Job ID = 6368565 SRX = SRX5020791 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:31:57 prefetch.2.10.7: 1) Downloading 'SRR8201414'... 2020-06-16T00:31:57 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:32:49 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:32:49 prefetch.2.10.7: 'SRR8201414' is valid 2020-06-16T00:32:49 prefetch.2.10.7: 1) 'SRR8201414' was downloaded successfully Read 5640309 spots for SRR8201414/SRR8201414.sra Written 5640309 spots for SRR8201414/SRR8201414.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: 00:01:07 5640309 reads; of these: 5640309 (100.00%) were unpaired; of these: 917658 (16.27%) aligned 0 times 4068631 (72.13%) aligned exactly 1 time 654020 (11.60%) aligned >1 times 83.73% overall alignment rate Time searching: 00:01:07 Overall time: 00:01:07 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] 585764 / 4722651 = 0.1240 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 09:35:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020791/SRX5020791.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020791/SRX5020791.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020791/SRX5020791.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020791/SRX5020791.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 09:35:57: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:35:57: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:36:03: 1000000 INFO @ Tue, 16 Jun 2020 09:36:10: 2000000 INFO @ Tue, 16 Jun 2020 09:36:16: 3000000 INFO @ Tue, 16 Jun 2020 09:36:22: 4000000 INFO @ Tue, 16 Jun 2020 09:36:22: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:36:22: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:36:22: #1 total tags in treatment: 4136887 INFO @ Tue, 16 Jun 2020 09:36:22: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:36:22: #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 09:36:22: #1 tags after filtering in treatment: 4136887 INFO @ Tue, 16 Jun 2020 09:36:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:36:22: #1 finished! INFO @ Tue, 16 Jun 2020 09:36:22: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:36:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:36:23: #2 number of paired peaks: 1666 INFO @ Tue, 16 Jun 2020 09:36:23: start model_add_line... INFO @ Tue, 16 Jun 2020 09:36:23: start X-correlation... INFO @ Tue, 16 Jun 2020 09:36:23: end of X-cor INFO @ Tue, 16 Jun 2020 09:36:23: #2 finished! INFO @ Tue, 16 Jun 2020 09:36:23: #2 predicted fragment length is 193 bps INFO @ Tue, 16 Jun 2020 09:36:23: #2 alternative fragment length(s) may be 193 bps INFO @ Tue, 16 Jun 2020 09:36:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020791/SRX5020791.05_model.r INFO @ Tue, 16 Jun 2020 09:36:23: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:36:23: #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 09:36:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020791/SRX5020791.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020791/SRX5020791.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020791/SRX5020791.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020791/SRX5020791.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 09:36:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:36:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:36:33: 1000000 INFO @ Tue, 16 Jun 2020 09:36:35: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:36:39: 2000000 INFO @ Tue, 16 Jun 2020 09:36:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020791/SRX5020791.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:36:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020791/SRX5020791.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:36:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020791/SRX5020791.05_summits.bed INFO @ Tue, 16 Jun 2020 09:36:40: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1561 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:36:45: 3000000 INFO @ Tue, 16 Jun 2020 09:36:51: 4000000 INFO @ Tue, 16 Jun 2020 09:36:52: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:36:52: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:36:52: #1 total tags in treatment: 4136887 INFO @ Tue, 16 Jun 2020 09:36:52: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:36:52: #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 09:36:52: #1 tags after filtering in treatment: 4136887 INFO @ Tue, 16 Jun 2020 09:36:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:36:52: #1 finished! INFO @ Tue, 16 Jun 2020 09:36:52: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:36:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:36:52: #2 number of paired peaks: 1666 INFO @ Tue, 16 Jun 2020 09:36:52: start model_add_line... INFO @ Tue, 16 Jun 2020 09:36:52: start X-correlation... INFO @ Tue, 16 Jun 2020 09:36:52: end of X-cor INFO @ Tue, 16 Jun 2020 09:36:52: #2 finished! INFO @ Tue, 16 Jun 2020 09:36:52: #2 predicted fragment length is 193 bps INFO @ Tue, 16 Jun 2020 09:36:52: #2 alternative fragment length(s) may be 193 bps INFO @ Tue, 16 Jun 2020 09:36:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020791/SRX5020791.10_model.r INFO @ Tue, 16 Jun 2020 09:36:52: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:36:52: #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 09:36:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020791/SRX5020791.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020791/SRX5020791.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020791/SRX5020791.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020791/SRX5020791.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 09:36:57: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:36:57: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:37:03: 1000000 INFO @ Tue, 16 Jun 2020 09:37:04: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:37:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020791/SRX5020791.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:37:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020791/SRX5020791.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:37:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020791/SRX5020791.10_summits.bed INFO @ Tue, 16 Jun 2020 09:37:09: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (937 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:37:09: 2000000 INFO @ Tue, 16 Jun 2020 09:37:15: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:37:21: 4000000 INFO @ Tue, 16 Jun 2020 09:37:22: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:37:22: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:37:22: #1 total tags in treatment: 4136887 INFO @ Tue, 16 Jun 2020 09:37:22: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:37:22: #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 09:37:22: #1 tags after filtering in treatment: 4136887 INFO @ Tue, 16 Jun 2020 09:37:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:37:22: #1 finished! INFO @ Tue, 16 Jun 2020 09:37:22: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:37:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:37:23: #2 number of paired peaks: 1666 INFO @ Tue, 16 Jun 2020 09:37:23: start model_add_line... INFO @ Tue, 16 Jun 2020 09:37:23: start X-correlation... INFO @ Tue, 16 Jun 2020 09:37:23: end of X-cor INFO @ Tue, 16 Jun 2020 09:37:23: #2 finished! INFO @ Tue, 16 Jun 2020 09:37:23: #2 predicted fragment length is 193 bps INFO @ Tue, 16 Jun 2020 09:37:23: #2 alternative fragment length(s) may be 193 bps INFO @ Tue, 16 Jun 2020 09:37:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020791/SRX5020791.20_model.r INFO @ Tue, 16 Jun 2020 09:37:23: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:37:23: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:37:34: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:37:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020791/SRX5020791.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:37:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020791/SRX5020791.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:37:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020791/SRX5020791.20_summits.bed INFO @ Tue, 16 Jun 2020 09:37:39: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (498 records, 4 fields): 1 millis CompletedMACS2peakCalling