Job ID = 6507924 SRX = SRX495020 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T13:44:31 prefetch.2.10.7: 1) Downloading 'SRR1198552'... 2020-06-26T13:44:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:48:01 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:48:01 prefetch.2.10.7: 1) 'SRR1198552' was downloaded successfully Read 19841011 spots for SRR1198552/SRR1198552.sra Written 19841011 spots for SRR1198552/SRR1198552.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: 00:03:23 19841011 reads; of these: 19841011 (100.00%) were unpaired; of these: 3918810 (19.75%) aligned 0 times 12951479 (65.28%) aligned exactly 1 time 2970722 (14.97%) aligned >1 times 80.25% overall alignment rate Time searching: 00:03:23 Overall time: 00:03:23 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_sort_core] merging from 8 files... [bam_rmdupse_core] 5781312 / 15922201 = 0.3631 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 22:56:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495020/SRX495020.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495020/SRX495020.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495020/SRX495020.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495020/SRX495020.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 22:56:00: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:56:00: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:56:06: 1000000 INFO @ Fri, 26 Jun 2020 22:56:12: 2000000 INFO @ Fri, 26 Jun 2020 22:56:18: 3000000 INFO @ Fri, 26 Jun 2020 22:56:24: 4000000 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 22:56:30: 5000000 INFO @ Fri, 26 Jun 2020 22:56:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495020/SRX495020.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495020/SRX495020.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495020/SRX495020.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495020/SRX495020.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 22:56:30: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:56:30: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:56:36: 6000000 INFO @ Fri, 26 Jun 2020 22:56:36: 1000000 INFO @ Fri, 26 Jun 2020 22:56:42: 7000000 INFO @ Fri, 26 Jun 2020 22:56:42: 2000000 INFO @ Fri, 26 Jun 2020 22:56:48: 8000000 INFO @ Fri, 26 Jun 2020 22:56:49: 3000000 INFO @ Fri, 26 Jun 2020 22:56:54: 9000000 INFO @ Fri, 26 Jun 2020 22:56:55: 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 @ Fri, 26 Jun 2020 22:57:00: 10000000 INFO @ Fri, 26 Jun 2020 22:57:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495020/SRX495020.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495020/SRX495020.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495020/SRX495020.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495020/SRX495020.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 22:57:00: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:57:00: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:57:01: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 22:57:01: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 22:57:01: #1 total tags in treatment: 10140889 INFO @ Fri, 26 Jun 2020 22:57:01: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:57:01: #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 22:57:01: #1 tags after filtering in treatment: 10140889 INFO @ Fri, 26 Jun 2020 22:57:01: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:57:01: #1 finished! INFO @ Fri, 26 Jun 2020 22:57:01: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:57:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:57:01: 5000000 INFO @ Fri, 26 Jun 2020 22:57:02: #2 number of paired peaks: 610 WARNING @ Fri, 26 Jun 2020 22:57:02: Fewer paired peaks (610) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 610 pairs to build model! INFO @ Fri, 26 Jun 2020 22:57:02: start model_add_line... INFO @ Fri, 26 Jun 2020 22:57:02: start X-correlation... INFO @ Fri, 26 Jun 2020 22:57:02: end of X-cor INFO @ Fri, 26 Jun 2020 22:57:02: #2 finished! INFO @ Fri, 26 Jun 2020 22:57:02: #2 predicted fragment length is 154 bps INFO @ Fri, 26 Jun 2020 22:57:02: #2 alternative fragment length(s) may be 4,154 bps INFO @ Fri, 26 Jun 2020 22:57:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495020/SRX495020.05_model.r INFO @ Fri, 26 Jun 2020 22:57:02: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:57:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:57:06: 1000000 INFO @ Fri, 26 Jun 2020 22:57:07: 6000000 INFO @ Fri, 26 Jun 2020 22:57:12: 2000000 INFO @ Fri, 26 Jun 2020 22:57:13: 7000000 INFO @ Fri, 26 Jun 2020 22:57:17: 3000000 INFO @ Fri, 26 Jun 2020 22:57:19: 8000000 INFO @ Fri, 26 Jun 2020 22:57:23: 4000000 INFO @ Fri, 26 Jun 2020 22:57:25: 9000000 INFO @ Fri, 26 Jun 2020 22:57:26: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:57:29: 5000000 INFO @ Fri, 26 Jun 2020 22:57:31: 10000000 INFO @ Fri, 26 Jun 2020 22:57:32: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 22:57:32: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 22:57:32: #1 total tags in treatment: 10140889 INFO @ Fri, 26 Jun 2020 22:57:32: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:57:32: #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 22:57:32: #1 tags after filtering in treatment: 10140889 INFO @ Fri, 26 Jun 2020 22:57:32: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:57:32: #1 finished! INFO @ Fri, 26 Jun 2020 22:57:32: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:57:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:57:33: #2 number of paired peaks: 610 WARNING @ Fri, 26 Jun 2020 22:57:33: Fewer paired peaks (610) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 610 pairs to build model! INFO @ Fri, 26 Jun 2020 22:57:33: start model_add_line... INFO @ Fri, 26 Jun 2020 22:57:33: start X-correlation... INFO @ Fri, 26 Jun 2020 22:57:33: end of X-cor INFO @ Fri, 26 Jun 2020 22:57:33: #2 finished! INFO @ Fri, 26 Jun 2020 22:57:33: #2 predicted fragment length is 154 bps INFO @ Fri, 26 Jun 2020 22:57:33: #2 alternative fragment length(s) may be 4,154 bps INFO @ Fri, 26 Jun 2020 22:57:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495020/SRX495020.10_model.r INFO @ Fri, 26 Jun 2020 22:57:33: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:57:33: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:57:34: 6000000 INFO @ Fri, 26 Jun 2020 22:57:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495020/SRX495020.05_peaks.xls INFO @ Fri, 26 Jun 2020 22:57:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495020/SRX495020.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:57:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495020/SRX495020.05_summits.bed INFO @ Fri, 26 Jun 2020 22:57:37: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1334 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:57:40: 7000000 INFO @ Fri, 26 Jun 2020 22:57:45: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 22:57:50: 9000000 INFO @ Fri, 26 Jun 2020 22:57:56: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:57:56: 10000000 INFO @ Fri, 26 Jun 2020 22:57:57: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 22:57:57: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 22:57:57: #1 total tags in treatment: 10140889 INFO @ Fri, 26 Jun 2020 22:57:57: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:57:57: #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 22:57:57: #1 tags after filtering in treatment: 10140889 INFO @ Fri, 26 Jun 2020 22:57:57: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:57:57: #1 finished! INFO @ Fri, 26 Jun 2020 22:57:57: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:57:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:57:58: #2 number of paired peaks: 610 WARNING @ Fri, 26 Jun 2020 22:57:58: Fewer paired peaks (610) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 610 pairs to build model! INFO @ Fri, 26 Jun 2020 22:57:58: start model_add_line... INFO @ Fri, 26 Jun 2020 22:57:58: start X-correlation... INFO @ Fri, 26 Jun 2020 22:57:58: end of X-cor INFO @ Fri, 26 Jun 2020 22:57:58: #2 finished! INFO @ Fri, 26 Jun 2020 22:57:58: #2 predicted fragment length is 154 bps INFO @ Fri, 26 Jun 2020 22:57:58: #2 alternative fragment length(s) may be 4,154 bps INFO @ Fri, 26 Jun 2020 22:57:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495020/SRX495020.20_model.r INFO @ Fri, 26 Jun 2020 22:57:58: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:57:58: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:58:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495020/SRX495020.10_peaks.xls INFO @ Fri, 26 Jun 2020 22:58:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495020/SRX495020.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:58:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495020/SRX495020.10_summits.bed INFO @ Fri, 26 Jun 2020 22:58:07: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (717 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 22:58:22: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:58:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495020/SRX495020.20_peaks.xls INFO @ Fri, 26 Jun 2020 22:58:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495020/SRX495020.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:58:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495020/SRX495020.20_summits.bed INFO @ Fri, 26 Jun 2020 22:58:34: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (441 records, 4 fields): 2 millis CompletedMACS2peakCalling