Job ID = 6367970 SRX = SRX4456929 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:47:32 prefetch.2.10.7: 1) Downloading 'SRR7591870'... 2020-06-15T23:47:32 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:48:49 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:48:50 prefetch.2.10.7: 'SRR7591870' is valid 2020-06-15T23:48:50 prefetch.2.10.7: 1) 'SRR7591870' was downloaded successfully Read 6057430 spots for SRR7591870/SRR7591870.sra Written 6057430 spots for SRR7591870/SRR7591870.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: 00:00:01 Multiseed full-index search: 00:01:07 6057430 reads; of these: 6057430 (100.00%) were unpaired; of these: 2255220 (37.23%) aligned 0 times 3225278 (53.24%) aligned exactly 1 time 576932 (9.52%) aligned >1 times 62.77% overall alignment rate Time searching: 00:01:08 Overall time: 00:01:08 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] 262949 / 3802210 = 0.0692 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 08:51:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4456929/SRX4456929.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4456929/SRX4456929.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4456929/SRX4456929.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4456929/SRX4456929.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 08:51:52: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:51:52: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:51:57: 1000000 INFO @ Tue, 16 Jun 2020 08:52:03: 2000000 INFO @ Tue, 16 Jun 2020 08:52:08: 3000000 INFO @ Tue, 16 Jun 2020 08:52:11: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:52:11: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:52:11: #1 total tags in treatment: 3539261 INFO @ Tue, 16 Jun 2020 08:52:11: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:52:11: #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 08:52:11: #1 tags after filtering in treatment: 3539261 INFO @ Tue, 16 Jun 2020 08:52:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:52:11: #1 finished! INFO @ Tue, 16 Jun 2020 08:52:11: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:52:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:52:12: #2 number of paired peaks: 1027 INFO @ Tue, 16 Jun 2020 08:52:12: start model_add_line... INFO @ Tue, 16 Jun 2020 08:52:12: start X-correlation... INFO @ Tue, 16 Jun 2020 08:52:12: end of X-cor INFO @ Tue, 16 Jun 2020 08:52:12: #2 finished! INFO @ Tue, 16 Jun 2020 08:52:12: #2 predicted fragment length is 112 bps INFO @ Tue, 16 Jun 2020 08:52:12: #2 alternative fragment length(s) may be 71,112 bps INFO @ Tue, 16 Jun 2020 08:52:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4456929/SRX4456929.05_model.r INFO @ Tue, 16 Jun 2020 08:52:12: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:52:12: #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 08:52:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4456929/SRX4456929.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4456929/SRX4456929.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4456929/SRX4456929.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4456929/SRX4456929.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 08:52:19: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:52:19: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:52:19: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:52:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4456929/SRX4456929.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:52:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4456929/SRX4456929.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:52:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4456929/SRX4456929.05_summits.bed INFO @ Tue, 16 Jun 2020 08:52:23: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (1129 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:52:24: 1000000 INFO @ Tue, 16 Jun 2020 08:52:29: 2000000 INFO @ Tue, 16 Jun 2020 08:52:34: 3000000 INFO @ Tue, 16 Jun 2020 08:52:37: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:52:37: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:52:37: #1 total tags in treatment: 3539261 INFO @ Tue, 16 Jun 2020 08:52:37: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:52:37: #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 08:52:37: #1 tags after filtering in treatment: 3539261 INFO @ Tue, 16 Jun 2020 08:52:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:52:37: #1 finished! INFO @ Tue, 16 Jun 2020 08:52:37: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:52:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:52:37: #2 number of paired peaks: 1027 INFO @ Tue, 16 Jun 2020 08:52:37: start model_add_line... INFO @ Tue, 16 Jun 2020 08:52:37: start X-correlation... INFO @ Tue, 16 Jun 2020 08:52:37: end of X-cor INFO @ Tue, 16 Jun 2020 08:52:37: #2 finished! INFO @ Tue, 16 Jun 2020 08:52:37: #2 predicted fragment length is 112 bps INFO @ Tue, 16 Jun 2020 08:52:37: #2 alternative fragment length(s) may be 71,112 bps INFO @ Tue, 16 Jun 2020 08:52:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4456929/SRX4456929.10_model.r INFO @ Tue, 16 Jun 2020 08:52:37: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:52:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:52:45: #3 Call peaks for each chromosome... 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 08:52:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4456929/SRX4456929.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:52:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4456929/SRX4456929.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:52:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4456929/SRX4456929.10_summits.bed INFO @ Tue, 16 Jun 2020 08:52:49: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (442 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:52:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4456929/SRX4456929.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4456929/SRX4456929.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4456929/SRX4456929.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4456929/SRX4456929.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 08:52:49: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:52:49: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:52:54: 1000000 INFO @ Tue, 16 Jun 2020 08:52:59: 2000000 INFO @ Tue, 16 Jun 2020 08:53:04: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:53:07: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:53:07: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:53:07: #1 total tags in treatment: 3539261 INFO @ Tue, 16 Jun 2020 08:53:07: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:53:07: #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 08:53:07: #1 tags after filtering in treatment: 3539261 INFO @ Tue, 16 Jun 2020 08:53:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:53:07: #1 finished! INFO @ Tue, 16 Jun 2020 08:53:07: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:53:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:53:07: #2 number of paired peaks: 1027 INFO @ Tue, 16 Jun 2020 08:53:07: start model_add_line... INFO @ Tue, 16 Jun 2020 08:53:07: start X-correlation... INFO @ Tue, 16 Jun 2020 08:53:07: end of X-cor INFO @ Tue, 16 Jun 2020 08:53:07: #2 finished! INFO @ Tue, 16 Jun 2020 08:53:07: #2 predicted fragment length is 112 bps INFO @ Tue, 16 Jun 2020 08:53:07: #2 alternative fragment length(s) may be 71,112 bps INFO @ Tue, 16 Jun 2020 08:53:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4456929/SRX4456929.20_model.r INFO @ Tue, 16 Jun 2020 08:53:07: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:53:07: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:53:15: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:53:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4456929/SRX4456929.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:53:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4456929/SRX4456929.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:53:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4456929/SRX4456929.20_summits.bed INFO @ Tue, 16 Jun 2020 08:53:18: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (126 records, 4 fields): 1 millis CompletedMACS2peakCalling