Job ID = 6366635 SRX = SRX2144182 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:52:41 prefetch.2.10.7: 1) Downloading 'SRR4188786'... 2020-06-15T22:52:41 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:53:22 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:53:23 prefetch.2.10.7: 'SRR4188786' is valid 2020-06-15T22:53:23 prefetch.2.10.7: 1) 'SRR4188786' was downloaded successfully Read 7550443 spots for SRR4188786/SRR4188786.sra Written 7550443 spots for SRR4188786/SRR4188786.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: 00:01:17 7550443 reads; of these: 7550443 (100.00%) were unpaired; of these: 2417382 (32.02%) aligned 0 times 4403276 (58.32%) aligned exactly 1 time 729785 (9.67%) aligned >1 times 67.98% overall alignment rate Time searching: 00:01:17 Overall time: 00:01:17 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] 352538 / 5133061 = 0.0687 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 07:56:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2144182/SRX2144182.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2144182/SRX2144182.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2144182/SRX2144182.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2144182/SRX2144182.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 07:56:39: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:56:39: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:56:44: 1000000 INFO @ Tue, 16 Jun 2020 07:56:49: 2000000 INFO @ Tue, 16 Jun 2020 07:56:54: 3000000 INFO @ Tue, 16 Jun 2020 07:56:59: 4000000 INFO @ Tue, 16 Jun 2020 07:57:03: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 07:57:03: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 07:57:03: #1 total tags in treatment: 4780523 INFO @ Tue, 16 Jun 2020 07:57:03: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:57:03: #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 07:57:03: #1 tags after filtering in treatment: 4780523 INFO @ Tue, 16 Jun 2020 07:57:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:57:03: #1 finished! INFO @ Tue, 16 Jun 2020 07:57:03: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:57:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:57:03: #2 number of paired peaks: 1446 INFO @ Tue, 16 Jun 2020 07:57:03: start model_add_line... INFO @ Tue, 16 Jun 2020 07:57:03: start X-correlation... INFO @ Tue, 16 Jun 2020 07:57:03: end of X-cor INFO @ Tue, 16 Jun 2020 07:57:03: #2 finished! INFO @ Tue, 16 Jun 2020 07:57:03: #2 predicted fragment length is 120 bps INFO @ Tue, 16 Jun 2020 07:57:03: #2 alternative fragment length(s) may be 120,132 bps INFO @ Tue, 16 Jun 2020 07:57:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2144182/SRX2144182.05_model.r INFO @ Tue, 16 Jun 2020 07:57:03: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:57:03: #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 07:57:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2144182/SRX2144182.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2144182/SRX2144182.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2144182/SRX2144182.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2144182/SRX2144182.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 07:57:10: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:57:10: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:57:14: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:57:15: 1000000 INFO @ Tue, 16 Jun 2020 07:57:19: 2000000 INFO @ Tue, 16 Jun 2020 07:57:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2144182/SRX2144182.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:57:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2144182/SRX2144182.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:57:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2144182/SRX2144182.05_summits.bed INFO @ Tue, 16 Jun 2020 07:57:20: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2328 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:57:24: 3000000 INFO @ Tue, 16 Jun 2020 07:57:29: 4000000 INFO @ Tue, 16 Jun 2020 07:57:33: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 07:57:33: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 07:57:33: #1 total tags in treatment: 4780523 INFO @ Tue, 16 Jun 2020 07:57:33: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:57:33: #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 07:57:33: #1 tags after filtering in treatment: 4780523 INFO @ Tue, 16 Jun 2020 07:57:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:57:33: #1 finished! INFO @ Tue, 16 Jun 2020 07:57:33: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:57:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:57:33: #2 number of paired peaks: 1446 INFO @ Tue, 16 Jun 2020 07:57:33: start model_add_line... INFO @ Tue, 16 Jun 2020 07:57:34: start X-correlation... INFO @ Tue, 16 Jun 2020 07:57:34: end of X-cor INFO @ Tue, 16 Jun 2020 07:57:34: #2 finished! INFO @ Tue, 16 Jun 2020 07:57:34: #2 predicted fragment length is 120 bps INFO @ Tue, 16 Jun 2020 07:57:34: #2 alternative fragment length(s) may be 120,132 bps INFO @ Tue, 16 Jun 2020 07:57:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2144182/SRX2144182.10_model.r INFO @ Tue, 16 Jun 2020 07:57:34: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:57:34: #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 07:57:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2144182/SRX2144182.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2144182/SRX2144182.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2144182/SRX2144182.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2144182/SRX2144182.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 07:57:39: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:57:39: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:57:45: 1000000 INFO @ Tue, 16 Jun 2020 07:57:45: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:57:50: 2000000 INFO @ Tue, 16 Jun 2020 07:57:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2144182/SRX2144182.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:57:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2144182/SRX2144182.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:57:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2144182/SRX2144182.10_summits.bed INFO @ Tue, 16 Jun 2020 07:57:51: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (950 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:57:55: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:58:00: 4000000 INFO @ Tue, 16 Jun 2020 07:58:05: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 07:58:05: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 07:58:05: #1 total tags in treatment: 4780523 INFO @ Tue, 16 Jun 2020 07:58:05: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:58:05: #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 07:58:05: #1 tags after filtering in treatment: 4780523 INFO @ Tue, 16 Jun 2020 07:58:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:58:05: #1 finished! INFO @ Tue, 16 Jun 2020 07:58:05: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:58:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:58:05: #2 number of paired peaks: 1446 INFO @ Tue, 16 Jun 2020 07:58:05: start model_add_line... INFO @ Tue, 16 Jun 2020 07:58:05: start X-correlation... INFO @ Tue, 16 Jun 2020 07:58:05: end of X-cor INFO @ Tue, 16 Jun 2020 07:58:05: #2 finished! INFO @ Tue, 16 Jun 2020 07:58:05: #2 predicted fragment length is 120 bps INFO @ Tue, 16 Jun 2020 07:58:05: #2 alternative fragment length(s) may be 120,132 bps INFO @ Tue, 16 Jun 2020 07:58:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2144182/SRX2144182.20_model.r INFO @ Tue, 16 Jun 2020 07:58:05: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:58:05: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:58:17: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:58:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2144182/SRX2144182.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:58:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2144182/SRX2144182.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:58:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2144182/SRX2144182.20_summits.bed INFO @ Tue, 16 Jun 2020 07:58:23: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (310 records, 4 fields): 2 millis CompletedMACS2peakCalling