Job ID = 6507944 SRX = SRX495104 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T13:44:00 prefetch.2.10.7: 1) Downloading 'SRR1198636'... 2020-06-26T13:44:00 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:46:36 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:46:36 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:02 13968794 reads; of these: 13968794 (100.00%) were unpaired; of these: 6373823 (45.63%) aligned 0 times 6537408 (46.80%) aligned exactly 1 time 1057563 (7.57%) aligned >1 times 54.37% overall alignment rate Time searching: 00:02:03 Overall time: 00:02:03 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] 3828438 / 7594971 = 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 22:51:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495104/SRX495104.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495104/SRX495104.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495104/SRX495104.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/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 22:51:19: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:51:19: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:51:24: 1000000 INFO @ Fri, 26 Jun 2020 22:51:30: 2000000 INFO @ Fri, 26 Jun 2020 22:51:35: 3000000 INFO @ Fri, 26 Jun 2020 22:51:40: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 22:51:40: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 22:51:40: #1 total tags in treatment: 3766533 INFO @ Fri, 26 Jun 2020 22:51:40: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:51:40: #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 22:51:40: #1 tags after filtering in treatment: 3766533 INFO @ Fri, 26 Jun 2020 22:51:40: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:51:40: #1 finished! INFO @ Fri, 26 Jun 2020 22:51:40: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:51:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:51:40: #2 number of paired peaks: 701 WARNING @ Fri, 26 Jun 2020 22:51:40: 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 22:51:40: start model_add_line... INFO @ Fri, 26 Jun 2020 22:51:40: start X-correlation... INFO @ Fri, 26 Jun 2020 22:51:40: end of X-cor INFO @ Fri, 26 Jun 2020 22:51:40: #2 finished! INFO @ Fri, 26 Jun 2020 22:51:40: #2 predicted fragment length is 104 bps INFO @ Fri, 26 Jun 2020 22:51:40: #2 alternative fragment length(s) may be 4,104 bps INFO @ Fri, 26 Jun 2020 22:51:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495104/SRX495104.05_model.r INFO @ Fri, 26 Jun 2020 22:51:40: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:51:40: #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 22:51:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495104/SRX495104.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495104/SRX495104.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495104/SRX495104.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/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 22:51:49: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:51:49: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:51:49: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:51:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495104/SRX495104.05_peaks.xls INFO @ Fri, 26 Jun 2020 22:51:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495104/SRX495104.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:51:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495104/SRX495104.05_summits.bed INFO @ Fri, 26 Jun 2020 22:51:54: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (571 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:51:54: 1000000 INFO @ Fri, 26 Jun 2020 22:52:00: 2000000 INFO @ Fri, 26 Jun 2020 22:52:05: 3000000 INFO @ Fri, 26 Jun 2020 22:52:09: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 22:52:09: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 22:52:09: #1 total tags in treatment: 3766533 INFO @ Fri, 26 Jun 2020 22:52:09: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:52:09: #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 22:52:09: #1 tags after filtering in treatment: 3766533 INFO @ Fri, 26 Jun 2020 22:52:09: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:52:09: #1 finished! INFO @ Fri, 26 Jun 2020 22:52:09: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:52:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:52:10: #2 number of paired peaks: 701 WARNING @ Fri, 26 Jun 2020 22:52:10: 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 22:52:10: start model_add_line... INFO @ Fri, 26 Jun 2020 22:52:10: start X-correlation... INFO @ Fri, 26 Jun 2020 22:52:10: end of X-cor INFO @ Fri, 26 Jun 2020 22:52:10: #2 finished! INFO @ Fri, 26 Jun 2020 22:52:10: #2 predicted fragment length is 104 bps INFO @ Fri, 26 Jun 2020 22:52:10: #2 alternative fragment length(s) may be 4,104 bps INFO @ Fri, 26 Jun 2020 22:52:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495104/SRX495104.10_model.r INFO @ Fri, 26 Jun 2020 22:52:10: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:52:10: #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 22:52:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495104/SRX495104.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495104/SRX495104.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495104/SRX495104.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/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 22:52:19: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:52:19: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:52:19: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:52:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495104/SRX495104.10_peaks.xls INFO @ Fri, 26 Jun 2020 22:52:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495104/SRX495104.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:52:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495104/SRX495104.10_summits.bed INFO @ Fri, 26 Jun 2020 22:52:24: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (328 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:52:24: 1000000 INFO @ Fri, 26 Jun 2020 22:52:30: 2000000 INFO @ Fri, 26 Jun 2020 22:52:35: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 22:52:39: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 22:52:39: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 22:52:39: #1 total tags in treatment: 3766533 INFO @ Fri, 26 Jun 2020 22:52:39: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:52:39: #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 22:52:39: #1 tags after filtering in treatment: 3766533 INFO @ Fri, 26 Jun 2020 22:52:39: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:52:39: #1 finished! INFO @ Fri, 26 Jun 2020 22:52:39: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:52:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:52:40: #2 number of paired peaks: 701 WARNING @ Fri, 26 Jun 2020 22:52:40: 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 22:52:40: start model_add_line... INFO @ Fri, 26 Jun 2020 22:52:40: start X-correlation... INFO @ Fri, 26 Jun 2020 22:52:40: end of X-cor INFO @ Fri, 26 Jun 2020 22:52:40: #2 finished! INFO @ Fri, 26 Jun 2020 22:52:40: #2 predicted fragment length is 104 bps INFO @ Fri, 26 Jun 2020 22:52:40: #2 alternative fragment length(s) may be 4,104 bps INFO @ Fri, 26 Jun 2020 22:52:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495104/SRX495104.20_model.r INFO @ Fri, 26 Jun 2020 22:52:40: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:52:40: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 22:52:49: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:52:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495104/SRX495104.20_peaks.xls INFO @ Fri, 26 Jun 2020 22:52:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495104/SRX495104.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:52:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495104/SRX495104.20_summits.bed INFO @ Fri, 26 Jun 2020 22:52:54: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (165 records, 4 fields): 2 millis CompletedMACS2peakCalling