Job ID = 6367446 SRX = SRX331204 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:24:20 prefetch.2.10.7: 1) Downloading 'SRR947436'... 2020-06-15T23:24:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:24:46 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:24:46 prefetch.2.10.7: 'SRR947436' is valid 2020-06-15T23:24:46 prefetch.2.10.7: 1) 'SRR947436' was downloaded successfully Read 7997830 spots for SRR947436/SRR947436.sra Written 7997830 spots for SRR947436/SRR947436.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: 00:01:03 7997830 reads; of these: 7997830 (100.00%) were unpaired; of these: 2841549 (35.53%) aligned 0 times 4300718 (53.77%) aligned exactly 1 time 855563 (10.70%) aligned >1 times 64.47% overall alignment rate Time searching: 00:01:03 Overall time: 00:01:03 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] 376737 / 5156281 = 0.0731 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 08:27:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331204/SRX331204.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331204/SRX331204.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331204/SRX331204.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331204/SRX331204.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 08:27:42: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:27:42: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:27:49: 1000000 INFO @ Tue, 16 Jun 2020 08:27:56: 2000000 INFO @ Tue, 16 Jun 2020 08:28:02: 3000000 INFO @ Tue, 16 Jun 2020 08:28:09: 4000000 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 08:28:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331204/SRX331204.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331204/SRX331204.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331204/SRX331204.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331204/SRX331204.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 08:28:13: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:28:13: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:28:14: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:28:14: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:28:14: #1 total tags in treatment: 4779544 INFO @ Tue, 16 Jun 2020 08:28:14: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:28:14: #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 08:28:14: #1 tags after filtering in treatment: 4779544 INFO @ Tue, 16 Jun 2020 08:28:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:28:14: #1 finished! INFO @ Tue, 16 Jun 2020 08:28:14: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:28:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:28:14: #2 number of paired peaks: 497 WARNING @ Tue, 16 Jun 2020 08:28:14: Fewer paired peaks (497) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 497 pairs to build model! INFO @ Tue, 16 Jun 2020 08:28:14: start model_add_line... INFO @ Tue, 16 Jun 2020 08:28:14: start X-correlation... INFO @ Tue, 16 Jun 2020 08:28:14: end of X-cor INFO @ Tue, 16 Jun 2020 08:28:14: #2 finished! INFO @ Tue, 16 Jun 2020 08:28:14: #2 predicted fragment length is 104 bps INFO @ Tue, 16 Jun 2020 08:28:14: #2 alternative fragment length(s) may be 4,104 bps INFO @ Tue, 16 Jun 2020 08:28:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331204/SRX331204.05_model.r INFO @ Tue, 16 Jun 2020 08:28:14: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:28:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:28:18: 1000000 INFO @ Tue, 16 Jun 2020 08:28:23: 2000000 INFO @ Tue, 16 Jun 2020 08:28:25: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:28:28: 3000000 INFO @ Tue, 16 Jun 2020 08:28:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331204/SRX331204.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:28:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331204/SRX331204.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:28:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331204/SRX331204.05_summits.bed INFO @ Tue, 16 Jun 2020 08:28:30: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1036 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:28:33: 4000000 INFO @ Tue, 16 Jun 2020 08:28:38: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:28:38: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:28:38: #1 total tags in treatment: 4779544 INFO @ Tue, 16 Jun 2020 08:28:38: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:28:38: #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 08:28:38: #1 tags after filtering in treatment: 4779544 INFO @ Tue, 16 Jun 2020 08:28:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:28:38: #1 finished! INFO @ Tue, 16 Jun 2020 08:28:38: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:28:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:28:38: #2 number of paired peaks: 497 WARNING @ Tue, 16 Jun 2020 08:28:38: Fewer paired peaks (497) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 497 pairs to build model! INFO @ Tue, 16 Jun 2020 08:28:38: start model_add_line... INFO @ Tue, 16 Jun 2020 08:28:38: start X-correlation... INFO @ Tue, 16 Jun 2020 08:28:38: end of X-cor INFO @ Tue, 16 Jun 2020 08:28:38: #2 finished! INFO @ Tue, 16 Jun 2020 08:28:38: #2 predicted fragment length is 104 bps INFO @ Tue, 16 Jun 2020 08:28:38: #2 alternative fragment length(s) may be 4,104 bps INFO @ Tue, 16 Jun 2020 08:28:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331204/SRX331204.10_model.r INFO @ Tue, 16 Jun 2020 08:28:38: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:28:38: #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 08:28:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331204/SRX331204.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331204/SRX331204.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331204/SRX331204.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331204/SRX331204.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 08:28:42: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:28:42: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:28:48: 1000000 INFO @ Tue, 16 Jun 2020 08:28:50: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:28:53: 2000000 INFO @ Tue, 16 Jun 2020 08:28:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331204/SRX331204.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:28:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331204/SRX331204.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:28:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331204/SRX331204.10_summits.bed INFO @ Tue, 16 Jun 2020 08:28:55: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (523 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:28:58: 3000000 INFO @ Tue, 16 Jun 2020 08:29:03: 4000000 INFO @ Tue, 16 Jun 2020 08:29:07: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:29:07: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:29:07: #1 total tags in treatment: 4779544 INFO @ Tue, 16 Jun 2020 08:29:07: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:29:07: #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 08:29:07: #1 tags after filtering in treatment: 4779544 INFO @ Tue, 16 Jun 2020 08:29:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:29:07: #1 finished! INFO @ Tue, 16 Jun 2020 08:29:07: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:29:07: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:29:07: #2 number of paired peaks: 497 WARNING @ Tue, 16 Jun 2020 08:29:07: Fewer paired peaks (497) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 497 pairs to build model! INFO @ Tue, 16 Jun 2020 08:29:07: start model_add_line... INFO @ Tue, 16 Jun 2020 08:29:07: start X-correlation... INFO @ Tue, 16 Jun 2020 08:29:07: end of X-cor INFO @ Tue, 16 Jun 2020 08:29:07: #2 finished! INFO @ Tue, 16 Jun 2020 08:29:07: #2 predicted fragment length is 104 bps INFO @ Tue, 16 Jun 2020 08:29:07: #2 alternative fragment length(s) may be 4,104 bps INFO @ Tue, 16 Jun 2020 08:29:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331204/SRX331204.20_model.r INFO @ Tue, 16 Jun 2020 08:29:07: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:29:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:29:18: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:29:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331204/SRX331204.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:29:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331204/SRX331204.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:29:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331204/SRX331204.20_summits.bed INFO @ Tue, 16 Jun 2020 08:29:24: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (188 records, 4 fields): 1 millis CompletedMACS2peakCalling