Job ID = 6366533 SRX = SRX1769988 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:57:53 prefetch.2.10.7: 1) Downloading 'SRR3535766'... 2020-06-15T22:57:53 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:58:33 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:58:33 prefetch.2.10.7: 'SRR3535766' is valid 2020-06-15T22:58:33 prefetch.2.10.7: 1) 'SRR3535766' was downloaded successfully Read 6113677 spots for SRR3535766/SRR3535766.sra Written 6113677 spots for SRR3535766/SRR3535766.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: 00:01:20 6113677 reads; of these: 6113677 (100.00%) were unpaired; of these: 523628 (8.56%) aligned 0 times 4711449 (77.06%) aligned exactly 1 time 878600 (14.37%) aligned >1 times 91.44% overall alignment rate Time searching: 00:01:20 Overall time: 00:01:20 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] 1905363 / 5590049 = 0.3408 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 08:02:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1769988/SRX1769988.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1769988/SRX1769988.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1769988/SRX1769988.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1769988/SRX1769988.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 08:02:04: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:02:04: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:02:10: 1000000 INFO @ Tue, 16 Jun 2020 08:02:16: 2000000 INFO @ Tue, 16 Jun 2020 08:02:22: 3000000 INFO @ Tue, 16 Jun 2020 08:02:27: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:02:27: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:02:27: #1 total tags in treatment: 3684686 INFO @ Tue, 16 Jun 2020 08:02:27: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:02:27: #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 08:02:27: #1 tags after filtering in treatment: 3684686 INFO @ Tue, 16 Jun 2020 08:02:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:02:27: #1 finished! INFO @ Tue, 16 Jun 2020 08:02:27: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:02:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:02:27: #2 number of paired peaks: 3062 INFO @ Tue, 16 Jun 2020 08:02:27: start model_add_line... INFO @ Tue, 16 Jun 2020 08:02:27: start X-correlation... INFO @ Tue, 16 Jun 2020 08:02:27: end of X-cor INFO @ Tue, 16 Jun 2020 08:02:27: #2 finished! INFO @ Tue, 16 Jun 2020 08:02:27: #2 predicted fragment length is 230 bps INFO @ Tue, 16 Jun 2020 08:02:27: #2 alternative fragment length(s) may be 230 bps INFO @ Tue, 16 Jun 2020 08:02:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1769988/SRX1769988.05_model.r INFO @ Tue, 16 Jun 2020 08:02:27: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:02:27: #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 08:02:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1769988/SRX1769988.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1769988/SRX1769988.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1769988/SRX1769988.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1769988/SRX1769988.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 08:02:34: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:02:34: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:02:40: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:02:40: 1000000 INFO @ Tue, 16 Jun 2020 08:02:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1769988/SRX1769988.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:02:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1769988/SRX1769988.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:02:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1769988/SRX1769988.05_summits.bed INFO @ Tue, 16 Jun 2020 08:02:45: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3889 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:02:46: 2000000 INFO @ Tue, 16 Jun 2020 08:02:53: 3000000 INFO @ Tue, 16 Jun 2020 08:02:57: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:02:57: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:02:57: #1 total tags in treatment: 3684686 INFO @ Tue, 16 Jun 2020 08:02:57: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:02:57: #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 08:02:57: #1 tags after filtering in treatment: 3684686 INFO @ Tue, 16 Jun 2020 08:02:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:02:57: #1 finished! INFO @ Tue, 16 Jun 2020 08:02:57: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:02:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:02:57: #2 number of paired peaks: 3062 INFO @ Tue, 16 Jun 2020 08:02:57: start model_add_line... INFO @ Tue, 16 Jun 2020 08:02:57: start X-correlation... INFO @ Tue, 16 Jun 2020 08:02:57: end of X-cor INFO @ Tue, 16 Jun 2020 08:02:57: #2 finished! INFO @ Tue, 16 Jun 2020 08:02:57: #2 predicted fragment length is 230 bps INFO @ Tue, 16 Jun 2020 08:02:57: #2 alternative fragment length(s) may be 230 bps INFO @ Tue, 16 Jun 2020 08:02:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1769988/SRX1769988.10_model.r INFO @ Tue, 16 Jun 2020 08:02:57: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:02:57: #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 08:03:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1769988/SRX1769988.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1769988/SRX1769988.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1769988/SRX1769988.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1769988/SRX1769988.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 08:03:04: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:03:04: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:03:10: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:03:10: 1000000 INFO @ Tue, 16 Jun 2020 08:03:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1769988/SRX1769988.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:03:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1769988/SRX1769988.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:03:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1769988/SRX1769988.10_summits.bed INFO @ Tue, 16 Jun 2020 08:03:15: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2621 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:03:17: 2000000 INFO @ Tue, 16 Jun 2020 08:03:23: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:03:28: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:03:28: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:03:28: #1 total tags in treatment: 3684686 INFO @ Tue, 16 Jun 2020 08:03:28: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:03:28: #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 08:03:28: #1 tags after filtering in treatment: 3684686 INFO @ Tue, 16 Jun 2020 08:03:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:03:28: #1 finished! INFO @ Tue, 16 Jun 2020 08:03:28: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:03:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:03:28: #2 number of paired peaks: 3062 INFO @ Tue, 16 Jun 2020 08:03:28: start model_add_line... INFO @ Tue, 16 Jun 2020 08:03:28: start X-correlation... INFO @ Tue, 16 Jun 2020 08:03:28: end of X-cor INFO @ Tue, 16 Jun 2020 08:03:28: #2 finished! INFO @ Tue, 16 Jun 2020 08:03:28: #2 predicted fragment length is 230 bps INFO @ Tue, 16 Jun 2020 08:03:28: #2 alternative fragment length(s) may be 230 bps INFO @ Tue, 16 Jun 2020 08:03:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1769988/SRX1769988.20_model.r INFO @ Tue, 16 Jun 2020 08:03:28: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:03:28: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:03:41: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:03:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1769988/SRX1769988.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:03:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1769988/SRX1769988.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:03:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1769988/SRX1769988.20_summits.bed INFO @ Tue, 16 Jun 2020 08:03:47: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1622 records, 4 fields): 3 millis CompletedMACS2peakCalling