Job ID = 6366388 SRX = SRX1388762 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:35:36 prefetch.2.10.7: 1) Downloading 'SRR2832478'... 2020-06-15T22:35:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:35:58 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:35:58 prefetch.2.10.7: 'SRR2832478' is valid 2020-06-15T22:35:58 prefetch.2.10.7: 1) 'SRR2832478' was downloaded successfully Read 3585613 spots for SRR2832478/SRR2832478.sra Written 3585613 spots for SRR2832478/SRR2832478.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: 00:00:51 3585613 reads; of these: 3585613 (100.00%) were unpaired; of these: 137344 (3.83%) aligned 0 times 2987743 (83.33%) aligned exactly 1 time 460526 (12.84%) aligned >1 times 96.17% overall alignment rate Time searching: 00:00:51 Overall time: 00:00:51 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] 295289 / 3448269 = 0.0856 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 07:38:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1388762/SRX1388762.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1388762/SRX1388762.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1388762/SRX1388762.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1388762/SRX1388762.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 07:38:20: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:38:20: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:38:28: 1000000 INFO @ Tue, 16 Jun 2020 07:38:36: 2000000 INFO @ Tue, 16 Jun 2020 07:38:44: 3000000 INFO @ Tue, 16 Jun 2020 07:38:45: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 07:38:45: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 07:38:45: #1 total tags in treatment: 3152980 INFO @ Tue, 16 Jun 2020 07:38:45: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:38:45: #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 07:38:45: #1 tags after filtering in treatment: 3152980 INFO @ Tue, 16 Jun 2020 07:38:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:38:45: #1 finished! INFO @ Tue, 16 Jun 2020 07:38:45: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:38:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:38:45: #2 number of paired peaks: 3104 INFO @ Tue, 16 Jun 2020 07:38:45: start model_add_line... INFO @ Tue, 16 Jun 2020 07:38:45: start X-correlation... INFO @ Tue, 16 Jun 2020 07:38:45: end of X-cor INFO @ Tue, 16 Jun 2020 07:38:45: #2 finished! INFO @ Tue, 16 Jun 2020 07:38:45: #2 predicted fragment length is 170 bps INFO @ Tue, 16 Jun 2020 07:38:45: #2 alternative fragment length(s) may be 170 bps INFO @ Tue, 16 Jun 2020 07:38:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1388762/SRX1388762.05_model.r INFO @ Tue, 16 Jun 2020 07:38:45: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:38:45: #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 07:38:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1388762/SRX1388762.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1388762/SRX1388762.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1388762/SRX1388762.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1388762/SRX1388762.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 07:38:49: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:38:49: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:38:54: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:38:56: 1000000 INFO @ Tue, 16 Jun 2020 07:38:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1388762/SRX1388762.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:38:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1388762/SRX1388762.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:38:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1388762/SRX1388762.05_summits.bed INFO @ Tue, 16 Jun 2020 07:38:58: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2730 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:39:03: 2000000 INFO @ Tue, 16 Jun 2020 07:39:09: 3000000 INFO @ Tue, 16 Jun 2020 07:39:10: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 07:39:10: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 07:39:10: #1 total tags in treatment: 3152980 INFO @ Tue, 16 Jun 2020 07:39:10: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:39:10: #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 07:39:10: #1 tags after filtering in treatment: 3152980 INFO @ Tue, 16 Jun 2020 07:39:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:39:10: #1 finished! INFO @ Tue, 16 Jun 2020 07:39:10: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:39:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:39:11: #2 number of paired peaks: 3104 INFO @ Tue, 16 Jun 2020 07:39:11: start model_add_line... INFO @ Tue, 16 Jun 2020 07:39:11: start X-correlation... INFO @ Tue, 16 Jun 2020 07:39:11: end of X-cor INFO @ Tue, 16 Jun 2020 07:39:11: #2 finished! INFO @ Tue, 16 Jun 2020 07:39:11: #2 predicted fragment length is 170 bps INFO @ Tue, 16 Jun 2020 07:39:11: #2 alternative fragment length(s) may be 170 bps INFO @ Tue, 16 Jun 2020 07:39:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1388762/SRX1388762.10_model.r INFO @ Tue, 16 Jun 2020 07:39:11: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:39:11: #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 07:39:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1388762/SRX1388762.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1388762/SRX1388762.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1388762/SRX1388762.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1388762/SRX1388762.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 07:39:19: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:39:19: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:39:20: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:39:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1388762/SRX1388762.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:39:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1388762/SRX1388762.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:39:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1388762/SRX1388762.10_summits.bed INFO @ Tue, 16 Jun 2020 07:39:25: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1224 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:39:27: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:39:35: 2000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:39:42: 3000000 INFO @ Tue, 16 Jun 2020 07:39:43: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 07:39:43: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 07:39:43: #1 total tags in treatment: 3152980 INFO @ Tue, 16 Jun 2020 07:39:43: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:39:43: #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 07:39:43: #1 tags after filtering in treatment: 3152980 INFO @ Tue, 16 Jun 2020 07:39:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:39:43: #1 finished! INFO @ Tue, 16 Jun 2020 07:39:43: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:39:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:39:44: #2 number of paired peaks: 3104 INFO @ Tue, 16 Jun 2020 07:39:44: start model_add_line... INFO @ Tue, 16 Jun 2020 07:39:44: start X-correlation... INFO @ Tue, 16 Jun 2020 07:39:44: end of X-cor INFO @ Tue, 16 Jun 2020 07:39:44: #2 finished! INFO @ Tue, 16 Jun 2020 07:39:44: #2 predicted fragment length is 170 bps INFO @ Tue, 16 Jun 2020 07:39:44: #2 alternative fragment length(s) may be 170 bps INFO @ Tue, 16 Jun 2020 07:39:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1388762/SRX1388762.20_model.r INFO @ Tue, 16 Jun 2020 07:39:44: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:39:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:39:53: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:39:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1388762/SRX1388762.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:39:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1388762/SRX1388762.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:39:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1388762/SRX1388762.20_summits.bed INFO @ Tue, 16 Jun 2020 07:39:57: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (438 records, 4 fields): 2 millis CompletedMACS2peakCalling