Job ID = 6366512 SRX = SRX1674092 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:55:44 prefetch.2.10.7: 1) Downloading 'SRR3320138'... 2020-06-15T22:55:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:01:26 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:01:26 prefetch.2.10.7: 1) 'SRR3320138' was downloaded successfully Read 70154866 spots for SRR3320138/SRR3320138.sra Written 70154866 spots for SRR3320138/SRR3320138.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: 00:14:29 70154866 reads; of these: 70154866 (100.00%) were unpaired; of these: 14913291 (21.26%) aligned 0 times 44943583 (64.06%) aligned exactly 1 time 10297992 (14.68%) aligned >1 times 78.74% overall alignment rate Time searching: 00:14:29 Overall time: 00:14:29 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 24 files... [bam_rmdupse_core] 49294601 / 55241575 = 0.8923 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 08:28:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1674092/SRX1674092.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1674092/SRX1674092.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1674092/SRX1674092.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1674092/SRX1674092.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 08:28:29: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:28:29: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:28:34: 1000000 INFO @ Tue, 16 Jun 2020 08:28:39: 2000000 INFO @ Tue, 16 Jun 2020 08:28:44: 3000000 INFO @ Tue, 16 Jun 2020 08:28:49: 4000000 INFO @ Tue, 16 Jun 2020 08:28:54: 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 08:28:59: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:28:59: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:28:59: #1 total tags in treatment: 5946974 INFO @ Tue, 16 Jun 2020 08:28:59: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:28:59: #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 08:28:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1674092/SRX1674092.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1674092/SRX1674092.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1674092/SRX1674092.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1674092/SRX1674092.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 08:28:59: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:28:59: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:28:59: #1 tags after filtering in treatment: 5946974 INFO @ Tue, 16 Jun 2020 08:28:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:28:59: #1 finished! INFO @ Tue, 16 Jun 2020 08:28:59: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:28:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:29:00: #2 number of paired peaks: 2407 INFO @ Tue, 16 Jun 2020 08:29:00: start model_add_line... INFO @ Tue, 16 Jun 2020 08:29:00: start X-correlation... INFO @ Tue, 16 Jun 2020 08:29:00: end of X-cor INFO @ Tue, 16 Jun 2020 08:29:00: #2 finished! INFO @ Tue, 16 Jun 2020 08:29:00: #2 predicted fragment length is 129 bps INFO @ Tue, 16 Jun 2020 08:29:00: #2 alternative fragment length(s) may be 129 bps INFO @ Tue, 16 Jun 2020 08:29:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1674092/SRX1674092.05_model.r INFO @ Tue, 16 Jun 2020 08:29:00: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:29:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:29:04: 1000000 INFO @ Tue, 16 Jun 2020 08:29:09: 2000000 INFO @ Tue, 16 Jun 2020 08:29:15: 3000000 INFO @ Tue, 16 Jun 2020 08:29:17: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:29:20: 4000000 INFO @ Tue, 16 Jun 2020 08:29:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1674092/SRX1674092.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:29:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1674092/SRX1674092.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:29:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1674092/SRX1674092.05_summits.bed INFO @ Tue, 16 Jun 2020 08:29:25: Done! INFO @ Tue, 16 Jun 2020 08:29:25: 5000000 pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (8905 records, 4 fields): 9 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 08:29:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1674092/SRX1674092.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1674092/SRX1674092.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1674092/SRX1674092.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1674092/SRX1674092.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 08:29:29: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:29:29: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:29:30: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:29:30: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:29:30: #1 total tags in treatment: 5946974 INFO @ Tue, 16 Jun 2020 08:29:30: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:29:30: #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 08:29:30: #1 tags after filtering in treatment: 5946974 INFO @ Tue, 16 Jun 2020 08:29:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:29:30: #1 finished! INFO @ Tue, 16 Jun 2020 08:29:30: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:29:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:29:31: #2 number of paired peaks: 2407 INFO @ Tue, 16 Jun 2020 08:29:31: start model_add_line... INFO @ Tue, 16 Jun 2020 08:29:31: start X-correlation... INFO @ Tue, 16 Jun 2020 08:29:31: end of X-cor INFO @ Tue, 16 Jun 2020 08:29:31: #2 finished! INFO @ Tue, 16 Jun 2020 08:29:31: #2 predicted fragment length is 129 bps INFO @ Tue, 16 Jun 2020 08:29:31: #2 alternative fragment length(s) may be 129 bps INFO @ Tue, 16 Jun 2020 08:29:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1674092/SRX1674092.10_model.r INFO @ Tue, 16 Jun 2020 08:29:31: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:29:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:29:34: 1000000 INFO @ Tue, 16 Jun 2020 08:29:40: 2000000 INFO @ Tue, 16 Jun 2020 08:29:45: 3000000 INFO @ Tue, 16 Jun 2020 08:29:48: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:29:51: 4000000 INFO @ Tue, 16 Jun 2020 08:29:56: 5000000 INFO @ Tue, 16 Jun 2020 08:29:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1674092/SRX1674092.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:29:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1674092/SRX1674092.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:29:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1674092/SRX1674092.10_summits.bed INFO @ Tue, 16 Jun 2020 08:29:56: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4473 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:30:01: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:30:01: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:30:01: #1 total tags in treatment: 5946974 INFO @ Tue, 16 Jun 2020 08:30:01: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:30:01: #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 08:30:01: #1 tags after filtering in treatment: 5946974 INFO @ Tue, 16 Jun 2020 08:30:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:30:01: #1 finished! INFO @ Tue, 16 Jun 2020 08:30:01: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:30:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:30:01: #2 number of paired peaks: 2407 INFO @ Tue, 16 Jun 2020 08:30:01: start model_add_line... INFO @ Tue, 16 Jun 2020 08:30:01: start X-correlation... INFO @ Tue, 16 Jun 2020 08:30:01: end of X-cor INFO @ Tue, 16 Jun 2020 08:30:01: #2 finished! INFO @ Tue, 16 Jun 2020 08:30:01: #2 predicted fragment length is 129 bps INFO @ Tue, 16 Jun 2020 08:30:01: #2 alternative fragment length(s) may be 129 bps INFO @ Tue, 16 Jun 2020 08:30:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1674092/SRX1674092.20_model.r INFO @ Tue, 16 Jun 2020 08:30:01: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:30:01: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:30:17: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:30:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1674092/SRX1674092.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:30:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1674092/SRX1674092.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:30:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1674092/SRX1674092.20_summits.bed INFO @ Tue, 16 Jun 2020 08:30:25: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1953 records, 4 fields): 4 millis CompletedMACS2peakCalling