Job ID = 6366250 SRX = SRX080104 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:09:01 prefetch.2.10.7: 1) Downloading 'SRR298924'... 2020-06-15T23:09:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:09:31 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:09:32 prefetch.2.10.7: 'SRR298924' is valid 2020-06-15T23:09:32 prefetch.2.10.7: 1) 'SRR298924' was downloaded successfully Read 6438791 spots for SRR298924/SRR298924.sra Written 6438791 spots for SRR298924/SRR298924.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: 00:00:34 6438791 reads; of these: 6438791 (100.00%) were unpaired; of these: 4595956 (71.38%) aligned 0 times 1529181 (23.75%) aligned exactly 1 time 313654 (4.87%) aligned >1 times 28.62% overall alignment rate Time searching: 00:00:34 Overall time: 00:00:34 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] 290183 / 1842835 = 0.1575 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 08:11:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX080104/SRX080104.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX080104/SRX080104.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX080104/SRX080104.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX080104/SRX080104.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 08:11:13: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:11:13: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:11:18: 1000000 INFO @ Tue, 16 Jun 2020 08:11:20: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:11:20: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:11:20: #1 total tags in treatment: 1552652 INFO @ Tue, 16 Jun 2020 08:11:20: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:11:20: #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 08:11:20: #1 tags after filtering in treatment: 1552652 INFO @ Tue, 16 Jun 2020 08:11:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:11:20: #1 finished! INFO @ Tue, 16 Jun 2020 08:11:20: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:11:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:11:21: #2 number of paired peaks: 484 WARNING @ Tue, 16 Jun 2020 08:11:21: Fewer paired peaks (484) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 484 pairs to build model! INFO @ Tue, 16 Jun 2020 08:11:21: start model_add_line... INFO @ Tue, 16 Jun 2020 08:11:21: start X-correlation... INFO @ Tue, 16 Jun 2020 08:11:21: end of X-cor INFO @ Tue, 16 Jun 2020 08:11:21: #2 finished! INFO @ Tue, 16 Jun 2020 08:11:21: #2 predicted fragment length is 90 bps INFO @ Tue, 16 Jun 2020 08:11:21: #2 alternative fragment length(s) may be 37,90 bps INFO @ Tue, 16 Jun 2020 08:11:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX080104/SRX080104.05_model.r INFO @ Tue, 16 Jun 2020 08:11:21: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:11:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:11:24: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:11:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX080104/SRX080104.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:11:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX080104/SRX080104.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:11:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX080104/SRX080104.05_summits.bed INFO @ Tue, 16 Jun 2020 08:11:26: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (462 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 08:11:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX080104/SRX080104.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX080104/SRX080104.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX080104/SRX080104.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX080104/SRX080104.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 08:11:43: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:11:43: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:11:48: 1000000 INFO @ Tue, 16 Jun 2020 08:11:51: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:11:51: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:11:51: #1 total tags in treatment: 1552652 INFO @ Tue, 16 Jun 2020 08:11:51: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:11:51: #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 08:11:51: #1 tags after filtering in treatment: 1552652 INFO @ Tue, 16 Jun 2020 08:11:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:11:51: #1 finished! INFO @ Tue, 16 Jun 2020 08:11:51: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:11:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:11:51: #2 number of paired peaks: 484 WARNING @ Tue, 16 Jun 2020 08:11:51: Fewer paired peaks (484) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 484 pairs to build model! INFO @ Tue, 16 Jun 2020 08:11:51: start model_add_line... INFO @ Tue, 16 Jun 2020 08:11:51: start X-correlation... INFO @ Tue, 16 Jun 2020 08:11:51: end of X-cor INFO @ Tue, 16 Jun 2020 08:11:51: #2 finished! INFO @ Tue, 16 Jun 2020 08:11:51: #2 predicted fragment length is 90 bps INFO @ Tue, 16 Jun 2020 08:11:51: #2 alternative fragment length(s) may be 37,90 bps INFO @ Tue, 16 Jun 2020 08:11:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX080104/SRX080104.10_model.r INFO @ Tue, 16 Jun 2020 08:11:51: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:11:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:11:55: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:11:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX080104/SRX080104.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:11:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX080104/SRX080104.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:11:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX080104/SRX080104.10_summits.bed INFO @ Tue, 16 Jun 2020 08:11:57: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (192 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 08:12:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX080104/SRX080104.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX080104/SRX080104.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX080104/SRX080104.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX080104/SRX080104.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 08:12:13: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:12:13: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:12:19: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:12:22: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:12:22: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:12:22: #1 total tags in treatment: 1552652 INFO @ Tue, 16 Jun 2020 08:12:22: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:12:22: #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 08:12:22: #1 tags after filtering in treatment: 1552652 INFO @ Tue, 16 Jun 2020 08:12:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:12:22: #1 finished! INFO @ Tue, 16 Jun 2020 08:12:22: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:12:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:12:22: #2 number of paired peaks: 484 WARNING @ Tue, 16 Jun 2020 08:12:22: Fewer paired peaks (484) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 484 pairs to build model! INFO @ Tue, 16 Jun 2020 08:12:22: start model_add_line... INFO @ Tue, 16 Jun 2020 08:12:22: start X-correlation... INFO @ Tue, 16 Jun 2020 08:12:22: end of X-cor INFO @ Tue, 16 Jun 2020 08:12:22: #2 finished! INFO @ Tue, 16 Jun 2020 08:12:22: #2 predicted fragment length is 90 bps INFO @ Tue, 16 Jun 2020 08:12:22: #2 alternative fragment length(s) may be 37,90 bps INFO @ Tue, 16 Jun 2020 08:12:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX080104/SRX080104.20_model.r INFO @ Tue, 16 Jun 2020 08:12:22: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:12:22: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:12:26: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:12:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX080104/SRX080104.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:12:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX080104/SRX080104.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:12:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX080104/SRX080104.20_summits.bed INFO @ Tue, 16 Jun 2020 08:12:28: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (53 records, 4 fields): 2 millis CompletedMACS2peakCalling