Job ID = 6367730 SRX = SRX4082344 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:37:14 prefetch.2.10.7: 1) Downloading 'SRR7164162'... 2020-06-15T23:37:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:39:51 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:39:52 prefetch.2.10.7: 'SRR7164162' is valid 2020-06-15T23:39:52 prefetch.2.10.7: 1) 'SRR7164162' was downloaded successfully 2020-06-15T23:39:52 prefetch.2.10.7: 'SRR7164162' has 0 unresolved dependencies Read 16780662 spots for SRR7164162/SRR7164162.sra Written 16780662 spots for SRR7164162/SRR7164162.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: 00:03:32 16780662 reads; of these: 16780662 (100.00%) were unpaired; of these: 500786 (2.98%) aligned 0 times 14876402 (88.65%) aligned exactly 1 time 1403474 (8.36%) aligned >1 times 97.02% overall alignment rate Time searching: 00:03:32 Overall time: 00:03:32 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] 4772440 / 16279876 = 0.2931 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 08:48:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082344/SRX4082344.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082344/SRX4082344.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082344/SRX4082344.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082344/SRX4082344.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 08:48:15: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:48:15: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:48:21: 1000000 INFO @ Tue, 16 Jun 2020 08:48:28: 2000000 INFO @ Tue, 16 Jun 2020 08:48:34: 3000000 INFO @ Tue, 16 Jun 2020 08:48:40: 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 08:48:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082344/SRX4082344.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082344/SRX4082344.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082344/SRX4082344.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082344/SRX4082344.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 08:48:45: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:48:45: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:48:47: 5000000 INFO @ Tue, 16 Jun 2020 08:48:52: 1000000 INFO @ Tue, 16 Jun 2020 08:48:54: 6000000 INFO @ Tue, 16 Jun 2020 08:48:59: 2000000 INFO @ Tue, 16 Jun 2020 08:49:00: 7000000 INFO @ Tue, 16 Jun 2020 08:49:05: 3000000 INFO @ Tue, 16 Jun 2020 08:49:07: 8000000 INFO @ Tue, 16 Jun 2020 08:49:12: 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 08:49:14: 9000000 INFO @ Tue, 16 Jun 2020 08:49:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082344/SRX4082344.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082344/SRX4082344.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082344/SRX4082344.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082344/SRX4082344.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 08:49:15: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:49:15: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:49:19: 5000000 INFO @ Tue, 16 Jun 2020 08:49:21: 10000000 INFO @ Tue, 16 Jun 2020 08:49:21: 1000000 INFO @ Tue, 16 Jun 2020 08:49:26: 6000000 INFO @ Tue, 16 Jun 2020 08:49:28: 2000000 INFO @ Tue, 16 Jun 2020 08:49:28: 11000000 INFO @ Tue, 16 Jun 2020 08:49:31: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:49:31: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:49:31: #1 total tags in treatment: 11507436 INFO @ Tue, 16 Jun 2020 08:49:31: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:49:31: #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 08:49:32: #1 tags after filtering in treatment: 11507436 INFO @ Tue, 16 Jun 2020 08:49:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:49:32: #1 finished! INFO @ Tue, 16 Jun 2020 08:49:32: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:49:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:49:33: 7000000 INFO @ Tue, 16 Jun 2020 08:49:33: #2 number of paired peaks: 5404 INFO @ Tue, 16 Jun 2020 08:49:33: start model_add_line... INFO @ Tue, 16 Jun 2020 08:49:33: start X-correlation... INFO @ Tue, 16 Jun 2020 08:49:33: end of X-cor INFO @ Tue, 16 Jun 2020 08:49:33: #2 finished! INFO @ Tue, 16 Jun 2020 08:49:33: #2 predicted fragment length is 149 bps INFO @ Tue, 16 Jun 2020 08:49:33: #2 alternative fragment length(s) may be 149 bps INFO @ Tue, 16 Jun 2020 08:49:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082344/SRX4082344.05_model.r INFO @ Tue, 16 Jun 2020 08:49:33: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:49:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:49:34: 3000000 INFO @ Tue, 16 Jun 2020 08:49:40: 8000000 INFO @ Tue, 16 Jun 2020 08:49:40: 4000000 INFO @ Tue, 16 Jun 2020 08:49:46: 5000000 INFO @ Tue, 16 Jun 2020 08:49:46: 9000000 INFO @ Tue, 16 Jun 2020 08:49:52: 6000000 INFO @ Tue, 16 Jun 2020 08:49:53: 10000000 INFO @ Tue, 16 Jun 2020 08:49:58: 7000000 INFO @ Tue, 16 Jun 2020 08:50:00: 11000000 INFO @ Tue, 16 Jun 2020 08:50:03: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:50:03: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:50:03: #1 total tags in treatment: 11507436 INFO @ Tue, 16 Jun 2020 08:50:03: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:50:03: #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 08:50:03: #1 tags after filtering in treatment: 11507436 INFO @ Tue, 16 Jun 2020 08:50:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:50:03: #1 finished! INFO @ Tue, 16 Jun 2020 08:50:03: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:50:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:50:04: 8000000 INFO @ Tue, 16 Jun 2020 08:50:05: #2 number of paired peaks: 5404 INFO @ Tue, 16 Jun 2020 08:50:05: start model_add_line... INFO @ Tue, 16 Jun 2020 08:50:05: start X-correlation... INFO @ Tue, 16 Jun 2020 08:50:05: end of X-cor INFO @ Tue, 16 Jun 2020 08:50:05: #2 finished! INFO @ Tue, 16 Jun 2020 08:50:05: #2 predicted fragment length is 149 bps INFO @ Tue, 16 Jun 2020 08:50:05: #2 alternative fragment length(s) may be 149 bps INFO @ Tue, 16 Jun 2020 08:50:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082344/SRX4082344.10_model.r INFO @ Tue, 16 Jun 2020 08:50:05: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:50:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:50:05: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:50:10: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:50:15: 10000000 INFO @ Tue, 16 Jun 2020 08:50:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082344/SRX4082344.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:50:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082344/SRX4082344.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:50:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082344/SRX4082344.05_summits.bed INFO @ Tue, 16 Jun 2020 08:50:19: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (7361 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:50:21: 11000000 INFO @ Tue, 16 Jun 2020 08:50:24: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:50:24: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:50:24: #1 total tags in treatment: 11507436 INFO @ Tue, 16 Jun 2020 08:50:24: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:50:24: #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 08:50:24: #1 tags after filtering in treatment: 11507436 INFO @ Tue, 16 Jun 2020 08:50:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:50:24: #1 finished! INFO @ Tue, 16 Jun 2020 08:50:24: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:50:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:50:25: #2 number of paired peaks: 5404 INFO @ Tue, 16 Jun 2020 08:50:25: start model_add_line... INFO @ Tue, 16 Jun 2020 08:50:25: start X-correlation... INFO @ Tue, 16 Jun 2020 08:50:25: end of X-cor INFO @ Tue, 16 Jun 2020 08:50:25: #2 finished! INFO @ Tue, 16 Jun 2020 08:50:25: #2 predicted fragment length is 149 bps INFO @ Tue, 16 Jun 2020 08:50:25: #2 alternative fragment length(s) may be 149 bps INFO @ Tue, 16 Jun 2020 08:50:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082344/SRX4082344.20_model.r INFO @ Tue, 16 Jun 2020 08:50:25: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:50:25: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:50:36: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:50:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082344/SRX4082344.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:50:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082344/SRX4082344.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:50:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082344/SRX4082344.10_summits.bed INFO @ Tue, 16 Jun 2020 08:50:50: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (5715 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:50:57: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:51:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082344/SRX4082344.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:51:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082344/SRX4082344.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:51:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082344/SRX4082344.20_summits.bed INFO @ Tue, 16 Jun 2020 08:51:11: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (4188 records, 4 fields): 5 millis CompletedMACS2peakCalling