Job ID = 6367754 SRX = SRX4082368 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:45:59 prefetch.2.10.7: 1) Downloading 'SRR7164186'... 2020-06-15T23:45:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:47:43 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:47:44 prefetch.2.10.7: 'SRR7164186' is valid 2020-06-15T23:47:44 prefetch.2.10.7: 1) 'SRR7164186' was downloaded successfully 2020-06-15T23:47:44 prefetch.2.10.7: 'SRR7164186' has 0 unresolved dependencies Read 14888088 spots for SRR7164186/SRR7164186.sra Written 14888088 spots for SRR7164186/SRR7164186.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: 00:03:19 14888088 reads; of these: 14888088 (100.00%) were unpaired; of these: 525718 (3.53%) aligned 0 times 13121959 (88.14%) aligned exactly 1 time 1240411 (8.33%) aligned >1 times 96.47% overall alignment rate Time searching: 00:03:19 Overall time: 00:03:19 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_sort_core] merging from 8 files... [bam_rmdupse_core] 3131608 / 14362370 = 0.2180 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 08:55:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082368/SRX4082368.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082368/SRX4082368.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082368/SRX4082368.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082368/SRX4082368.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 08:55:40: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:55:40: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:55:46: 1000000 INFO @ Tue, 16 Jun 2020 08:55:52: 2000000 INFO @ Tue, 16 Jun 2020 08:55:59: 3000000 INFO @ Tue, 16 Jun 2020 08:56:05: 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 08:56:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082368/SRX4082368.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082368/SRX4082368.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082368/SRX4082368.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082368/SRX4082368.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 08:56:10: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:56:10: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:56:12: 5000000 INFO @ Tue, 16 Jun 2020 08:56:16: 1000000 INFO @ Tue, 16 Jun 2020 08:56:18: 6000000 INFO @ Tue, 16 Jun 2020 08:56:22: 2000000 INFO @ Tue, 16 Jun 2020 08:56:25: 7000000 INFO @ Tue, 16 Jun 2020 08:56:28: 3000000 INFO @ Tue, 16 Jun 2020 08:56:31: 8000000 INFO @ Tue, 16 Jun 2020 08:56:34: 4000000 INFO @ Tue, 16 Jun 2020 08:56:38: 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 08:56:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082368/SRX4082368.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082368/SRX4082368.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082368/SRX4082368.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082368/SRX4082368.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 08:56:40: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:56:40: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:56:40: 5000000 INFO @ Tue, 16 Jun 2020 08:56:44: 10000000 INFO @ Tue, 16 Jun 2020 08:56:46: 6000000 INFO @ Tue, 16 Jun 2020 08:56:47: 1000000 INFO @ Tue, 16 Jun 2020 08:56:51: 11000000 INFO @ Tue, 16 Jun 2020 08:56:52: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:56:52: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:56:52: #1 total tags in treatment: 11230762 INFO @ Tue, 16 Jun 2020 08:56:52: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:56:52: #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 08:56:53: #1 tags after filtering in treatment: 11230762 INFO @ Tue, 16 Jun 2020 08:56:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:56:53: #1 finished! INFO @ Tue, 16 Jun 2020 08:56:53: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:56:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:56:53: 7000000 INFO @ Tue, 16 Jun 2020 08:56:53: 2000000 INFO @ Tue, 16 Jun 2020 08:56:54: #2 number of paired peaks: 5430 INFO @ Tue, 16 Jun 2020 08:56:54: start model_add_line... INFO @ Tue, 16 Jun 2020 08:56:54: start X-correlation... INFO @ Tue, 16 Jun 2020 08:56:54: end of X-cor INFO @ Tue, 16 Jun 2020 08:56:54: #2 finished! INFO @ Tue, 16 Jun 2020 08:56:54: #2 predicted fragment length is 169 bps INFO @ Tue, 16 Jun 2020 08:56:54: #2 alternative fragment length(s) may be 4,169 bps INFO @ Tue, 16 Jun 2020 08:56:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082368/SRX4082368.05_model.r INFO @ Tue, 16 Jun 2020 08:56:54: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:56:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:56:59: 8000000 INFO @ Tue, 16 Jun 2020 08:57:00: 3000000 INFO @ Tue, 16 Jun 2020 08:57:05: 9000000 INFO @ Tue, 16 Jun 2020 08:57:06: 4000000 INFO @ Tue, 16 Jun 2020 08:57:11: 10000000 INFO @ Tue, 16 Jun 2020 08:57:13: 5000000 INFO @ Tue, 16 Jun 2020 08:57:17: 11000000 INFO @ Tue, 16 Jun 2020 08:57:18: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:57:18: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:57:18: #1 total tags in treatment: 11230762 INFO @ Tue, 16 Jun 2020 08:57:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:57:18: #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 08:57:18: #1 tags after filtering in treatment: 11230762 INFO @ Tue, 16 Jun 2020 08:57:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:57:18: #1 finished! INFO @ Tue, 16 Jun 2020 08:57:18: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:57:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:57:20: #2 number of paired peaks: 5430 INFO @ Tue, 16 Jun 2020 08:57:20: start model_add_line... INFO @ Tue, 16 Jun 2020 08:57:20: 6000000 INFO @ Tue, 16 Jun 2020 08:57:20: start X-correlation... INFO @ Tue, 16 Jun 2020 08:57:20: end of X-cor INFO @ Tue, 16 Jun 2020 08:57:20: #2 finished! INFO @ Tue, 16 Jun 2020 08:57:20: #2 predicted fragment length is 169 bps INFO @ Tue, 16 Jun 2020 08:57:20: #2 alternative fragment length(s) may be 4,169 bps INFO @ Tue, 16 Jun 2020 08:57:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082368/SRX4082368.10_model.r INFO @ Tue, 16 Jun 2020 08:57:20: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:57:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:57:23: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:57:26: 7000000 INFO @ Tue, 16 Jun 2020 08:57:32: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:57:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082368/SRX4082368.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:57:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082368/SRX4082368.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:57:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082368/SRX4082368.05_summits.bed INFO @ Tue, 16 Jun 2020 08:57:38: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (10592 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:57:38: 9000000 INFO @ Tue, 16 Jun 2020 08:57:45: 10000000 INFO @ Tue, 16 Jun 2020 08:57:48: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:57:51: 11000000 INFO @ Tue, 16 Jun 2020 08:57:53: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:57:53: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:57:53: #1 total tags in treatment: 11230762 INFO @ Tue, 16 Jun 2020 08:57:53: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:57:53: #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 08:57:53: #1 tags after filtering in treatment: 11230762 INFO @ Tue, 16 Jun 2020 08:57:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:57:53: #1 finished! INFO @ Tue, 16 Jun 2020 08:57:53: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:57:53: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:57:54: #2 number of paired peaks: 5430 INFO @ Tue, 16 Jun 2020 08:57:54: start model_add_line... INFO @ Tue, 16 Jun 2020 08:57:54: start X-correlation... INFO @ Tue, 16 Jun 2020 08:57:54: end of X-cor INFO @ Tue, 16 Jun 2020 08:57:54: #2 finished! INFO @ Tue, 16 Jun 2020 08:57:54: #2 predicted fragment length is 169 bps INFO @ Tue, 16 Jun 2020 08:57:54: #2 alternative fragment length(s) may be 4,169 bps INFO @ Tue, 16 Jun 2020 08:57:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082368/SRX4082368.20_model.r INFO @ Tue, 16 Jun 2020 08:57:54: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:57:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:58:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082368/SRX4082368.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:58:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082368/SRX4082368.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:58:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082368/SRX4082368.10_summits.bed INFO @ Tue, 16 Jun 2020 08:58:02: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (6505 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:58:23: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:58:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082368/SRX4082368.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:58:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082368/SRX4082368.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:58:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082368/SRX4082368.20_summits.bed INFO @ Tue, 16 Jun 2020 08:58:36: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2288 records, 4 fields): 3 millis CompletedMACS2peakCalling