Job ID = 6367857 SRX = SRX4085425 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T23:35:59 prefetch.2.10.7: 1) Downloading 'SRR7167454'... 2020-06-15T23:35:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:39:24 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:39:24 prefetch.2.10.7: 1) 'SRR7167454' was downloaded successfully Read 10971740 spots for SRR7167454/SRR7167454.sra Written 10971740 spots for SRR7167454/SRR7167454.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: 00:05:37 10971740 reads; of these: 10971740 (100.00%) were paired; of these: 8522346 (77.68%) aligned concordantly 0 times 2128930 (19.40%) aligned concordantly exactly 1 time 320464 (2.92%) aligned concordantly >1 times ---- 8522346 pairs aligned concordantly 0 times; of these: 212376 (2.49%) aligned discordantly 1 time ---- 8309970 pairs aligned 0 times concordantly or discordantly; of these: 16619940 mates make up the pairs; of these: 11399770 (68.59%) aligned 0 times 4600230 (27.68%) aligned exactly 1 time 619940 (3.73%) aligned >1 times 48.05% overall alignment rate Time searching: 00:05:37 Overall time: 00:05:37 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] 94382 / 2543859 = 0.0371 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 08:49:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085425/SRX4085425.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085425/SRX4085425.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085425/SRX4085425.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085425/SRX4085425.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 08:49:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:49:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:49:32: 1000000 INFO @ Tue, 16 Jun 2020 08:49:38: 2000000 INFO @ Tue, 16 Jun 2020 08:49:43: 3000000 INFO @ Tue, 16 Jun 2020 08:49:49: 4000000 INFO @ Tue, 16 Jun 2020 08:49:55: 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 08:49:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085425/SRX4085425.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085425/SRX4085425.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085425/SRX4085425.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085425/SRX4085425.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 08:49:57: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:49:57: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:50:01: 6000000 INFO @ Tue, 16 Jun 2020 08:50:02: 1000000 INFO @ Tue, 16 Jun 2020 08:50:06: 7000000 INFO @ Tue, 16 Jun 2020 08:50:08: 2000000 INFO @ Tue, 16 Jun 2020 08:50:12: 8000000 INFO @ Tue, 16 Jun 2020 08:50:13: 3000000 INFO @ Tue, 16 Jun 2020 08:50:18: 9000000 INFO @ Tue, 16 Jun 2020 08:50:19: 4000000 INFO @ Tue, 16 Jun 2020 08:50:24: 10000000 INFO @ Tue, 16 Jun 2020 08:50:24: 5000000 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 08:50:26: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:50:26: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:50:26: #1 total tags in treatment: 2356756 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: 2260982 INFO @ Tue, 16 Jun 2020 08:50:26: #1 Redundant rate of treatment: 0.04 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: 289 WARNING @ Tue, 16 Jun 2020 08:50:26: Fewer paired peaks (289) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 289 pairs to build model! 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 192 bps INFO @ Tue, 16 Jun 2020 08:50:26: #2 alternative fragment length(s) may be 128,163,192,221,591 bps INFO @ Tue, 16 Jun 2020 08:50:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085425/SRX4085425.05_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 08:50:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085425/SRX4085425.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085425/SRX4085425.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085425/SRX4085425.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085425/SRX4085425.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 08:50:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:50:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:50:30: 6000000 INFO @ Tue, 16 Jun 2020 08:50:32: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:50:32: 1000000 INFO @ Tue, 16 Jun 2020 08:50:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085425/SRX4085425.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:50:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085425/SRX4085425.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:50:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085425/SRX4085425.05_summits.bed INFO @ Tue, 16 Jun 2020 08:50:34: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (183 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:50:36: 7000000 INFO @ Tue, 16 Jun 2020 08:50:38: 2000000 INFO @ Tue, 16 Jun 2020 08:50:41: 8000000 INFO @ Tue, 16 Jun 2020 08:50:43: 3000000 INFO @ Tue, 16 Jun 2020 08:50:47: 9000000 INFO @ Tue, 16 Jun 2020 08:50:49: 4000000 INFO @ Tue, 16 Jun 2020 08:50:53: 10000000 INFO @ Tue, 16 Jun 2020 08:50:54: 5000000 INFO @ Tue, 16 Jun 2020 08:50:54: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:50:54: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:50:54: #1 total tags in treatment: 2356756 INFO @ Tue, 16 Jun 2020 08:50:54: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:50:54: #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 08:50:54: #1 tags after filtering in treatment: 2260982 INFO @ Tue, 16 Jun 2020 08:50:54: #1 Redundant rate of treatment: 0.04 INFO @ Tue, 16 Jun 2020 08:50:54: #1 finished! INFO @ Tue, 16 Jun 2020 08:50:54: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:50:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:50:55: #2 number of paired peaks: 289 WARNING @ Tue, 16 Jun 2020 08:50:55: Fewer paired peaks (289) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 289 pairs to build model! INFO @ Tue, 16 Jun 2020 08:50:55: start model_add_line... INFO @ Tue, 16 Jun 2020 08:50:55: start X-correlation... INFO @ Tue, 16 Jun 2020 08:50:55: end of X-cor INFO @ Tue, 16 Jun 2020 08:50:55: #2 finished! INFO @ Tue, 16 Jun 2020 08:50:55: #2 predicted fragment length is 192 bps INFO @ Tue, 16 Jun 2020 08:50:55: #2 alternative fragment length(s) may be 128,163,192,221,591 bps INFO @ Tue, 16 Jun 2020 08:50:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085425/SRX4085425.10_model.r INFO @ Tue, 16 Jun 2020 08:50:55: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:50:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:51:00: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:51:00: 6000000 INFO @ Tue, 16 Jun 2020 08:51:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085425/SRX4085425.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:51:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085425/SRX4085425.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:51:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085425/SRX4085425.10_summits.bed INFO @ Tue, 16 Jun 2020 08:51:02: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (120 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:51:05: 7000000 INFO @ Tue, 16 Jun 2020 08:51:11: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:51:16: 9000000 INFO @ Tue, 16 Jun 2020 08:51:22: 10000000 INFO @ Tue, 16 Jun 2020 08:51:24: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:51:24: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:51:24: #1 total tags in treatment: 2356756 INFO @ Tue, 16 Jun 2020 08:51:24: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:51:24: #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 08:51:24: #1 tags after filtering in treatment: 2260982 INFO @ Tue, 16 Jun 2020 08:51:24: #1 Redundant rate of treatment: 0.04 INFO @ Tue, 16 Jun 2020 08:51:24: #1 finished! INFO @ Tue, 16 Jun 2020 08:51:24: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:51:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:51:24: #2 number of paired peaks: 289 WARNING @ Tue, 16 Jun 2020 08:51:24: Fewer paired peaks (289) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 289 pairs to build model! INFO @ Tue, 16 Jun 2020 08:51:24: start model_add_line... INFO @ Tue, 16 Jun 2020 08:51:24: start X-correlation... INFO @ Tue, 16 Jun 2020 08:51:24: end of X-cor INFO @ Tue, 16 Jun 2020 08:51:24: #2 finished! INFO @ Tue, 16 Jun 2020 08:51:24: #2 predicted fragment length is 192 bps INFO @ Tue, 16 Jun 2020 08:51:24: #2 alternative fragment length(s) may be 128,163,192,221,591 bps INFO @ Tue, 16 Jun 2020 08:51:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085425/SRX4085425.20_model.r INFO @ Tue, 16 Jun 2020 08:51:24: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:51:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:51:29: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:51:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085425/SRX4085425.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:51:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085425/SRX4085425.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:51:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085425/SRX4085425.20_summits.bed INFO @ Tue, 16 Jun 2020 08:51:31: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (53 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。