Job ID = 6366389 SRX = SRX1388763 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:57:54 prefetch.2.10.7: 1) Downloading 'SRR2832479'... 2020-06-15T22:57:54 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:58:17 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:58:17 prefetch.2.10.7: 'SRR2832479' is valid 2020-06-15T22:58:17 prefetch.2.10.7: 1) 'SRR2832479' was downloaded successfully Read 4976690 spots for SRR2832479/SRR2832479.sra Written 4976690 spots for SRR2832479/SRR2832479.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: 00:01:09 4976690 reads; of these: 4976690 (100.00%) were unpaired; of these: 243608 (4.89%) aligned 0 times 4105319 (82.49%) aligned exactly 1 time 627763 (12.61%) aligned >1 times 95.11% overall alignment rate Time searching: 00:01:09 Overall time: 00:01:09 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] 397878 / 4733082 = 0.0841 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 08:01:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1388763/SRX1388763.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1388763/SRX1388763.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1388763/SRX1388763.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1388763/SRX1388763.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 08:01:30: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:01:30: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:01:37: 1000000 INFO @ Tue, 16 Jun 2020 08:01:43: 2000000 INFO @ Tue, 16 Jun 2020 08:01:49: 3000000 INFO @ Tue, 16 Jun 2020 08:01:56: 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 08:01:58: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:01:58: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:01:58: #1 total tags in treatment: 4335204 INFO @ Tue, 16 Jun 2020 08:01:58: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:01:58: #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 08:01:58: #1 tags after filtering in treatment: 4335204 INFO @ Tue, 16 Jun 2020 08:01:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:01:58: #1 finished! INFO @ Tue, 16 Jun 2020 08:01:58: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:01:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:01:59: #2 number of paired peaks: 2864 INFO @ Tue, 16 Jun 2020 08:01:59: start model_add_line... INFO @ Tue, 16 Jun 2020 08:01:59: start X-correlation... INFO @ Tue, 16 Jun 2020 08:01:59: end of X-cor INFO @ Tue, 16 Jun 2020 08:01:59: #2 finished! INFO @ Tue, 16 Jun 2020 08:01:59: #2 predicted fragment length is 177 bps INFO @ Tue, 16 Jun 2020 08:01:59: #2 alternative fragment length(s) may be 4,166,177 bps INFO @ Tue, 16 Jun 2020 08:01:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1388763/SRX1388763.05_model.r INFO @ Tue, 16 Jun 2020 08:01:59: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:01:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:02:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1388763/SRX1388763.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1388763/SRX1388763.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1388763/SRX1388763.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1388763/SRX1388763.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 08:02:00: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:02:00: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:02:07: 1000000 INFO @ Tue, 16 Jun 2020 08:02:11: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:02:15: 2000000 INFO @ Tue, 16 Jun 2020 08:02:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1388763/SRX1388763.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:02:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1388763/SRX1388763.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:02:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1388763/SRX1388763.05_summits.bed INFO @ Tue, 16 Jun 2020 08:02:17: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2907 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:02:22: 3000000 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 08:02:30: 4000000 INFO @ Tue, 16 Jun 2020 08:02:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1388763/SRX1388763.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1388763/SRX1388763.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1388763/SRX1388763.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1388763/SRX1388763.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 08:02:30: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:02:30: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:02:32: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:02:32: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:02:32: #1 total tags in treatment: 4335204 INFO @ Tue, 16 Jun 2020 08:02:32: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:02:32: #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 08:02:32: #1 tags after filtering in treatment: 4335204 INFO @ Tue, 16 Jun 2020 08:02:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:02:32: #1 finished! INFO @ Tue, 16 Jun 2020 08:02:32: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:02:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:02:32: #2 number of paired peaks: 2864 INFO @ Tue, 16 Jun 2020 08:02:32: start model_add_line... INFO @ Tue, 16 Jun 2020 08:02:33: start X-correlation... INFO @ Tue, 16 Jun 2020 08:02:33: end of X-cor INFO @ Tue, 16 Jun 2020 08:02:33: #2 finished! INFO @ Tue, 16 Jun 2020 08:02:33: #2 predicted fragment length is 177 bps INFO @ Tue, 16 Jun 2020 08:02:33: #2 alternative fragment length(s) may be 4,166,177 bps INFO @ Tue, 16 Jun 2020 08:02:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1388763/SRX1388763.10_model.r INFO @ Tue, 16 Jun 2020 08:02:33: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:02:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:02:37: 1000000 INFO @ Tue, 16 Jun 2020 08:02:43: 2000000 INFO @ Tue, 16 Jun 2020 08:02:45: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:02:50: 3000000 INFO @ Tue, 16 Jun 2020 08:02:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1388763/SRX1388763.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:02:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1388763/SRX1388763.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:02:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1388763/SRX1388763.10_summits.bed INFO @ Tue, 16 Jun 2020 08:02:51: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1388 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:02:56: 4000000 INFO @ Tue, 16 Jun 2020 08:02:58: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:02:58: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:02:58: #1 total tags in treatment: 4335204 INFO @ Tue, 16 Jun 2020 08:02:58: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:02:58: #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 08:02:58: #1 tags after filtering in treatment: 4335204 INFO @ Tue, 16 Jun 2020 08:02:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:02:58: #1 finished! INFO @ Tue, 16 Jun 2020 08:02:58: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:02:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:02:59: #2 number of paired peaks: 2864 INFO @ Tue, 16 Jun 2020 08:02:59: start model_add_line... INFO @ Tue, 16 Jun 2020 08:02:59: start X-correlation... INFO @ Tue, 16 Jun 2020 08:02:59: end of X-cor INFO @ Tue, 16 Jun 2020 08:02:59: #2 finished! INFO @ Tue, 16 Jun 2020 08:02:59: #2 predicted fragment length is 177 bps INFO @ Tue, 16 Jun 2020 08:02:59: #2 alternative fragment length(s) may be 4,166,177 bps INFO @ Tue, 16 Jun 2020 08:02:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1388763/SRX1388763.20_model.r INFO @ Tue, 16 Jun 2020 08:02:59: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:02:59: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:03:10: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:03:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1388763/SRX1388763.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:03:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1388763/SRX1388763.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:03:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1388763/SRX1388763.20_summits.bed INFO @ Tue, 16 Jun 2020 08:03:16: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (465 records, 4 fields): 2 millis CompletedMACS2peakCalling