Job ID = 6368170 SRX = SRX494854 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:54:33 prefetch.2.10.7: 1) Downloading 'SRR1198386'... 2020-06-15T23:54:33 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:55:30 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:55:30 prefetch.2.10.7: 'SRR1198386' is valid 2020-06-15T23:55:30 prefetch.2.10.7: 1) 'SRR1198386' was downloaded successfully Read 8666051 spots for SRR1198386/SRR1198386.sra Written 8666051 spots for SRR1198386/SRR1198386.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: 00:01:13 8666051 reads; of these: 8666051 (100.00%) were unpaired; of these: 992878 (11.46%) aligned 0 times 6677785 (77.06%) aligned exactly 1 time 995388 (11.49%) aligned >1 times 88.54% overall alignment rate Time searching: 00:01:13 Overall time: 00:01:13 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_rmdupse_core] 1695030 / 7673173 = 0.2209 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 08:59:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494854/SRX494854.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494854/SRX494854.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494854/SRX494854.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494854/SRX494854.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 08:59:24: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:59:24: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:59:30: 1000000 INFO @ Tue, 16 Jun 2020 08:59:37: 2000000 INFO @ Tue, 16 Jun 2020 08:59:43: 3000000 INFO @ Tue, 16 Jun 2020 08:59:49: 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 08:59:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494854/SRX494854.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494854/SRX494854.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494854/SRX494854.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494854/SRX494854.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 08:59:54: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:59:54: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:59:55: 5000000 INFO @ Tue, 16 Jun 2020 09:00:00: 1000000 INFO @ Tue, 16 Jun 2020 09:00:01: #1 tag size is determined as 29 bps INFO @ Tue, 16 Jun 2020 09:00:01: #1 tag size = 29 INFO @ Tue, 16 Jun 2020 09:00:01: #1 total tags in treatment: 5978143 INFO @ Tue, 16 Jun 2020 09:00:01: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:00:01: #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 09:00:01: #1 tags after filtering in treatment: 5978143 INFO @ Tue, 16 Jun 2020 09:00:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:00:01: #1 finished! INFO @ Tue, 16 Jun 2020 09:00:01: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:00:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:00:02: #2 number of paired peaks: 1807 INFO @ Tue, 16 Jun 2020 09:00:02: start model_add_line... INFO @ Tue, 16 Jun 2020 09:00:02: start X-correlation... INFO @ Tue, 16 Jun 2020 09:00:02: end of X-cor INFO @ Tue, 16 Jun 2020 09:00:02: #2 finished! INFO @ Tue, 16 Jun 2020 09:00:02: #2 predicted fragment length is 204 bps INFO @ Tue, 16 Jun 2020 09:00:02: #2 alternative fragment length(s) may be 4,204 bps INFO @ Tue, 16 Jun 2020 09:00:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494854/SRX494854.05_model.r INFO @ Tue, 16 Jun 2020 09:00:02: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:00:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:00:07: 2000000 INFO @ Tue, 16 Jun 2020 09:00:13: 3000000 INFO @ Tue, 16 Jun 2020 09:00:17: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:00:20: 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 09:00:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494854/SRX494854.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494854/SRX494854.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494854/SRX494854.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494854/SRX494854.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 09:00:24: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:00:24: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:00:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494854/SRX494854.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:00:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494854/SRX494854.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:00:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494854/SRX494854.05_summits.bed INFO @ Tue, 16 Jun 2020 09:00:25: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3779 records, 4 fields): 404 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:00:26: 5000000 INFO @ Tue, 16 Jun 2020 09:00:31: 1000000 INFO @ Tue, 16 Jun 2020 09:00:32: #1 tag size is determined as 29 bps INFO @ Tue, 16 Jun 2020 09:00:32: #1 tag size = 29 INFO @ Tue, 16 Jun 2020 09:00:32: #1 total tags in treatment: 5978143 INFO @ Tue, 16 Jun 2020 09:00:32: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:00:32: #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 09:00:33: #1 tags after filtering in treatment: 5978143 INFO @ Tue, 16 Jun 2020 09:00:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:00:33: #1 finished! INFO @ Tue, 16 Jun 2020 09:00:33: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:00:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:00:33: #2 number of paired peaks: 1807 INFO @ Tue, 16 Jun 2020 09:00:33: start model_add_line... INFO @ Tue, 16 Jun 2020 09:00:33: start X-correlation... INFO @ Tue, 16 Jun 2020 09:00:33: end of X-cor INFO @ Tue, 16 Jun 2020 09:00:33: #2 finished! INFO @ Tue, 16 Jun 2020 09:00:33: #2 predicted fragment length is 204 bps INFO @ Tue, 16 Jun 2020 09:00:33: #2 alternative fragment length(s) may be 4,204 bps INFO @ Tue, 16 Jun 2020 09:00:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494854/SRX494854.10_model.r INFO @ Tue, 16 Jun 2020 09:00:33: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:00:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:00:37: 2000000 INFO @ Tue, 16 Jun 2020 09:00:43: 3000000 INFO @ Tue, 16 Jun 2020 09:00:48: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:00:50: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:00:56: 5000000 INFO @ Tue, 16 Jun 2020 09:00:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494854/SRX494854.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:00:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494854/SRX494854.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:00:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494854/SRX494854.10_summits.bed INFO @ Tue, 16 Jun 2020 09:00:56: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1307 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:01:02: #1 tag size is determined as 29 bps INFO @ Tue, 16 Jun 2020 09:01:02: #1 tag size = 29 INFO @ Tue, 16 Jun 2020 09:01:02: #1 total tags in treatment: 5978143 INFO @ Tue, 16 Jun 2020 09:01:02: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:01:02: #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 09:01:02: #1 tags after filtering in treatment: 5978143 INFO @ Tue, 16 Jun 2020 09:01:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:01:02: #1 finished! INFO @ Tue, 16 Jun 2020 09:01:02: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:01:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:01:03: #2 number of paired peaks: 1807 INFO @ Tue, 16 Jun 2020 09:01:03: start model_add_line... INFO @ Tue, 16 Jun 2020 09:01:03: start X-correlation... INFO @ Tue, 16 Jun 2020 09:01:03: end of X-cor INFO @ Tue, 16 Jun 2020 09:01:03: #2 finished! INFO @ Tue, 16 Jun 2020 09:01:03: #2 predicted fragment length is 204 bps INFO @ Tue, 16 Jun 2020 09:01:03: #2 alternative fragment length(s) may be 4,204 bps INFO @ Tue, 16 Jun 2020 09:01:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494854/SRX494854.20_model.r INFO @ Tue, 16 Jun 2020 09:01:03: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:01:03: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:01:19: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:01:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494854/SRX494854.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:01:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494854/SRX494854.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:01:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494854/SRX494854.20_summits.bed INFO @ Tue, 16 Jun 2020 09:01:26: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (192 records, 4 fields): 1 millis CompletedMACS2peakCalling