Job ID = 6368400 SRX = SRX495079 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:08:54 prefetch.2.10.7: 1) Downloading 'SRR1198611'... 2020-06-16T00:08:54 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:12:12 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:12:12 prefetch.2.10.7: 1) 'SRR1198611' was downloaded successfully Read 14382334 spots for SRR1198611/SRR1198611.sra Written 14382334 spots for SRR1198611/SRR1198611.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: 00:02:34 14382334 reads; of these: 14382334 (100.00%) were unpaired; of these: 1868249 (12.99%) aligned 0 times 10981844 (76.36%) aligned exactly 1 time 1532241 (10.65%) aligned >1 times 87.01% overall alignment rate Time searching: 00:02:34 Overall time: 00:02:34 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] 4779558 / 12514085 = 0.3819 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 09:18:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495079/SRX495079.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495079/SRX495079.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495079/SRX495079.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495079/SRX495079.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 09:18:16: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:18:16: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:18:21: 1000000 INFO @ Tue, 16 Jun 2020 09:18:26: 2000000 INFO @ Tue, 16 Jun 2020 09:18:32: 3000000 INFO @ Tue, 16 Jun 2020 09:18:37: 4000000 INFO @ Tue, 16 Jun 2020 09:18:42: 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 09:18:47: 6000000 INFO @ Tue, 16 Jun 2020 09:18:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495079/SRX495079.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495079/SRX495079.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495079/SRX495079.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495079/SRX495079.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 09:18:47: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:18:47: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:18:52: 7000000 INFO @ Tue, 16 Jun 2020 09:18:53: 1000000 INFO @ Tue, 16 Jun 2020 09:18:56: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:18:56: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:18:56: #1 total tags in treatment: 7734527 INFO @ Tue, 16 Jun 2020 09:18:56: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:18:56: #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 09:18:57: #1 tags after filtering in treatment: 7734527 INFO @ Tue, 16 Jun 2020 09:18:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:18:57: #1 finished! INFO @ Tue, 16 Jun 2020 09:18:57: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:18:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:18:57: #2 number of paired peaks: 366 WARNING @ Tue, 16 Jun 2020 09:18:57: Fewer paired peaks (366) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 366 pairs to build model! INFO @ Tue, 16 Jun 2020 09:18:57: start model_add_line... INFO @ Tue, 16 Jun 2020 09:18:57: start X-correlation... INFO @ Tue, 16 Jun 2020 09:18:57: end of X-cor INFO @ Tue, 16 Jun 2020 09:18:57: #2 finished! INFO @ Tue, 16 Jun 2020 09:18:57: #2 predicted fragment length is 107 bps INFO @ Tue, 16 Jun 2020 09:18:57: #2 alternative fragment length(s) may be 4,107,594 bps INFO @ Tue, 16 Jun 2020 09:18:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495079/SRX495079.05_model.r INFO @ Tue, 16 Jun 2020 09:18:57: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:18:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:18:59: 2000000 INFO @ Tue, 16 Jun 2020 09:19:05: 3000000 INFO @ Tue, 16 Jun 2020 09:19:11: 4000000 INFO @ Tue, 16 Jun 2020 09:19:13: #3 Call peaks for each chromosome... 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 09:19:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495079/SRX495079.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495079/SRX495079.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495079/SRX495079.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495079/SRX495079.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 09:19:16: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:19:16: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:19:17: 5000000 INFO @ Tue, 16 Jun 2020 09:19:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495079/SRX495079.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:19:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495079/SRX495079.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:19:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495079/SRX495079.05_summits.bed INFO @ Tue, 16 Jun 2020 09:19:22: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (519 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:19:22: 1000000 INFO @ Tue, 16 Jun 2020 09:19:23: 6000000 INFO @ Tue, 16 Jun 2020 09:19:28: 2000000 INFO @ Tue, 16 Jun 2020 09:19:29: 7000000 INFO @ Tue, 16 Jun 2020 09:19:33: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:19:33: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:19:33: #1 total tags in treatment: 7734527 INFO @ Tue, 16 Jun 2020 09:19:33: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:19:33: #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 09:19:33: #1 tags after filtering in treatment: 7734527 INFO @ Tue, 16 Jun 2020 09:19:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:19:33: #1 finished! INFO @ Tue, 16 Jun 2020 09:19:33: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:19:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:19:34: 3000000 INFO @ Tue, 16 Jun 2020 09:19:34: #2 number of paired peaks: 366 WARNING @ Tue, 16 Jun 2020 09:19:34: Fewer paired peaks (366) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 366 pairs to build model! INFO @ Tue, 16 Jun 2020 09:19:34: start model_add_line... INFO @ Tue, 16 Jun 2020 09:19:34: start X-correlation... INFO @ Tue, 16 Jun 2020 09:19:34: end of X-cor INFO @ Tue, 16 Jun 2020 09:19:34: #2 finished! INFO @ Tue, 16 Jun 2020 09:19:34: #2 predicted fragment length is 107 bps INFO @ Tue, 16 Jun 2020 09:19:34: #2 alternative fragment length(s) may be 4,107,594 bps INFO @ Tue, 16 Jun 2020 09:19:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495079/SRX495079.10_model.r INFO @ Tue, 16 Jun 2020 09:19:34: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:19:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:19:39: 4000000 INFO @ Tue, 16 Jun 2020 09:19:44: 5000000 INFO @ Tue, 16 Jun 2020 09:19:50: 6000000 INFO @ Tue, 16 Jun 2020 09:19:50: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:19:55: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:19:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495079/SRX495079.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:19:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495079/SRX495079.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:19:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495079/SRX495079.10_summits.bed INFO @ Tue, 16 Jun 2020 09:19:58: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (221 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:19:59: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:19:59: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:19:59: #1 total tags in treatment: 7734527 INFO @ Tue, 16 Jun 2020 09:19:59: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:19:59: #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 09:19:59: #1 tags after filtering in treatment: 7734527 INFO @ Tue, 16 Jun 2020 09:19:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:19:59: #1 finished! INFO @ Tue, 16 Jun 2020 09:19:59: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:19:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:19:59: #2 number of paired peaks: 366 WARNING @ Tue, 16 Jun 2020 09:19:59: Fewer paired peaks (366) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 366 pairs to build model! INFO @ Tue, 16 Jun 2020 09:19:59: start model_add_line... INFO @ Tue, 16 Jun 2020 09:20:00: start X-correlation... INFO @ Tue, 16 Jun 2020 09:20:00: end of X-cor INFO @ Tue, 16 Jun 2020 09:20:00: #2 finished! INFO @ Tue, 16 Jun 2020 09:20:00: #2 predicted fragment length is 107 bps INFO @ Tue, 16 Jun 2020 09:20:00: #2 alternative fragment length(s) may be 4,107,594 bps INFO @ Tue, 16 Jun 2020 09:20:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495079/SRX495079.20_model.r INFO @ Tue, 16 Jun 2020 09:20:00: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:20:00: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:20:16: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:20:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495079/SRX495079.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:20:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495079/SRX495079.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:20:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495079/SRX495079.20_summits.bed INFO @ Tue, 16 Jun 2020 09:20:24: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (99 records, 4 fields): 1 millis CompletedMACS2peakCalling