Job ID = 6366935 SRX = SRX2576637 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:07:38 prefetch.2.10.7: 1) Downloading 'SRR5272594'... 2020-06-15T23:07:38 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:08:29 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:08:30 prefetch.2.10.7: 'SRR5272594' is valid 2020-06-15T23:08:30 prefetch.2.10.7: 1) 'SRR5272594' was downloaded successfully Read 8677034 spots for SRR5272594/SRR5272594.sra Written 8677034 spots for SRR5272594/SRR5272594.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: 00:01:19 8677034 reads; of these: 8677034 (100.00%) were unpaired; of these: 1459163 (16.82%) aligned 0 times 5973419 (68.84%) aligned exactly 1 time 1244452 (14.34%) aligned >1 times 83.18% overall alignment rate Time searching: 00:01:19 Overall time: 00:01:19 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] 1634796 / 7217871 = 0.2265 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 08:12:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576637/SRX2576637.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576637/SRX2576637.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576637/SRX2576637.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576637/SRX2576637.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 08:12:12: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:12:12: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:12:17: 1000000 INFO @ Tue, 16 Jun 2020 08:12:22: 2000000 INFO @ Tue, 16 Jun 2020 08:12:27: 3000000 INFO @ Tue, 16 Jun 2020 08:12:33: 4000000 INFO @ Tue, 16 Jun 2020 08:12:38: 5000000 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 08:12:41: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 08:12:41: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 08:12:41: #1 total tags in treatment: 5583075 INFO @ Tue, 16 Jun 2020 08:12:41: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:12:41: #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 08:12:41: #1 tags after filtering in treatment: 5583075 INFO @ Tue, 16 Jun 2020 08:12:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:12:41: #1 finished! INFO @ Tue, 16 Jun 2020 08:12:41: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:12:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:12:42: #2 number of paired peaks: 1526 INFO @ Tue, 16 Jun 2020 08:12:42: start model_add_line... INFO @ Tue, 16 Jun 2020 08:12:42: start X-correlation... INFO @ Tue, 16 Jun 2020 08:12:42: end of X-cor INFO @ Tue, 16 Jun 2020 08:12:42: #2 finished! INFO @ Tue, 16 Jun 2020 08:12:42: #2 predicted fragment length is 115 bps INFO @ Tue, 16 Jun 2020 08:12:42: #2 alternative fragment length(s) may be 115 bps INFO @ Tue, 16 Jun 2020 08:12:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576637/SRX2576637.05_model.r INFO @ Tue, 16 Jun 2020 08:12:42: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:12:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:12:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576637/SRX2576637.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576637/SRX2576637.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576637/SRX2576637.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576637/SRX2576637.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 08:12:42: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:12:42: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:12:47: 1000000 INFO @ Tue, 16 Jun 2020 08:12:53: 2000000 INFO @ Tue, 16 Jun 2020 08:12:55: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:12:58: 3000000 INFO @ Tue, 16 Jun 2020 08:13:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576637/SRX2576637.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:13:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576637/SRX2576637.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:13:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576637/SRX2576637.05_summits.bed INFO @ Tue, 16 Jun 2020 08:13:01: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (4308 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:13:03: 4000000 INFO @ Tue, 16 Jun 2020 08:13:09: 5000000 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 08:13:12: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 08:13:12: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 08:13:12: #1 total tags in treatment: 5583075 INFO @ Tue, 16 Jun 2020 08:13:12: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:13:12: #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 08:13:12: #1 tags after filtering in treatment: 5583075 INFO @ Tue, 16 Jun 2020 08:13:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:13:12: #1 finished! INFO @ Tue, 16 Jun 2020 08:13:12: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:13:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:13:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576637/SRX2576637.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576637/SRX2576637.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576637/SRX2576637.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576637/SRX2576637.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 08:13:12: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:13:12: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:13:12: #2 number of paired peaks: 1526 INFO @ Tue, 16 Jun 2020 08:13:12: start model_add_line... INFO @ Tue, 16 Jun 2020 08:13:12: start X-correlation... INFO @ Tue, 16 Jun 2020 08:13:12: end of X-cor INFO @ Tue, 16 Jun 2020 08:13:12: #2 finished! INFO @ Tue, 16 Jun 2020 08:13:12: #2 predicted fragment length is 115 bps INFO @ Tue, 16 Jun 2020 08:13:12: #2 alternative fragment length(s) may be 115 bps INFO @ Tue, 16 Jun 2020 08:13:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576637/SRX2576637.10_model.r INFO @ Tue, 16 Jun 2020 08:13:12: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:13:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:13:17: 1000000 INFO @ Tue, 16 Jun 2020 08:13:23: 2000000 INFO @ Tue, 16 Jun 2020 08:13:25: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:13:28: 3000000 INFO @ Tue, 16 Jun 2020 08:13:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576637/SRX2576637.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:13:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576637/SRX2576637.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:13:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576637/SRX2576637.10_summits.bed INFO @ Tue, 16 Jun 2020 08:13:31: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2632 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:13:33: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:13:39: 5000000 INFO @ Tue, 16 Jun 2020 08:13:42: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 08:13:42: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 08:13:42: #1 total tags in treatment: 5583075 INFO @ Tue, 16 Jun 2020 08:13:42: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:13:42: #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 08:13:42: #1 tags after filtering in treatment: 5583075 INFO @ Tue, 16 Jun 2020 08:13:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:13:42: #1 finished! INFO @ Tue, 16 Jun 2020 08:13:42: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:13:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:13:42: #2 number of paired peaks: 1526 INFO @ Tue, 16 Jun 2020 08:13:42: start model_add_line... INFO @ Tue, 16 Jun 2020 08:13:42: start X-correlation... INFO @ Tue, 16 Jun 2020 08:13:42: end of X-cor INFO @ Tue, 16 Jun 2020 08:13:42: #2 finished! INFO @ Tue, 16 Jun 2020 08:13:42: #2 predicted fragment length is 115 bps INFO @ Tue, 16 Jun 2020 08:13:42: #2 alternative fragment length(s) may be 115 bps INFO @ Tue, 16 Jun 2020 08:13:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576637/SRX2576637.20_model.r INFO @ Tue, 16 Jun 2020 08:13:42: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:13:42: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:13:55: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:14:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576637/SRX2576637.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:14:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576637/SRX2576637.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:14:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576637/SRX2576637.20_summits.bed INFO @ Tue, 16 Jun 2020 08:14:01: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (1633 records, 4 fields): 4 millis CompletedMACS2peakCalling