Job ID = 6367848 SRX = SRX4085416 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T23:35:50 prefetch.2.10.7: 1) Downloading 'SRR7167445'... 2020-06-15T23:35:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:40:23 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:40:23 prefetch.2.10.7: 1) 'SRR7167445' was downloaded successfully Read 13804034 spots for SRR7167445/SRR7167445.sra Written 13804034 spots for SRR7167445/SRR7167445.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: 00:06:28 13804034 reads; of these: 13804034 (100.00%) were paired; of these: 11596350 (84.01%) aligned concordantly 0 times 1924631 (13.94%) aligned concordantly exactly 1 time 283053 (2.05%) aligned concordantly >1 times ---- 11596350 pairs aligned concordantly 0 times; of these: 243635 (2.10%) aligned discordantly 1 time ---- 11352715 pairs aligned 0 times concordantly or discordantly; of these: 22705430 mates make up the pairs; of these: 16144315 (71.10%) aligned 0 times 5765847 (25.39%) aligned exactly 1 time 795268 (3.50%) aligned >1 times 41.52% overall alignment rate Time searching: 00:06:28 Overall time: 00:06:28 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_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 166036 / 2305776 = 0.0720 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 08:51:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085416/SRX4085416.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085416/SRX4085416.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085416/SRX4085416.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085416/SRX4085416.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 08:51:45: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:51:45: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:51:51: 1000000 INFO @ Tue, 16 Jun 2020 08:51:56: 2000000 INFO @ Tue, 16 Jun 2020 08:52:01: 3000000 INFO @ Tue, 16 Jun 2020 08:52:06: 4000000 INFO @ Tue, 16 Jun 2020 08:52:11: 5000000 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 08:52:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085416/SRX4085416.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085416/SRX4085416.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085416/SRX4085416.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085416/SRX4085416.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 08:52:15: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:52:15: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:52:16: 6000000 INFO @ Tue, 16 Jun 2020 08:52:21: 1000000 INFO @ Tue, 16 Jun 2020 08:52:21: 7000000 INFO @ Tue, 16 Jun 2020 08:52:27: 2000000 INFO @ Tue, 16 Jun 2020 08:52:27: 8000000 INFO @ Tue, 16 Jun 2020 08:52:32: 3000000 INFO @ Tue, 16 Jun 2020 08:52:33: 9000000 INFO @ Tue, 16 Jun 2020 08:52:38: 4000000 INFO @ Tue, 16 Jun 2020 08:52:38: 10000000 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 08:52:44: 5000000 INFO @ Tue, 16 Jun 2020 08:52:44: 11000000 INFO @ Tue, 16 Jun 2020 08:52:45: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:52:45: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:52:45: #1 total tags in treatment: 2045487 INFO @ Tue, 16 Jun 2020 08:52:45: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:52:45: #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 08:52:45: #1 tags after filtering in treatment: 1977437 INFO @ Tue, 16 Jun 2020 08:52:45: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 16 Jun 2020 08:52:45: #1 finished! INFO @ Tue, 16 Jun 2020 08:52:45: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:52:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:52:45: #2 number of paired peaks: 260 WARNING @ Tue, 16 Jun 2020 08:52:45: Fewer paired peaks (260) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 260 pairs to build model! INFO @ Tue, 16 Jun 2020 08:52:45: start model_add_line... INFO @ Tue, 16 Jun 2020 08:52:45: start X-correlation... INFO @ Tue, 16 Jun 2020 08:52:45: end of X-cor INFO @ Tue, 16 Jun 2020 08:52:45: #2 finished! INFO @ Tue, 16 Jun 2020 08:52:45: #2 predicted fragment length is 223 bps INFO @ Tue, 16 Jun 2020 08:52:45: #2 alternative fragment length(s) may be 91,123,156,190,223,250,288,419,489,560,592 bps INFO @ Tue, 16 Jun 2020 08:52:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085416/SRX4085416.05_model.r INFO @ Tue, 16 Jun 2020 08:52:45: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:52:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:52:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085416/SRX4085416.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085416/SRX4085416.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085416/SRX4085416.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085416/SRX4085416.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 08:52:46: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:52:46: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:52:49: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:52:49: 6000000 INFO @ Tue, 16 Jun 2020 08:52:51: 1000000 INFO @ Tue, 16 Jun 2020 08:52:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085416/SRX4085416.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:52:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085416/SRX4085416.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:52:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085416/SRX4085416.05_summits.bed INFO @ Tue, 16 Jun 2020 08:52:52: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (208 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:52:55: 7000000 INFO @ Tue, 16 Jun 2020 08:52:57: 2000000 INFO @ Tue, 16 Jun 2020 08:53:01: 8000000 INFO @ Tue, 16 Jun 2020 08:53:03: 3000000 INFO @ Tue, 16 Jun 2020 08:53:07: 9000000 INFO @ Tue, 16 Jun 2020 08:53:09: 4000000 INFO @ Tue, 16 Jun 2020 08:53:13: 10000000 INFO @ Tue, 16 Jun 2020 08:53:15: 5000000 INFO @ Tue, 16 Jun 2020 08:53:19: 11000000 INFO @ Tue, 16 Jun 2020 08:53:19: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:53:19: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:53:19: #1 total tags in treatment: 2045487 INFO @ Tue, 16 Jun 2020 08:53:19: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:53:19: #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 08:53:19: #1 tags after filtering in treatment: 1977437 INFO @ Tue, 16 Jun 2020 08:53:19: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 16 Jun 2020 08:53:19: #1 finished! INFO @ Tue, 16 Jun 2020 08:53:19: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:53:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:53:20: #2 number of paired peaks: 260 WARNING @ Tue, 16 Jun 2020 08:53:20: Fewer paired peaks (260) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 260 pairs to build model! INFO @ Tue, 16 Jun 2020 08:53:20: start model_add_line... INFO @ Tue, 16 Jun 2020 08:53:20: start X-correlation... INFO @ Tue, 16 Jun 2020 08:53:20: end of X-cor INFO @ Tue, 16 Jun 2020 08:53:20: #2 finished! INFO @ Tue, 16 Jun 2020 08:53:20: #2 predicted fragment length is 223 bps INFO @ Tue, 16 Jun 2020 08:53:20: #2 alternative fragment length(s) may be 91,123,156,190,223,250,288,419,489,560,592 bps INFO @ Tue, 16 Jun 2020 08:53:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085416/SRX4085416.10_model.r INFO @ Tue, 16 Jun 2020 08:53:20: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:53:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:53:20: 6000000 INFO @ Tue, 16 Jun 2020 08:53:24: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:53:26: 7000000 INFO @ Tue, 16 Jun 2020 08:53:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085416/SRX4085416.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:53:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085416/SRX4085416.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:53:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085416/SRX4085416.10_summits.bed INFO @ Tue, 16 Jun 2020 08:53:27: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (101 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:53:32: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:53:38: 9000000 INFO @ Tue, 16 Jun 2020 08:53:43: 10000000 INFO @ Tue, 16 Jun 2020 08:53:48: 11000000 INFO @ Tue, 16 Jun 2020 08:53:49: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:53:49: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:53:49: #1 total tags in treatment: 2045487 INFO @ Tue, 16 Jun 2020 08:53:49: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:53:49: #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 08:53:49: #1 tags after filtering in treatment: 1977437 INFO @ Tue, 16 Jun 2020 08:53:49: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 16 Jun 2020 08:53:49: #1 finished! INFO @ Tue, 16 Jun 2020 08:53:49: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:53:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:53:49: #2 number of paired peaks: 260 WARNING @ Tue, 16 Jun 2020 08:53:49: Fewer paired peaks (260) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 260 pairs to build model! INFO @ Tue, 16 Jun 2020 08:53:49: start model_add_line... INFO @ Tue, 16 Jun 2020 08:53:49: start X-correlation... INFO @ Tue, 16 Jun 2020 08:53:49: end of X-cor INFO @ Tue, 16 Jun 2020 08:53:49: #2 finished! INFO @ Tue, 16 Jun 2020 08:53:49: #2 predicted fragment length is 223 bps INFO @ Tue, 16 Jun 2020 08:53:49: #2 alternative fragment length(s) may be 91,123,156,190,223,250,288,419,489,560,592 bps INFO @ Tue, 16 Jun 2020 08:53:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085416/SRX4085416.20_model.r INFO @ Tue, 16 Jun 2020 08:53:49: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:53:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:53:54: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:53:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085416/SRX4085416.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:53:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085416/SRX4085416.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:53:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085416/SRX4085416.20_summits.bed INFO @ Tue, 16 Jun 2020 08:53:57: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (46 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。