Job ID = 6366921 SRX = SRX2576624 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:14:01 prefetch.2.10.7: 1) Downloading 'SRR5272581'... 2020-06-15T23:14:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:16:21 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:16:21 prefetch.2.10.7: 1) 'SRR5272581' was downloaded successfully Read 21023417 spots for SRR5272581/SRR5272581.sra Written 21023417 spots for SRR5272581/SRR5272581.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: 00:04:56 21023417 reads; of these: 21023417 (100.00%) were unpaired; of these: 3577993 (17.02%) aligned 0 times 14315372 (68.09%) aligned exactly 1 time 3130052 (14.89%) aligned >1 times 82.98% overall alignment rate Time searching: 00:04:56 Overall time: 00:04:56 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_sort_core] merging from 8 files... [bam_rmdupse_core] 10627441 / 17445424 = 0.6092 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 08:26:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576624/SRX2576624.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576624/SRX2576624.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576624/SRX2576624.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576624/SRX2576624.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 08:26:31: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:26:31: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:26:38: 1000000 INFO @ Tue, 16 Jun 2020 08:26:45: 2000000 INFO @ Tue, 16 Jun 2020 08:26:52: 3000000 INFO @ Tue, 16 Jun 2020 08:26:59: 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 08:27:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576624/SRX2576624.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576624/SRX2576624.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576624/SRX2576624.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576624/SRX2576624.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 08:27:01: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:27:01: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:27:05: 5000000 INFO @ Tue, 16 Jun 2020 08:27:08: 1000000 INFO @ Tue, 16 Jun 2020 08:27:12: 6000000 INFO @ Tue, 16 Jun 2020 08:27:15: 2000000 INFO @ Tue, 16 Jun 2020 08:27:18: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:27:18: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:27:18: #1 total tags in treatment: 6817983 INFO @ Tue, 16 Jun 2020 08:27:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:27:18: #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 08:27:18: #1 tags after filtering in treatment: 6817983 INFO @ Tue, 16 Jun 2020 08:27:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:27:18: #1 finished! INFO @ Tue, 16 Jun 2020 08:27:18: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:27:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:27:19: #2 number of paired peaks: 1212 INFO @ Tue, 16 Jun 2020 08:27:19: start model_add_line... INFO @ Tue, 16 Jun 2020 08:27:19: start X-correlation... INFO @ Tue, 16 Jun 2020 08:27:19: end of X-cor INFO @ Tue, 16 Jun 2020 08:27:19: #2 finished! INFO @ Tue, 16 Jun 2020 08:27:19: #2 predicted fragment length is 149 bps INFO @ Tue, 16 Jun 2020 08:27:19: #2 alternative fragment length(s) may be 149 bps INFO @ Tue, 16 Jun 2020 08:27:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576624/SRX2576624.05_model.r INFO @ Tue, 16 Jun 2020 08:27:19: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:27:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:27:22: 3000000 INFO @ Tue, 16 Jun 2020 08:27:28: 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 08:27:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576624/SRX2576624.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576624/SRX2576624.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576624/SRX2576624.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576624/SRX2576624.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 08:27:31: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:27:31: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:27:35: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:27:35: 5000000 INFO @ Tue, 16 Jun 2020 08:27:38: 1000000 INFO @ Tue, 16 Jun 2020 08:27:41: 6000000 INFO @ Tue, 16 Jun 2020 08:27:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576624/SRX2576624.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:27:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576624/SRX2576624.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:27:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576624/SRX2576624.05_summits.bed INFO @ Tue, 16 Jun 2020 08:27:42: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2521 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:27:45: 2000000 INFO @ Tue, 16 Jun 2020 08:27:47: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:27:47: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:27:47: #1 total tags in treatment: 6817983 INFO @ Tue, 16 Jun 2020 08:27:47: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:27:47: #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 08:27:47: #1 tags after filtering in treatment: 6817983 INFO @ Tue, 16 Jun 2020 08:27:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:27:47: #1 finished! INFO @ Tue, 16 Jun 2020 08:27:47: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:27:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:27:48: #2 number of paired peaks: 1212 INFO @ Tue, 16 Jun 2020 08:27:48: start model_add_line... INFO @ Tue, 16 Jun 2020 08:27:48: start X-correlation... INFO @ Tue, 16 Jun 2020 08:27:48: end of X-cor INFO @ Tue, 16 Jun 2020 08:27:48: #2 finished! INFO @ Tue, 16 Jun 2020 08:27:48: #2 predicted fragment length is 149 bps INFO @ Tue, 16 Jun 2020 08:27:48: #2 alternative fragment length(s) may be 149 bps INFO @ Tue, 16 Jun 2020 08:27:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576624/SRX2576624.10_model.r INFO @ Tue, 16 Jun 2020 08:27:48: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:27:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:27:51: 3000000 INFO @ Tue, 16 Jun 2020 08:27:58: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:28:03: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:28:04: 5000000 INFO @ Tue, 16 Jun 2020 08:28:11: 6000000 INFO @ Tue, 16 Jun 2020 08:28:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576624/SRX2576624.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:28:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576624/SRX2576624.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:28:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576624/SRX2576624.10_summits.bed INFO @ Tue, 16 Jun 2020 08:28:11: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1811 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:28:16: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:28:16: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:28:16: #1 total tags in treatment: 6817983 INFO @ Tue, 16 Jun 2020 08:28:16: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:28:16: #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 08:28:16: #1 tags after filtering in treatment: 6817983 INFO @ Tue, 16 Jun 2020 08:28:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:28:16: #1 finished! INFO @ Tue, 16 Jun 2020 08:28:16: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:28:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:28:17: #2 number of paired peaks: 1212 INFO @ Tue, 16 Jun 2020 08:28:17: start model_add_line... INFO @ Tue, 16 Jun 2020 08:28:17: start X-correlation... INFO @ Tue, 16 Jun 2020 08:28:17: end of X-cor INFO @ Tue, 16 Jun 2020 08:28:17: #2 finished! INFO @ Tue, 16 Jun 2020 08:28:17: #2 predicted fragment length is 149 bps INFO @ Tue, 16 Jun 2020 08:28:17: #2 alternative fragment length(s) may be 149 bps INFO @ Tue, 16 Jun 2020 08:28:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576624/SRX2576624.20_model.r INFO @ Tue, 16 Jun 2020 08:28:17: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:28:17: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:28:33: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:28:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576624/SRX2576624.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:28:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576624/SRX2576624.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:28:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576624/SRX2576624.20_summits.bed INFO @ Tue, 16 Jun 2020 08:28:41: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1222 records, 4 fields): 3 millis CompletedMACS2peakCalling