Job ID = 6366339 SRX = SRX113617 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:44:22 prefetch.2.10.7: 1) Downloading 'SRR393717'... 2020-06-15T22:44:22 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:45:04 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:45:04 prefetch.2.10.7: 'SRR393717' is valid 2020-06-15T22:45:04 prefetch.2.10.7: 1) 'SRR393717' was downloaded successfully Read 6857333 spots for SRR393717/SRR393717.sra Written 6857333 spots for SRR393717/SRR393717.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: 00:01:43 6857333 reads; of these: 6857333 (100.00%) were unpaired; of these: 383143 (5.59%) aligned 0 times 4530612 (66.07%) aligned exactly 1 time 1943578 (28.34%) aligned >1 times 94.41% overall alignment rate Time searching: 00:01:43 Overall time: 00:01:43 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] 2113440 / 6474190 = 0.3264 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 07:49:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX113617/SRX113617.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX113617/SRX113617.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX113617/SRX113617.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX113617/SRX113617.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 07:49:02: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:49:02: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:49:08: 1000000 INFO @ Tue, 16 Jun 2020 07:49:14: 2000000 INFO @ Tue, 16 Jun 2020 07:49:20: 3000000 INFO @ Tue, 16 Jun 2020 07:49:26: 4000000 INFO @ Tue, 16 Jun 2020 07:49:28: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:49:28: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:49:28: #1 total tags in treatment: 4360750 INFO @ Tue, 16 Jun 2020 07:49:28: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:49:28: #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 07:49:28: #1 tags after filtering in treatment: 4360750 INFO @ Tue, 16 Jun 2020 07:49:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:49:28: #1 finished! INFO @ Tue, 16 Jun 2020 07:49:28: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:49:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:49:29: #2 number of paired peaks: 4887 INFO @ Tue, 16 Jun 2020 07:49:29: start model_add_line... INFO @ Tue, 16 Jun 2020 07:49:29: start X-correlation... INFO @ Tue, 16 Jun 2020 07:49:29: end of X-cor INFO @ Tue, 16 Jun 2020 07:49:29: #2 finished! INFO @ Tue, 16 Jun 2020 07:49:29: #2 predicted fragment length is 163 bps INFO @ Tue, 16 Jun 2020 07:49:29: #2 alternative fragment length(s) may be 108,163,264,525 bps INFO @ Tue, 16 Jun 2020 07:49:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX113617/SRX113617.05_model.r INFO @ Tue, 16 Jun 2020 07:49:29: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:49:29: #3 Pre-compute pvalue-qvalue table... 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 07:49:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX113617/SRX113617.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX113617/SRX113617.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX113617/SRX113617.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX113617/SRX113617.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 07:49:31: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:49:31: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:49:37: 1000000 INFO @ Tue, 16 Jun 2020 07:49:42: 2000000 INFO @ Tue, 16 Jun 2020 07:49:42: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:49:47: 3000000 INFO @ Tue, 16 Jun 2020 07:49:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX113617/SRX113617.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:49:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX113617/SRX113617.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:49:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX113617/SRX113617.05_summits.bed INFO @ Tue, 16 Jun 2020 07:49:48: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (626 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:49:53: 4000000 INFO @ Tue, 16 Jun 2020 07:49:55: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:49:55: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:49:55: #1 total tags in treatment: 4360750 INFO @ Tue, 16 Jun 2020 07:49:55: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:49:55: #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 07:49:55: #1 tags after filtering in treatment: 4360750 INFO @ Tue, 16 Jun 2020 07:49:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:49:55: #1 finished! INFO @ Tue, 16 Jun 2020 07:49:55: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:49:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:49:55: #2 number of paired peaks: 4887 INFO @ Tue, 16 Jun 2020 07:49:55: start model_add_line... INFO @ Tue, 16 Jun 2020 07:49:55: start X-correlation... INFO @ Tue, 16 Jun 2020 07:49:55: end of X-cor INFO @ Tue, 16 Jun 2020 07:49:55: #2 finished! INFO @ Tue, 16 Jun 2020 07:49:55: #2 predicted fragment length is 163 bps INFO @ Tue, 16 Jun 2020 07:49:55: #2 alternative fragment length(s) may be 108,163,264,525 bps INFO @ Tue, 16 Jun 2020 07:49:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX113617/SRX113617.10_model.r INFO @ Tue, 16 Jun 2020 07:49:55: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:49:55: #3 Pre-compute pvalue-qvalue table... 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 07:50:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX113617/SRX113617.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX113617/SRX113617.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX113617/SRX113617.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX113617/SRX113617.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 07:50:01: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:50:01: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:50:07: 1000000 INFO @ Tue, 16 Jun 2020 07:50:09: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:50:13: 2000000 INFO @ Tue, 16 Jun 2020 07:50:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX113617/SRX113617.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:50:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX113617/SRX113617.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:50:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX113617/SRX113617.10_summits.bed INFO @ Tue, 16 Jun 2020 07:50:15: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (254 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:50:18: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:50:24: 4000000 INFO @ Tue, 16 Jun 2020 07:50:26: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:50:26: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:50:26: #1 total tags in treatment: 4360750 INFO @ Tue, 16 Jun 2020 07:50:26: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:50:26: #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 07:50:26: #1 tags after filtering in treatment: 4360750 INFO @ Tue, 16 Jun 2020 07:50:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:50:26: #1 finished! INFO @ Tue, 16 Jun 2020 07:50:26: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:50:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:50:26: #2 number of paired peaks: 4887 INFO @ Tue, 16 Jun 2020 07:50:26: start model_add_line... INFO @ Tue, 16 Jun 2020 07:50:26: start X-correlation... INFO @ Tue, 16 Jun 2020 07:50:26: end of X-cor INFO @ Tue, 16 Jun 2020 07:50:26: #2 finished! INFO @ Tue, 16 Jun 2020 07:50:26: #2 predicted fragment length is 163 bps INFO @ Tue, 16 Jun 2020 07:50:26: #2 alternative fragment length(s) may be 108,163,264,525 bps INFO @ Tue, 16 Jun 2020 07:50:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX113617/SRX113617.20_model.r INFO @ Tue, 16 Jun 2020 07:50:26: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:50:26: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:50:39: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:50:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX113617/SRX113617.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:50:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX113617/SRX113617.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:50:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX113617/SRX113617.20_summits.bed INFO @ Tue, 16 Jun 2020 07:50:45: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (89 records, 4 fields): 1 millis CompletedMACS2peakCalling