Job ID = 6367195 SRX = SRX2978699 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T23:25:36 prefetch.2.10.7: 1) Downloading 'SRR5799206'... 2020-06-15T23:25:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:29:21 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:29:21 prefetch.2.10.7: 1) 'SRR5799206' was downloaded successfully 2020-06-15T23:29:21 prefetch.2.10.7: 'SRR5799206' has 0 unresolved dependencies Read 22272822 spots for SRR5799206/SRR5799206.sra Written 22272822 spots for SRR5799206/SRR5799206.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: 00:13:31 22272822 reads; of these: 22272822 (100.00%) were paired; of these: 10406978 (46.73%) aligned concordantly 0 times 10040437 (45.08%) aligned concordantly exactly 1 time 1825407 (8.20%) aligned concordantly >1 times ---- 10406978 pairs aligned concordantly 0 times; of these: 1491849 (14.34%) aligned discordantly 1 time ---- 8915129 pairs aligned 0 times concordantly or discordantly; of these: 17830258 mates make up the pairs; of these: 16252259 (91.15%) aligned 0 times 987429 (5.54%) aligned exactly 1 time 590570 (3.31%) aligned >1 times 63.52% overall alignment rate Time searching: 00:13:31 Overall time: 00:13:31 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 12 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] 11629933 / 13352982 = 0.8710 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 08:50:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2978699/SRX2978699.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2978699/SRX2978699.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2978699/SRX2978699.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2978699/SRX2978699.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 08:50:03: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:50:03: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:50:07: 1000000 INFO @ Tue, 16 Jun 2020 08:50:12: 2000000 INFO @ Tue, 16 Jun 2020 08:50:17: 3000000 INFO @ Tue, 16 Jun 2020 08:50:21: 4000000 INFO @ Tue, 16 Jun 2020 08:50:26: 5000000 INFO @ Tue, 16 Jun 2020 08:50:26: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:50:26: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:50:26: #1 total tags in treatment: 1456766 INFO @ Tue, 16 Jun 2020 08:50:26: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:50:26: #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 08:50:26: #1 tags after filtering in treatment: 1288116 INFO @ Tue, 16 Jun 2020 08:50:26: #1 Redundant rate of treatment: 0.12 INFO @ Tue, 16 Jun 2020 08:50:26: #1 finished! INFO @ Tue, 16 Jun 2020 08:50:26: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:50:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:50:26: #2 number of paired peaks: 1268 INFO @ Tue, 16 Jun 2020 08:50:26: start model_add_line... INFO @ Tue, 16 Jun 2020 08:50:26: start X-correlation... INFO @ Tue, 16 Jun 2020 08:50:26: end of X-cor INFO @ Tue, 16 Jun 2020 08:50:26: #2 finished! INFO @ Tue, 16 Jun 2020 08:50:26: #2 predicted fragment length is 196 bps INFO @ Tue, 16 Jun 2020 08:50:26: #2 alternative fragment length(s) may be 196 bps INFO @ Tue, 16 Jun 2020 08:50:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2978699/SRX2978699.05_model.r INFO @ Tue, 16 Jun 2020 08:50:26: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:50:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:50:30: #3 Call peaks for each chromosome... 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 08:50:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2978699/SRX2978699.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:50:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2978699/SRX2978699.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:50:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2978699/SRX2978699.05_summits.bed INFO @ Tue, 16 Jun 2020 08:50:31: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (778 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:50:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2978699/SRX2978699.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2978699/SRX2978699.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2978699/SRX2978699.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2978699/SRX2978699.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 08:50:33: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:50:33: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:50:37: 1000000 INFO @ Tue, 16 Jun 2020 08:50:42: 2000000 INFO @ Tue, 16 Jun 2020 08:50:47: 3000000 INFO @ Tue, 16 Jun 2020 08:50:52: 4000000 INFO @ Tue, 16 Jun 2020 08:50:57: 5000000 INFO @ Tue, 16 Jun 2020 08:50:57: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:50:57: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:50:57: #1 total tags in treatment: 1456766 INFO @ Tue, 16 Jun 2020 08:50:57: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:50:57: #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 08:50:57: #1 tags after filtering in treatment: 1288116 INFO @ Tue, 16 Jun 2020 08:50:57: #1 Redundant rate of treatment: 0.12 INFO @ Tue, 16 Jun 2020 08:50:57: #1 finished! INFO @ Tue, 16 Jun 2020 08:50:57: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:50:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:50:57: #2 number of paired peaks: 1268 INFO @ Tue, 16 Jun 2020 08:50:57: start model_add_line... INFO @ Tue, 16 Jun 2020 08:50:57: start X-correlation... INFO @ Tue, 16 Jun 2020 08:50:57: end of X-cor INFO @ Tue, 16 Jun 2020 08:50:57: #2 finished! INFO @ Tue, 16 Jun 2020 08:50:57: #2 predicted fragment length is 196 bps INFO @ Tue, 16 Jun 2020 08:50:57: #2 alternative fragment length(s) may be 196 bps INFO @ Tue, 16 Jun 2020 08:50:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2978699/SRX2978699.10_model.r INFO @ Tue, 16 Jun 2020 08:50:58: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:50:58: #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 @ Tue, 16 Jun 2020 08:51:01: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:51:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2978699/SRX2978699.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2978699/SRX2978699.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2978699/SRX2978699.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2978699/SRX2978699.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 08:51:03: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:51:03: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:51:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2978699/SRX2978699.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:51:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2978699/SRX2978699.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:51:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2978699/SRX2978699.10_summits.bed INFO @ Tue, 16 Jun 2020 08:51:03: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (440 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:51:07: 1000000 INFO @ Tue, 16 Jun 2020 08:51:12: 2000000 INFO @ Tue, 16 Jun 2020 08:51:17: 3000000 INFO @ Tue, 16 Jun 2020 08:51:21: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:51:26: 5000000 INFO @ Tue, 16 Jun 2020 08:51:26: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:51:26: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:51:26: #1 total tags in treatment: 1456766 INFO @ Tue, 16 Jun 2020 08:51:26: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:51:26: #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 08:51:26: #1 tags after filtering in treatment: 1288116 INFO @ Tue, 16 Jun 2020 08:51:26: #1 Redundant rate of treatment: 0.12 INFO @ Tue, 16 Jun 2020 08:51:26: #1 finished! INFO @ Tue, 16 Jun 2020 08:51:26: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:51:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:51:26: #2 number of paired peaks: 1268 INFO @ Tue, 16 Jun 2020 08:51:26: start model_add_line... INFO @ Tue, 16 Jun 2020 08:51:26: start X-correlation... INFO @ Tue, 16 Jun 2020 08:51:26: end of X-cor INFO @ Tue, 16 Jun 2020 08:51:26: #2 finished! INFO @ Tue, 16 Jun 2020 08:51:26: #2 predicted fragment length is 196 bps INFO @ Tue, 16 Jun 2020 08:51:26: #2 alternative fragment length(s) may be 196 bps INFO @ Tue, 16 Jun 2020 08:51:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2978699/SRX2978699.20_model.r INFO @ Tue, 16 Jun 2020 08:51:26: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:51:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:51:30: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:51:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2978699/SRX2978699.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:51:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2978699/SRX2978699.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:51:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2978699/SRX2978699.20_summits.bed INFO @ Tue, 16 Jun 2020 08:51:31: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (210 records, 4 fields): 2 millis CompletedMACS2peakCalling