Job ID = 6367243 SRX = SRX3104606 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:25:36 prefetch.2.10.7: 1) Downloading 'SRR5946211'... 2020-06-15T23:25:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:27:20 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:27:21 prefetch.2.10.7: 'SRR5946211' is valid 2020-06-15T23:27:21 prefetch.2.10.7: 1) 'SRR5946211' was downloaded successfully 2020-06-15T23:27:21 prefetch.2.10.7: 'SRR5946211' has 0 unresolved dependencies Read 21726070 spots for SRR5946211/SRR5946211.sra Written 21726070 spots for SRR5946211/SRR5946211.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: 00:04:13 21726070 reads; of these: 21726070 (100.00%) were unpaired; of these: 6681158 (30.75%) aligned 0 times 12902300 (59.39%) aligned exactly 1 time 2142612 (9.86%) aligned >1 times 69.25% overall alignment rate Time searching: 00:04:13 Overall time: 00:04:13 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] 8581434 / 15044912 = 0.5704 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 08:35:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3104606/SRX3104606.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3104606/SRX3104606.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3104606/SRX3104606.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3104606/SRX3104606.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 08:35:35: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:35:35: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:35:41: 1000000 INFO @ Tue, 16 Jun 2020 08:35:47: 2000000 INFO @ Tue, 16 Jun 2020 08:35:53: 3000000 INFO @ Tue, 16 Jun 2020 08:35:59: 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 08:36:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3104606/SRX3104606.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3104606/SRX3104606.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3104606/SRX3104606.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3104606/SRX3104606.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 08:36:05: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:36:05: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:36:05: 5000000 INFO @ Tue, 16 Jun 2020 08:36:12: 1000000 INFO @ Tue, 16 Jun 2020 08:36:12: 6000000 INFO @ Tue, 16 Jun 2020 08:36:15: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:36:15: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:36:15: #1 total tags in treatment: 6463478 INFO @ Tue, 16 Jun 2020 08:36:15: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:36:15: #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 08:36:15: #1 tags after filtering in treatment: 6463478 INFO @ Tue, 16 Jun 2020 08:36:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:36:15: #1 finished! INFO @ Tue, 16 Jun 2020 08:36:15: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:36:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:36:16: #2 number of paired peaks: 1578 INFO @ Tue, 16 Jun 2020 08:36:16: start model_add_line... INFO @ Tue, 16 Jun 2020 08:36:16: start X-correlation... INFO @ Tue, 16 Jun 2020 08:36:16: end of X-cor INFO @ Tue, 16 Jun 2020 08:36:16: #2 finished! INFO @ Tue, 16 Jun 2020 08:36:16: #2 predicted fragment length is 168 bps INFO @ Tue, 16 Jun 2020 08:36:16: #2 alternative fragment length(s) may be 168 bps INFO @ Tue, 16 Jun 2020 08:36:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3104606/SRX3104606.05_model.r INFO @ Tue, 16 Jun 2020 08:36:16: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:36:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:36:18: 2000000 INFO @ Tue, 16 Jun 2020 08:36:24: 3000000 INFO @ Tue, 16 Jun 2020 08:36:30: 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 08:36:34: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:36:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3104606/SRX3104606.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3104606/SRX3104606.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3104606/SRX3104606.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3104606/SRX3104606.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 08:36:35: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:36:35: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:36:36: 5000000 INFO @ Tue, 16 Jun 2020 08:36:41: 1000000 INFO @ Tue, 16 Jun 2020 08:36:42: 6000000 INFO @ Tue, 16 Jun 2020 08:36:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3104606/SRX3104606.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:36:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3104606/SRX3104606.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:36:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3104606/SRX3104606.05_summits.bed INFO @ Tue, 16 Jun 2020 08:36:44: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3776 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:36:45: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:36:45: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:36:45: #1 total tags in treatment: 6463478 INFO @ Tue, 16 Jun 2020 08:36:45: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:36:45: #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 08:36:45: #1 tags after filtering in treatment: 6463478 INFO @ Tue, 16 Jun 2020 08:36:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:36:45: #1 finished! INFO @ Tue, 16 Jun 2020 08:36:45: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:36:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:36:46: #2 number of paired peaks: 1578 INFO @ Tue, 16 Jun 2020 08:36:46: start model_add_line... INFO @ Tue, 16 Jun 2020 08:36:46: start X-correlation... INFO @ Tue, 16 Jun 2020 08:36:46: end of X-cor INFO @ Tue, 16 Jun 2020 08:36:46: #2 finished! INFO @ Tue, 16 Jun 2020 08:36:46: #2 predicted fragment length is 168 bps INFO @ Tue, 16 Jun 2020 08:36:46: #2 alternative fragment length(s) may be 168 bps INFO @ Tue, 16 Jun 2020 08:36:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3104606/SRX3104606.10_model.r INFO @ Tue, 16 Jun 2020 08:36:46: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:36:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:36:48: 2000000 INFO @ Tue, 16 Jun 2020 08:36:54: 3000000 INFO @ Tue, 16 Jun 2020 08:37:00: 4000000 INFO @ Tue, 16 Jun 2020 08:37:04: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:37:06: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:37:13: 6000000 INFO @ Tue, 16 Jun 2020 08:37:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3104606/SRX3104606.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:37:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3104606/SRX3104606.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:37:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3104606/SRX3104606.10_summits.bed INFO @ Tue, 16 Jun 2020 08:37:14: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2094 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:37:15: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:37:15: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:37:15: #1 total tags in treatment: 6463478 INFO @ Tue, 16 Jun 2020 08:37:15: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:37:15: #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 08:37:15: #1 tags after filtering in treatment: 6463478 INFO @ Tue, 16 Jun 2020 08:37:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:37:15: #1 finished! INFO @ Tue, 16 Jun 2020 08:37:15: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:37:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:37:16: #2 number of paired peaks: 1578 INFO @ Tue, 16 Jun 2020 08:37:16: start model_add_line... INFO @ Tue, 16 Jun 2020 08:37:16: start X-correlation... INFO @ Tue, 16 Jun 2020 08:37:16: end of X-cor INFO @ Tue, 16 Jun 2020 08:37:16: #2 finished! INFO @ Tue, 16 Jun 2020 08:37:16: #2 predicted fragment length is 168 bps INFO @ Tue, 16 Jun 2020 08:37:16: #2 alternative fragment length(s) may be 168 bps INFO @ Tue, 16 Jun 2020 08:37:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3104606/SRX3104606.20_model.r INFO @ Tue, 16 Jun 2020 08:37:16: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:37:16: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:37:34: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:37:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3104606/SRX3104606.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:37:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3104606/SRX3104606.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:37:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3104606/SRX3104606.20_summits.bed INFO @ Tue, 16 Jun 2020 08:37:43: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (960 records, 4 fields): 2 millis CompletedMACS2peakCalling