Job ID = 6365920 SRX = SRX043853 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:29:16 prefetch.2.10.7: 1) Downloading 'SRR107310'... 2020-06-15T22:29:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:29:41 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:29:42 prefetch.2.10.7: 'SRR107310' is valid 2020-06-15T22:29:42 prefetch.2.10.7: 1) 'SRR107310' was downloaded successfully Read 4175238 spots for SRR107310/SRR107310.sra Written 4175238 spots for SRR107310/SRR107310.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: 00:00:37 4175238 reads; of these: 4175238 (100.00%) were unpaired; of these: 1133804 (27.16%) aligned 0 times 2650731 (63.49%) aligned exactly 1 time 390703 (9.36%) aligned >1 times 72.84% overall alignment rate Time searching: 00:00:37 Overall time: 00:00:37 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_rmdupse_core] 229725 / 3041434 = 0.0755 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 07:31:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX043853/SRX043853.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX043853/SRX043853.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX043853/SRX043853.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX043853/SRX043853.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 07:31:47: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:31:47: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:31:53: 1000000 INFO @ Tue, 16 Jun 2020 07:31:58: 2000000 INFO @ Tue, 16 Jun 2020 07:32:02: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:32:02: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:32:02: #1 total tags in treatment: 2811709 INFO @ Tue, 16 Jun 2020 07:32:02: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:32:02: #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 07:32:02: #1 tags after filtering in treatment: 2811709 INFO @ Tue, 16 Jun 2020 07:32:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:32:02: #1 finished! INFO @ Tue, 16 Jun 2020 07:32:02: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:32:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:32:03: #2 number of paired peaks: 367 WARNING @ Tue, 16 Jun 2020 07:32:03: Fewer paired peaks (367) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 367 pairs to build model! INFO @ Tue, 16 Jun 2020 07:32:03: start model_add_line... INFO @ Tue, 16 Jun 2020 07:32:03: start X-correlation... INFO @ Tue, 16 Jun 2020 07:32:03: end of X-cor INFO @ Tue, 16 Jun 2020 07:32:03: #2 finished! INFO @ Tue, 16 Jun 2020 07:32:03: #2 predicted fragment length is 99 bps INFO @ Tue, 16 Jun 2020 07:32:03: #2 alternative fragment length(s) may be 99 bps INFO @ Tue, 16 Jun 2020 07:32:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX043853/SRX043853.05_model.r INFO @ Tue, 16 Jun 2020 07:32:03: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:32:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:32:09: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:32:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX043853/SRX043853.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:32:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX043853/SRX043853.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:32:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX043853/SRX043853.05_summits.bed INFO @ Tue, 16 Jun 2020 07:32:12: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1187 records, 4 fields): 2 millis CompletedMACS2peakCalling 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 07:32:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX043853/SRX043853.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX043853/SRX043853.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX043853/SRX043853.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX043853/SRX043853.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 07:32:17: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:32:17: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:32:23: 1000000 INFO @ Tue, 16 Jun 2020 07:32:28: 2000000 INFO @ Tue, 16 Jun 2020 07:32:33: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:32:33: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:32:33: #1 total tags in treatment: 2811709 INFO @ Tue, 16 Jun 2020 07:32:33: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:32:33: #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 07:32:33: #1 tags after filtering in treatment: 2811709 INFO @ Tue, 16 Jun 2020 07:32:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:32:33: #1 finished! INFO @ Tue, 16 Jun 2020 07:32:33: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:32:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:32:33: #2 number of paired peaks: 367 WARNING @ Tue, 16 Jun 2020 07:32:33: Fewer paired peaks (367) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 367 pairs to build model! INFO @ Tue, 16 Jun 2020 07:32:33: start model_add_line... INFO @ Tue, 16 Jun 2020 07:32:33: start X-correlation... INFO @ Tue, 16 Jun 2020 07:32:33: end of X-cor INFO @ Tue, 16 Jun 2020 07:32:33: #2 finished! INFO @ Tue, 16 Jun 2020 07:32:33: #2 predicted fragment length is 99 bps INFO @ Tue, 16 Jun 2020 07:32:33: #2 alternative fragment length(s) may be 99 bps INFO @ Tue, 16 Jun 2020 07:32:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX043853/SRX043853.10_model.r INFO @ Tue, 16 Jun 2020 07:32:33: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:32:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:32:39: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:32:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX043853/SRX043853.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:32:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX043853/SRX043853.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:32:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX043853/SRX043853.10_summits.bed INFO @ Tue, 16 Jun 2020 07:32:42: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (398 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 07:32:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX043853/SRX043853.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX043853/SRX043853.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX043853/SRX043853.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX043853/SRX043853.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 07:32:47: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:32:47: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:32:53: 1000000 INFO @ Tue, 16 Jun 2020 07:32:58: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:33:02: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:33:02: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:33:02: #1 total tags in treatment: 2811709 INFO @ Tue, 16 Jun 2020 07:33:02: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:33:02: #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 07:33:02: #1 tags after filtering in treatment: 2811709 INFO @ Tue, 16 Jun 2020 07:33:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:33:02: #1 finished! INFO @ Tue, 16 Jun 2020 07:33:02: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:33:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:33:02: #2 number of paired peaks: 367 WARNING @ Tue, 16 Jun 2020 07:33:02: Fewer paired peaks (367) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 367 pairs to build model! INFO @ Tue, 16 Jun 2020 07:33:02: start model_add_line... INFO @ Tue, 16 Jun 2020 07:33:02: start X-correlation... INFO @ Tue, 16 Jun 2020 07:33:02: end of X-cor INFO @ Tue, 16 Jun 2020 07:33:02: #2 finished! INFO @ Tue, 16 Jun 2020 07:33:02: #2 predicted fragment length is 99 bps INFO @ Tue, 16 Jun 2020 07:33:02: #2 alternative fragment length(s) may be 99 bps INFO @ Tue, 16 Jun 2020 07:33:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX043853/SRX043853.20_model.r INFO @ Tue, 16 Jun 2020 07:33:02: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:33:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:33:08: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:33:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX043853/SRX043853.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:33:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX043853/SRX043853.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:33:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX043853/SRX043853.20_summits.bed INFO @ Tue, 16 Jun 2020 07:33:11: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (45 records, 4 fields): 1 millis CompletedMACS2peakCalling