Job ID = 6368912 SRX = SRX6720190 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:44:27 prefetch.2.10.7: 1) Downloading 'SRR9972840'... 2020-06-16T00:44:27 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:49:11 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:49:11 prefetch.2.10.7: 1) 'SRR9972840' was downloaded successfully Read 22972055 spots for SRR9972840/SRR9972840.sra Written 22972055 spots for SRR9972840/SRR9972840.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: 00:05:10 22972055 reads; of these: 22972055 (100.00%) were unpaired; of these: 2024456 (8.81%) aligned 0 times 18241933 (79.41%) aligned exactly 1 time 2705666 (11.78%) aligned >1 times 91.19% overall alignment rate Time searching: 00:05:10 Overall time: 00:05:10 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 12 files... [bam_rmdupse_core] 6795154 / 20947599 = 0.3244 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 10:01:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6720190/SRX6720190.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6720190/SRX6720190.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6720190/SRX6720190.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6720190/SRX6720190.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 10:01:17: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:01:17: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:01:23: 1000000 INFO @ Tue, 16 Jun 2020 10:01:29: 2000000 INFO @ Tue, 16 Jun 2020 10:01:36: 3000000 INFO @ Tue, 16 Jun 2020 10:01:41: 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 10:01:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6720190/SRX6720190.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6720190/SRX6720190.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6720190/SRX6720190.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6720190/SRX6720190.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 10:01:47: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:01:47: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:01:47: 5000000 INFO @ Tue, 16 Jun 2020 10:01:53: 1000000 INFO @ Tue, 16 Jun 2020 10:01:54: 6000000 INFO @ Tue, 16 Jun 2020 10:02:00: 2000000 INFO @ Tue, 16 Jun 2020 10:02:00: 7000000 INFO @ Tue, 16 Jun 2020 10:02:06: 3000000 INFO @ Tue, 16 Jun 2020 10:02:06: 8000000 INFO @ Tue, 16 Jun 2020 10:02:12: 4000000 INFO @ Tue, 16 Jun 2020 10:02:12: 9000000 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 10:02:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6720190/SRX6720190.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6720190/SRX6720190.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6720190/SRX6720190.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6720190/SRX6720190.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 10:02:17: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:02:17: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:02:18: 5000000 INFO @ Tue, 16 Jun 2020 10:02:18: 10000000 INFO @ Tue, 16 Jun 2020 10:02:24: 1000000 INFO @ Tue, 16 Jun 2020 10:02:25: 6000000 INFO @ Tue, 16 Jun 2020 10:02:25: 11000000 INFO @ Tue, 16 Jun 2020 10:02:30: 2000000 INFO @ Tue, 16 Jun 2020 10:02:31: 7000000 INFO @ Tue, 16 Jun 2020 10:02:31: 12000000 INFO @ Tue, 16 Jun 2020 10:02:36: 3000000 INFO @ Tue, 16 Jun 2020 10:02:38: 13000000 INFO @ Tue, 16 Jun 2020 10:02:38: 8000000 INFO @ Tue, 16 Jun 2020 10:02:43: 4000000 INFO @ Tue, 16 Jun 2020 10:02:44: 14000000 INFO @ Tue, 16 Jun 2020 10:02:44: 9000000 INFO @ Tue, 16 Jun 2020 10:02:45: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 10:02:45: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 10:02:45: #1 total tags in treatment: 14152445 INFO @ Tue, 16 Jun 2020 10:02:45: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:02:45: #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 10:02:45: #1 tags after filtering in treatment: 14152445 INFO @ Tue, 16 Jun 2020 10:02:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:02:45: #1 finished! INFO @ Tue, 16 Jun 2020 10:02:45: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:02:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:02:46: #2 number of paired peaks: 1837 INFO @ Tue, 16 Jun 2020 10:02:46: start model_add_line... INFO @ Tue, 16 Jun 2020 10:02:47: start X-correlation... INFO @ Tue, 16 Jun 2020 10:02:47: end of X-cor INFO @ Tue, 16 Jun 2020 10:02:47: #2 finished! INFO @ Tue, 16 Jun 2020 10:02:47: #2 predicted fragment length is 128 bps INFO @ Tue, 16 Jun 2020 10:02:47: #2 alternative fragment length(s) may be 128 bps INFO @ Tue, 16 Jun 2020 10:02:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6720190/SRX6720190.05_model.r INFO @ Tue, 16 Jun 2020 10:02:47: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:02:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:02:49: 5000000 INFO @ Tue, 16 Jun 2020 10:02:50: 10000000 INFO @ Tue, 16 Jun 2020 10:02:55: 6000000 INFO @ Tue, 16 Jun 2020 10:02:56: 11000000 INFO @ Tue, 16 Jun 2020 10:03:01: 7000000 INFO @ Tue, 16 Jun 2020 10:03:03: 12000000 INFO @ Tue, 16 Jun 2020 10:03:07: 8000000 INFO @ Tue, 16 Jun 2020 10:03:09: 13000000 INFO @ Tue, 16 Jun 2020 10:03:13: 9000000 INFO @ Tue, 16 Jun 2020 10:03:15: 14000000 INFO @ Tue, 16 Jun 2020 10:03:16: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 10:03:16: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 10:03:16: #1 total tags in treatment: 14152445 INFO @ Tue, 16 Jun 2020 10:03:16: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:03:16: #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 10:03:16: #1 tags after filtering in treatment: 14152445 INFO @ Tue, 16 Jun 2020 10:03:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:03:16: #1 finished! INFO @ Tue, 16 Jun 2020 10:03:16: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:03:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:03:18: #2 number of paired peaks: 1837 INFO @ Tue, 16 Jun 2020 10:03:18: start model_add_line... INFO @ Tue, 16 Jun 2020 10:03:18: start X-correlation... INFO @ Tue, 16 Jun 2020 10:03:18: end of X-cor INFO @ Tue, 16 Jun 2020 10:03:18: #2 finished! INFO @ Tue, 16 Jun 2020 10:03:18: #2 predicted fragment length is 128 bps INFO @ Tue, 16 Jun 2020 10:03:18: #2 alternative fragment length(s) may be 128 bps INFO @ Tue, 16 Jun 2020 10:03:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6720190/SRX6720190.10_model.r INFO @ Tue, 16 Jun 2020 10:03:18: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:03:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:03:19: 10000000 INFO @ Tue, 16 Jun 2020 10:03:23: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:03:25: 11000000 INFO @ Tue, 16 Jun 2020 10:03:32: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 10:03:38: 13000000 INFO @ Tue, 16 Jun 2020 10:03:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6720190/SRX6720190.05_peaks.xls INFO @ Tue, 16 Jun 2020 10:03:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6720190/SRX6720190.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:03:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6720190/SRX6720190.05_summits.bed INFO @ Tue, 16 Jun 2020 10:03:43: Done! INFO @ Tue, 16 Jun 2020 10:03:44: 14000000 pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (8245 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:03:45: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 10:03:45: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 10:03:45: #1 total tags in treatment: 14152445 INFO @ Tue, 16 Jun 2020 10:03:45: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:03:45: #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 10:03:45: #1 tags after filtering in treatment: 14152445 INFO @ Tue, 16 Jun 2020 10:03:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:03:45: #1 finished! INFO @ Tue, 16 Jun 2020 10:03:45: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:03:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:03:46: #2 number of paired peaks: 1837 INFO @ Tue, 16 Jun 2020 10:03:46: start model_add_line... INFO @ Tue, 16 Jun 2020 10:03:46: start X-correlation... INFO @ Tue, 16 Jun 2020 10:03:46: end of X-cor INFO @ Tue, 16 Jun 2020 10:03:46: #2 finished! INFO @ Tue, 16 Jun 2020 10:03:46: #2 predicted fragment length is 128 bps INFO @ Tue, 16 Jun 2020 10:03:46: #2 alternative fragment length(s) may be 128 bps INFO @ Tue, 16 Jun 2020 10:03:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6720190/SRX6720190.20_model.r INFO @ Tue, 16 Jun 2020 10:03:46: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:03:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:03:54: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 10:04:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6720190/SRX6720190.10_peaks.xls INFO @ Tue, 16 Jun 2020 10:04:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6720190/SRX6720190.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:04:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6720190/SRX6720190.10_summits.bed INFO @ Tue, 16 Jun 2020 10:04:14: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (5293 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:04:23: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:04:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6720190/SRX6720190.20_peaks.xls INFO @ Tue, 16 Jun 2020 10:04:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6720190/SRX6720190.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:04:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6720190/SRX6720190.20_summits.bed INFO @ Tue, 16 Jun 2020 10:04:42: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2545 records, 4 fields): 4 millis CompletedMACS2peakCalling