Job ID = 6366930 SRX = SRX2576632 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:08:08 prefetch.2.10.7: 1) Downloading 'SRR5272589'... 2020-06-15T23:08:08 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:09:28 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:09:29 prefetch.2.10.7: 'SRR5272589' is valid 2020-06-15T23:09:29 prefetch.2.10.7: 1) 'SRR5272589' was downloaded successfully Read 18906900 spots for SRR5272589/SRR5272589.sra Written 18906900 spots for SRR5272589/SRR5272589.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:06 18906900 reads; of these: 18906900 (100.00%) were unpaired; of these: 483206 (2.56%) aligned 0 times 15157773 (80.17%) aligned exactly 1 time 3265921 (17.27%) aligned >1 times 97.44% overall alignment rate Time searching: 00:03:07 Overall time: 00:03:07 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_rmdupse_core] 2724218 / 18423694 = 0.1479 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 08:17:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576632/SRX2576632.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576632/SRX2576632.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576632/SRX2576632.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576632/SRX2576632.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 08:17:56: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:17:56: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:18:01: 1000000 INFO @ Tue, 16 Jun 2020 08:18:07: 2000000 INFO @ Tue, 16 Jun 2020 08:18:12: 3000000 INFO @ Tue, 16 Jun 2020 08:18:17: 4000000 INFO @ Tue, 16 Jun 2020 08:18:22: 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 08:18:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576632/SRX2576632.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576632/SRX2576632.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576632/SRX2576632.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576632/SRX2576632.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 08:18:26: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:18:26: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:18:28: 6000000 INFO @ Tue, 16 Jun 2020 08:18:32: 1000000 INFO @ Tue, 16 Jun 2020 08:18:34: 7000000 INFO @ Tue, 16 Jun 2020 08:18:39: 2000000 INFO @ Tue, 16 Jun 2020 08:18:40: 8000000 INFO @ Tue, 16 Jun 2020 08:18:45: 3000000 INFO @ Tue, 16 Jun 2020 08:18:46: 9000000 INFO @ Tue, 16 Jun 2020 08:18:52: 10000000 INFO @ Tue, 16 Jun 2020 08:18:52: 4000000 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 08:18:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576632/SRX2576632.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576632/SRX2576632.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576632/SRX2576632.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576632/SRX2576632.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 08:18:56: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:18:56: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:18:58: 11000000 INFO @ Tue, 16 Jun 2020 08:18:59: 5000000 INFO @ Tue, 16 Jun 2020 08:19:02: 1000000 INFO @ Tue, 16 Jun 2020 08:19:04: 12000000 INFO @ Tue, 16 Jun 2020 08:19:06: 6000000 INFO @ Tue, 16 Jun 2020 08:19:09: 2000000 INFO @ Tue, 16 Jun 2020 08:19:10: 13000000 INFO @ Tue, 16 Jun 2020 08:19:12: 7000000 INFO @ Tue, 16 Jun 2020 08:19:16: 3000000 INFO @ Tue, 16 Jun 2020 08:19:16: 14000000 INFO @ Tue, 16 Jun 2020 08:19:19: 8000000 INFO @ Tue, 16 Jun 2020 08:19:22: 15000000 INFO @ Tue, 16 Jun 2020 08:19:23: 4000000 INFO @ Tue, 16 Jun 2020 08:19:26: 9000000 INFO @ Tue, 16 Jun 2020 08:19:27: #1 tag size is determined as 35 bps INFO @ Tue, 16 Jun 2020 08:19:27: #1 tag size = 35 INFO @ Tue, 16 Jun 2020 08:19:27: #1 total tags in treatment: 15699476 INFO @ Tue, 16 Jun 2020 08:19:27: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:19:27: #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 08:19:27: #1 tags after filtering in treatment: 15699476 INFO @ Tue, 16 Jun 2020 08:19:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:19:27: #1 finished! INFO @ Tue, 16 Jun 2020 08:19:27: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:19:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:19:28: #2 number of paired peaks: 371 WARNING @ Tue, 16 Jun 2020 08:19:28: Fewer paired peaks (371) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 371 pairs to build model! INFO @ Tue, 16 Jun 2020 08:19:28: start model_add_line... INFO @ Tue, 16 Jun 2020 08:19:28: start X-correlation... INFO @ Tue, 16 Jun 2020 08:19:28: end of X-cor INFO @ Tue, 16 Jun 2020 08:19:28: #2 finished! INFO @ Tue, 16 Jun 2020 08:19:28: #2 predicted fragment length is 126 bps INFO @ Tue, 16 Jun 2020 08:19:28: #2 alternative fragment length(s) may be 126 bps INFO @ Tue, 16 Jun 2020 08:19:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576632/SRX2576632.05_model.r INFO @ Tue, 16 Jun 2020 08:19:28: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:19:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:19:30: 5000000 INFO @ Tue, 16 Jun 2020 08:19:32: 10000000 INFO @ Tue, 16 Jun 2020 08:19:36: 6000000 INFO @ Tue, 16 Jun 2020 08:19:39: 11000000 INFO @ Tue, 16 Jun 2020 08:19:43: 7000000 INFO @ Tue, 16 Jun 2020 08:19:45: 12000000 INFO @ Tue, 16 Jun 2020 08:19:49: 8000000 INFO @ Tue, 16 Jun 2020 08:19:52: 13000000 INFO @ Tue, 16 Jun 2020 08:19:56: 9000000 INFO @ Tue, 16 Jun 2020 08:19:59: 14000000 INFO @ Tue, 16 Jun 2020 08:20:02: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:20:02: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:20:05: 15000000 INFO @ Tue, 16 Jun 2020 08:20:09: 11000000 INFO @ Tue, 16 Jun 2020 08:20:10: #1 tag size is determined as 35 bps INFO @ Tue, 16 Jun 2020 08:20:10: #1 tag size = 35 INFO @ Tue, 16 Jun 2020 08:20:10: #1 total tags in treatment: 15699476 INFO @ Tue, 16 Jun 2020 08:20:10: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:20:10: #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 08:20:10: #1 tags after filtering in treatment: 15699476 INFO @ Tue, 16 Jun 2020 08:20:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:20:10: #1 finished! INFO @ Tue, 16 Jun 2020 08:20:10: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:20:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:20:11: #2 number of paired peaks: 371 WARNING @ Tue, 16 Jun 2020 08:20:11: Fewer paired peaks (371) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 371 pairs to build model! INFO @ Tue, 16 Jun 2020 08:20:11: start model_add_line... INFO @ Tue, 16 Jun 2020 08:20:11: start X-correlation... INFO @ Tue, 16 Jun 2020 08:20:11: end of X-cor INFO @ Tue, 16 Jun 2020 08:20:11: #2 finished! INFO @ Tue, 16 Jun 2020 08:20:11: #2 predicted fragment length is 126 bps INFO @ Tue, 16 Jun 2020 08:20:11: #2 alternative fragment length(s) may be 126 bps INFO @ Tue, 16 Jun 2020 08:20:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576632/SRX2576632.10_model.r INFO @ Tue, 16 Jun 2020 08:20:11: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:20:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:20:15: 12000000 INFO @ Tue, 16 Jun 2020 08:20:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576632/SRX2576632.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:20:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576632/SRX2576632.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:20:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576632/SRX2576632.05_summits.bed INFO @ Tue, 16 Jun 2020 08:20:19: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3071 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:20:21: 13000000 INFO @ Tue, 16 Jun 2020 08:20:27: 14000000 INFO @ Tue, 16 Jun 2020 08:20:34: 15000000 INFO @ Tue, 16 Jun 2020 08:20:38: #1 tag size is determined as 35 bps INFO @ Tue, 16 Jun 2020 08:20:38: #1 tag size = 35 INFO @ Tue, 16 Jun 2020 08:20:38: #1 total tags in treatment: 15699476 INFO @ Tue, 16 Jun 2020 08:20:38: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:20:38: #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 08:20:38: #1 tags after filtering in treatment: 15699476 INFO @ Tue, 16 Jun 2020 08:20:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:20:38: #1 finished! INFO @ Tue, 16 Jun 2020 08:20:38: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:20:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:20:39: #2 number of paired peaks: 371 WARNING @ Tue, 16 Jun 2020 08:20:39: Fewer paired peaks (371) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 371 pairs to build model! INFO @ Tue, 16 Jun 2020 08:20:39: start model_add_line... INFO @ Tue, 16 Jun 2020 08:20:39: start X-correlation... INFO @ Tue, 16 Jun 2020 08:20:39: end of X-cor INFO @ Tue, 16 Jun 2020 08:20:39: #2 finished! INFO @ Tue, 16 Jun 2020 08:20:39: #2 predicted fragment length is 126 bps INFO @ Tue, 16 Jun 2020 08:20:39: #2 alternative fragment length(s) may be 126 bps INFO @ Tue, 16 Jun 2020 08:20:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576632/SRX2576632.20_model.r INFO @ Tue, 16 Jun 2020 08:20:39: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:20:39: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:20:43: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:21:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576632/SRX2576632.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:21:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576632/SRX2576632.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:21:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576632/SRX2576632.10_summits.bed INFO @ Tue, 16 Jun 2020 08:21:00: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2037 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:21:11: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:21:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576632/SRX2576632.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:21:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576632/SRX2576632.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:21:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576632/SRX2576632.20_summits.bed INFO @ Tue, 16 Jun 2020 08:21:27: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1319 records, 4 fields): 2 millis CompletedMACS2peakCalling