Job ID = 6367503 SRX = SRX331260 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:27:51 prefetch.2.10.7: 1) Downloading 'SRR947492'... 2020-06-15T23:27:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:28:53 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:28:53 prefetch.2.10.7: 'SRR947492' is valid 2020-06-15T23:28:53 prefetch.2.10.7: 1) 'SRR947492' was downloaded successfully Read 8102787 spots for SRR947492/SRR947492.sra Written 8102787 spots for SRR947492/SRR947492.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: 00:00:54 8102787 reads; of these: 8102787 (100.00%) were unpaired; of these: 4183403 (51.63%) aligned 0 times 3292152 (40.63%) aligned exactly 1 time 627232 (7.74%) aligned >1 times 48.37% overall alignment rate Time searching: 00:00:54 Overall time: 00:00:54 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] 1300865 / 3919384 = 0.3319 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 08:31:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331260/SRX331260.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331260/SRX331260.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331260/SRX331260.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331260/SRX331260.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 08:31:18: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:31:18: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:31:22: 1000000 INFO @ Tue, 16 Jun 2020 08:31:27: 2000000 INFO @ Tue, 16 Jun 2020 08:31:30: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:31:30: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:31:30: #1 total tags in treatment: 2618519 INFO @ Tue, 16 Jun 2020 08:31:30: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:31:30: #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 08:31:30: #1 tags after filtering in treatment: 2618519 INFO @ Tue, 16 Jun 2020 08:31:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:31:30: #1 finished! INFO @ Tue, 16 Jun 2020 08:31:30: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:31:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:31:31: #2 number of paired peaks: 648 WARNING @ Tue, 16 Jun 2020 08:31:31: Fewer paired peaks (648) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 648 pairs to build model! INFO @ Tue, 16 Jun 2020 08:31:31: start model_add_line... INFO @ Tue, 16 Jun 2020 08:31:31: start X-correlation... INFO @ Tue, 16 Jun 2020 08:31:31: end of X-cor INFO @ Tue, 16 Jun 2020 08:31:31: #2 finished! INFO @ Tue, 16 Jun 2020 08:31:31: #2 predicted fragment length is 114 bps INFO @ Tue, 16 Jun 2020 08:31:31: #2 alternative fragment length(s) may be 114,558,581 bps INFO @ Tue, 16 Jun 2020 08:31:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331260/SRX331260.05_model.r INFO @ Tue, 16 Jun 2020 08:31:31: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:31:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:31:37: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:31:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331260/SRX331260.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:31:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331260/SRX331260.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:31:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331260/SRX331260.05_summits.bed INFO @ Tue, 16 Jun 2020 08:31:40: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1267 records, 4 fields): 3 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 08:31:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331260/SRX331260.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331260/SRX331260.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331260/SRX331260.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331260/SRX331260.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 08:31:48: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:31:48: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:31:52: 1000000 INFO @ Tue, 16 Jun 2020 08:31:56: 2000000 INFO @ Tue, 16 Jun 2020 08:31:59: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:31:59: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:31:59: #1 total tags in treatment: 2618519 INFO @ Tue, 16 Jun 2020 08:31:59: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:31:59: #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 08:31:59: #1 tags after filtering in treatment: 2618519 INFO @ Tue, 16 Jun 2020 08:31:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:31:59: #1 finished! INFO @ Tue, 16 Jun 2020 08:31:59: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:31:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:31:59: #2 number of paired peaks: 648 WARNING @ Tue, 16 Jun 2020 08:31:59: Fewer paired peaks (648) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 648 pairs to build model! INFO @ Tue, 16 Jun 2020 08:31:59: start model_add_line... INFO @ Tue, 16 Jun 2020 08:31:59: start X-correlation... INFO @ Tue, 16 Jun 2020 08:31:59: end of X-cor INFO @ Tue, 16 Jun 2020 08:31:59: #2 finished! INFO @ Tue, 16 Jun 2020 08:31:59: #2 predicted fragment length is 114 bps INFO @ Tue, 16 Jun 2020 08:31:59: #2 alternative fragment length(s) may be 114,558,581 bps INFO @ Tue, 16 Jun 2020 08:31:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331260/SRX331260.10_model.r INFO @ Tue, 16 Jun 2020 08:31:59: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:31:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:32:05: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:32:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331260/SRX331260.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:32:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331260/SRX331260.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:32:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331260/SRX331260.10_summits.bed INFO @ Tue, 16 Jun 2020 08:32:08: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (575 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 08:32:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331260/SRX331260.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331260/SRX331260.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331260/SRX331260.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331260/SRX331260.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 08:32:18: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:32:18: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:32:22: 1000000 INFO @ Tue, 16 Jun 2020 08:32:26: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:32:29: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:32:29: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:32:29: #1 total tags in treatment: 2618519 INFO @ Tue, 16 Jun 2020 08:32:29: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:32:29: #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 08:32:29: #1 tags after filtering in treatment: 2618519 INFO @ Tue, 16 Jun 2020 08:32:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:32:29: #1 finished! INFO @ Tue, 16 Jun 2020 08:32:29: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:32:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:32:29: #2 number of paired peaks: 648 WARNING @ Tue, 16 Jun 2020 08:32:29: Fewer paired peaks (648) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 648 pairs to build model! INFO @ Tue, 16 Jun 2020 08:32:29: start model_add_line... INFO @ Tue, 16 Jun 2020 08:32:29: start X-correlation... INFO @ Tue, 16 Jun 2020 08:32:29: end of X-cor INFO @ Tue, 16 Jun 2020 08:32:29: #2 finished! INFO @ Tue, 16 Jun 2020 08:32:29: #2 predicted fragment length is 114 bps INFO @ Tue, 16 Jun 2020 08:32:29: #2 alternative fragment length(s) may be 114,558,581 bps INFO @ Tue, 16 Jun 2020 08:32:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331260/SRX331260.20_model.r INFO @ Tue, 16 Jun 2020 08:32:29: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:32:29: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:32:35: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:32:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331260/SRX331260.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:32:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331260/SRX331260.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:32:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331260/SRX331260.20_summits.bed INFO @ Tue, 16 Jun 2020 08:32:38: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (221 records, 4 fields): 1 millis CompletedMACS2peakCalling