end of X-cor INFO @ Fri, 26 Jun 2020 07:36:39: #2 finished! INFO @ Fri, 26 Jun 2020 07:36:39: #2 predicted fragment length is 104 bps INFO @ Fri, 26 Jun 2020 07:36:39: #2 alternative fragment length(s) may be 4,104 bps INFO @ Fri, 26 Jun 2020 07:36:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495104/SRX495104.20_model.r INFO @ Fri, 26 Jun 2020 07:36:39: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:36:39: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 07:36:49: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:36:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495104/SRX495104.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:36:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495104/SRX495104.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:36:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495104/SRX495104.20_summits.bed INFO @ Fri, 26 Jun 2020 07:36:54: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (165 records, 4 fields): 6 millis CompletedMACS2peakCalling