Job ID = 6366726 SRX = SRX2228879 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:00:08 prefetch.2.10.7: 1) Downloading 'SRR4380335'... 2020-06-15T23:00:08 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:01:23 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:01:24 prefetch.2.10.7: 'SRR4380335' is valid 2020-06-15T23:01:24 prefetch.2.10.7: 1) 'SRR4380335' was downloaded successfully 2020-06-15T23:01:24 prefetch.2.10.7: 'SRR4380335' has 0 unresolved dependencies Read 19204008 spots for SRR4380335/SRR4380335.sra Written 19204008 spots for SRR4380335/SRR4380335.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: 00:02:35 19204008 reads; of these: 19204008 (100.00%) were unpaired; of these: 12927565 (67.32%) aligned 0 times 5179351 (26.97%) aligned exactly 1 time 1097092 (5.71%) aligned >1 times 32.68% overall alignment rate Time searching: 00:02:35 Overall time: 00:02:35 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] 869444 / 6276443 = 0.1385 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 08:07:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228879/SRX2228879.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228879/SRX2228879.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228879/SRX2228879.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228879/SRX2228879.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 08:07:22: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:07:22: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:07:29: 1000000 INFO @ Tue, 16 Jun 2020 08:07:35: 2000000 INFO @ Tue, 16 Jun 2020 08:07:42: 3000000 INFO @ Tue, 16 Jun 2020 08:07:49: 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 08:07:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228879/SRX2228879.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228879/SRX2228879.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228879/SRX2228879.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228879/SRX2228879.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 08:07:52: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:07:52: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:07:56: 5000000 INFO @ Tue, 16 Jun 2020 08:07:58: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:07:58: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:07:58: #1 total tags in treatment: 5406999 INFO @ Tue, 16 Jun 2020 08:07:58: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:07:58: #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 08:07:59: #1 tags after filtering in treatment: 5406999 INFO @ Tue, 16 Jun 2020 08:07:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:07:59: #1 finished! INFO @ Tue, 16 Jun 2020 08:07:59: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:07:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:07:59: 1000000 INFO @ Tue, 16 Jun 2020 08:07:59: #2 number of paired peaks: 756 WARNING @ Tue, 16 Jun 2020 08:07:59: Fewer paired peaks (756) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 756 pairs to build model! INFO @ Tue, 16 Jun 2020 08:07:59: start model_add_line... INFO @ Tue, 16 Jun 2020 08:07:59: start X-correlation... INFO @ Tue, 16 Jun 2020 08:07:59: end of X-cor INFO @ Tue, 16 Jun 2020 08:07:59: #2 finished! INFO @ Tue, 16 Jun 2020 08:07:59: #2 predicted fragment length is 112 bps INFO @ Tue, 16 Jun 2020 08:07:59: #2 alternative fragment length(s) may be 112 bps INFO @ Tue, 16 Jun 2020 08:07:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228879/SRX2228879.05_model.r INFO @ Tue, 16 Jun 2020 08:07:59: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:07:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:08:06: 2000000 INFO @ Tue, 16 Jun 2020 08:08:12: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:08:13: 3000000 INFO @ Tue, 16 Jun 2020 08:08:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228879/SRX2228879.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:08:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228879/SRX2228879.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:08:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228879/SRX2228879.05_summits.bed INFO @ Tue, 16 Jun 2020 08:08:19: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1573 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:08:20: 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 08:08:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228879/SRX2228879.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228879/SRX2228879.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228879/SRX2228879.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228879/SRX2228879.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 08:08:22: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:08:22: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:08:27: 5000000 INFO @ Tue, 16 Jun 2020 08:08:29: 1000000 INFO @ Tue, 16 Jun 2020 08:08:30: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:08:30: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:08:30: #1 total tags in treatment: 5406999 INFO @ Tue, 16 Jun 2020 08:08:30: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:08:30: #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 08:08:30: #1 tags after filtering in treatment: 5406999 INFO @ Tue, 16 Jun 2020 08:08:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:08:30: #1 finished! INFO @ Tue, 16 Jun 2020 08:08:30: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:08:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:08:30: #2 number of paired peaks: 756 WARNING @ Tue, 16 Jun 2020 08:08:30: Fewer paired peaks (756) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 756 pairs to build model! INFO @ Tue, 16 Jun 2020 08:08:30: start model_add_line... INFO @ Tue, 16 Jun 2020 08:08:30: start X-correlation... INFO @ Tue, 16 Jun 2020 08:08:30: end of X-cor INFO @ Tue, 16 Jun 2020 08:08:30: #2 finished! INFO @ Tue, 16 Jun 2020 08:08:30: #2 predicted fragment length is 112 bps INFO @ Tue, 16 Jun 2020 08:08:30: #2 alternative fragment length(s) may be 112 bps INFO @ Tue, 16 Jun 2020 08:08:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228879/SRX2228879.10_model.r INFO @ Tue, 16 Jun 2020 08:08:30: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:08:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:08:36: 2000000 INFO @ Tue, 16 Jun 2020 08:08:43: 3000000 INFO @ Tue, 16 Jun 2020 08:08:43: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:08:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228879/SRX2228879.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:08:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228879/SRX2228879.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:08:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228879/SRX2228879.10_summits.bed INFO @ Tue, 16 Jun 2020 08:08:49: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1001 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:08:50: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:08:56: 5000000 INFO @ Tue, 16 Jun 2020 08:08:59: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:08:59: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:08:59: #1 total tags in treatment: 5406999 INFO @ Tue, 16 Jun 2020 08:08:59: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:08:59: #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 08:08:59: #1 tags after filtering in treatment: 5406999 INFO @ Tue, 16 Jun 2020 08:08:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:08:59: #1 finished! INFO @ Tue, 16 Jun 2020 08:08:59: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:08:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:09:00: #2 number of paired peaks: 756 WARNING @ Tue, 16 Jun 2020 08:09:00: Fewer paired peaks (756) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 756 pairs to build model! INFO @ Tue, 16 Jun 2020 08:09:00: start model_add_line... INFO @ Tue, 16 Jun 2020 08:09:00: start X-correlation... INFO @ Tue, 16 Jun 2020 08:09:00: end of X-cor INFO @ Tue, 16 Jun 2020 08:09:00: #2 finished! INFO @ Tue, 16 Jun 2020 08:09:00: #2 predicted fragment length is 112 bps INFO @ Tue, 16 Jun 2020 08:09:00: #2 alternative fragment length(s) may be 112 bps INFO @ Tue, 16 Jun 2020 08:09:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228879/SRX2228879.20_model.r INFO @ Tue, 16 Jun 2020 08:09:00: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:09:00: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:09:12: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:09:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228879/SRX2228879.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:09:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228879/SRX2228879.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:09:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228879/SRX2228879.20_summits.bed INFO @ Tue, 16 Jun 2020 08:09:19: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (554 records, 4 fields): 1 millis CompletedMACS2peakCalling