Job ID = 6368694 SRX = SRX5402720 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:28:16 prefetch.2.10.7: 1) Downloading 'SRR8602954'... 2020-06-16T00:28:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:33:51 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:33:51 prefetch.2.10.7: 1) 'SRR8602954' was downloaded successfully Read 42267115 spots for SRR8602954/SRR8602954.sra Written 42267115 spots for SRR8602954/SRR8602954.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: 00:07:25 42267115 reads; of these: 42267115 (100.00%) were unpaired; of these: 10922055 (25.84%) aligned 0 times 28778562 (68.09%) aligned exactly 1 time 2566498 (6.07%) aligned >1 times 74.16% overall alignment rate Time searching: 00:07:25 Overall time: 00:07:25 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 16 files... [bam_rmdupse_core] 10609601 / 31345060 = 0.3385 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 09:50:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402720/SRX5402720.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402720/SRX5402720.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402720/SRX5402720.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402720/SRX5402720.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 09:50:34: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:50:34: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:50:39: 1000000 INFO @ Tue, 16 Jun 2020 09:50:45: 2000000 INFO @ Tue, 16 Jun 2020 09:50:50: 3000000 INFO @ Tue, 16 Jun 2020 09:50:55: 4000000 INFO @ Tue, 16 Jun 2020 09:51:01: 5000000 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 09:51:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402720/SRX5402720.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402720/SRX5402720.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402720/SRX5402720.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402720/SRX5402720.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 09:51:04: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:51:04: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:51:06: 6000000 INFO @ Tue, 16 Jun 2020 09:51:11: 1000000 INFO @ Tue, 16 Jun 2020 09:51:12: 7000000 INFO @ Tue, 16 Jun 2020 09:51:17: 2000000 INFO @ Tue, 16 Jun 2020 09:51:18: 8000000 INFO @ Tue, 16 Jun 2020 09:51:24: 9000000 INFO @ Tue, 16 Jun 2020 09:51:24: 3000000 INFO @ Tue, 16 Jun 2020 09:51:30: 10000000 INFO @ Tue, 16 Jun 2020 09:51:30: 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 09:51:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402720/SRX5402720.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402720/SRX5402720.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402720/SRX5402720.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402720/SRX5402720.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 09:51:34: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:51:34: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:51:35: 11000000 INFO @ Tue, 16 Jun 2020 09:51:37: 5000000 INFO @ Tue, 16 Jun 2020 09:51:41: 1000000 INFO @ Tue, 16 Jun 2020 09:51:41: 12000000 INFO @ Tue, 16 Jun 2020 09:51:44: 6000000 INFO @ Tue, 16 Jun 2020 09:51:47: 2000000 INFO @ Tue, 16 Jun 2020 09:51:47: 13000000 INFO @ Tue, 16 Jun 2020 09:51:50: 7000000 INFO @ Tue, 16 Jun 2020 09:51:53: 14000000 INFO @ Tue, 16 Jun 2020 09:51:54: 3000000 INFO @ Tue, 16 Jun 2020 09:51:57: 8000000 INFO @ Tue, 16 Jun 2020 09:51:59: 15000000 INFO @ Tue, 16 Jun 2020 09:52:00: 4000000 INFO @ Tue, 16 Jun 2020 09:52:03: 9000000 INFO @ Tue, 16 Jun 2020 09:52:05: 16000000 INFO @ Tue, 16 Jun 2020 09:52:07: 5000000 INFO @ Tue, 16 Jun 2020 09:52:10: 10000000 INFO @ Tue, 16 Jun 2020 09:52:11: 17000000 INFO @ Tue, 16 Jun 2020 09:52:13: 6000000 INFO @ Tue, 16 Jun 2020 09:52:17: 11000000 INFO @ Tue, 16 Jun 2020 09:52:17: 18000000 INFO @ Tue, 16 Jun 2020 09:52:20: 7000000 INFO @ Tue, 16 Jun 2020 09:52:23: 19000000 INFO @ Tue, 16 Jun 2020 09:52:23: 12000000 INFO @ Tue, 16 Jun 2020 09:52:26: 8000000 INFO @ Tue, 16 Jun 2020 09:52:29: 20000000 INFO @ Tue, 16 Jun 2020 09:52:30: 13000000 INFO @ Tue, 16 Jun 2020 09:52:33: 9000000 INFO @ Tue, 16 Jun 2020 09:52:33: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:52:33: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:52:33: #1 total tags in treatment: 20735459 INFO @ Tue, 16 Jun 2020 09:52:33: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:52:33: #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 09:52:34: #1 tags after filtering in treatment: 20735459 INFO @ Tue, 16 Jun 2020 09:52:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:52:34: #1 finished! INFO @ Tue, 16 Jun 2020 09:52:34: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:52:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:52:36: #2 number of paired peaks: 5455 INFO @ Tue, 16 Jun 2020 09:52:36: start model_add_line... INFO @ Tue, 16 Jun 2020 09:52:36: start X-correlation... INFO @ Tue, 16 Jun 2020 09:52:36: end of X-cor INFO @ Tue, 16 Jun 2020 09:52:36: #2 finished! INFO @ Tue, 16 Jun 2020 09:52:36: #2 predicted fragment length is 101 bps INFO @ Tue, 16 Jun 2020 09:52:36: #2 alternative fragment length(s) may be 3,101 bps INFO @ Tue, 16 Jun 2020 09:52:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402720/SRX5402720.05_model.r INFO @ Tue, 16 Jun 2020 09:52:36: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:52:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:52:36: 14000000 INFO @ Tue, 16 Jun 2020 09:52:39: 10000000 INFO @ Tue, 16 Jun 2020 09:52:43: 15000000 INFO @ Tue, 16 Jun 2020 09:52:46: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:52:50: 16000000 INFO @ Tue, 16 Jun 2020 09:52:52: 12000000 INFO @ Tue, 16 Jun 2020 09:52:57: 17000000 INFO @ Tue, 16 Jun 2020 09:52:59: 13000000 INFO @ Tue, 16 Jun 2020 09:53:04: 18000000 INFO @ Tue, 16 Jun 2020 09:53:06: 14000000 INFO @ Tue, 16 Jun 2020 09:53:11: 19000000 INFO @ Tue, 16 Jun 2020 09:53:13: 15000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:53:18: 20000000 INFO @ Tue, 16 Jun 2020 09:53:19: 16000000 INFO @ Tue, 16 Jun 2020 09:53:20: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:53:24: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:53:24: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:53:24: #1 total tags in treatment: 20735459 INFO @ Tue, 16 Jun 2020 09:53:24: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:53:24: #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 09:53:24: #1 tags after filtering in treatment: 20735459 INFO @ Tue, 16 Jun 2020 09:53:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:53:24: #1 finished! INFO @ Tue, 16 Jun 2020 09:53:24: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:53:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:53:26: #2 number of paired peaks: 5455 INFO @ Tue, 16 Jun 2020 09:53:26: start model_add_line... INFO @ Tue, 16 Jun 2020 09:53:26: 17000000 INFO @ Tue, 16 Jun 2020 09:53:26: start X-correlation... INFO @ Tue, 16 Jun 2020 09:53:26: end of X-cor INFO @ Tue, 16 Jun 2020 09:53:26: #2 finished! INFO @ Tue, 16 Jun 2020 09:53:26: #2 predicted fragment length is 101 bps INFO @ Tue, 16 Jun 2020 09:53:26: #2 alternative fragment length(s) may be 3,101 bps INFO @ Tue, 16 Jun 2020 09:53:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402720/SRX5402720.10_model.r INFO @ Tue, 16 Jun 2020 09:53:26: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:53:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:53:33: 18000000 INFO @ Tue, 16 Jun 2020 09:53:39: 19000000 INFO @ Tue, 16 Jun 2020 09:53:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402720/SRX5402720.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:53:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402720/SRX5402720.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:53:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402720/SRX5402720.05_summits.bed INFO @ Tue, 16 Jun 2020 09:53:41: Done! pass1 - making usageList (6 chroms): 3 millis pass2 - checking and writing primary data (17491 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:53:46: 20000000 INFO @ Tue, 16 Jun 2020 09:53:51: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:53:51: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:53:51: #1 total tags in treatment: 20735459 INFO @ Tue, 16 Jun 2020 09:53:51: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:53:51: #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 09:53:51: #1 tags after filtering in treatment: 20735459 INFO @ Tue, 16 Jun 2020 09:53:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:53:51: #1 finished! INFO @ Tue, 16 Jun 2020 09:53:51: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:53:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:53:53: #2 number of paired peaks: 5455 INFO @ Tue, 16 Jun 2020 09:53:53: start model_add_line... INFO @ Tue, 16 Jun 2020 09:53:53: start X-correlation... INFO @ Tue, 16 Jun 2020 09:53:53: end of X-cor INFO @ Tue, 16 Jun 2020 09:53:53: #2 finished! INFO @ Tue, 16 Jun 2020 09:53:53: #2 predicted fragment length is 101 bps INFO @ Tue, 16 Jun 2020 09:53:53: #2 alternative fragment length(s) may be 3,101 bps INFO @ Tue, 16 Jun 2020 09:53:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402720/SRX5402720.20_model.r INFO @ Tue, 16 Jun 2020 09:53:53: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:53:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:54:12: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:54:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402720/SRX5402720.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:54:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402720/SRX5402720.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:54:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402720/SRX5402720.10_summits.bed INFO @ Tue, 16 Jun 2020 09:54:33: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (13171 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:54:40: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:55:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402720/SRX5402720.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:55:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402720/SRX5402720.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:55:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402720/SRX5402720.20_summits.bed INFO @ Tue, 16 Jun 2020 09:55:00: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (6933 records, 4 fields): 8 millis CompletedMACS2peakCalling