Job ID = 6368820 SRX = SRX5985674 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:30:00 prefetch.2.10.7: 1) Downloading 'SRR9214979'... 2020-06-16T00:30:00 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:32:40 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:32:40 prefetch.2.10.7: 1) 'SRR9214979' was downloaded successfully Read 19194338 spots for SRR9214979/SRR9214979.sra Written 19194338 spots for SRR9214979/SRR9214979.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: 00:06:08 19194338 reads; of these: 19194338 (100.00%) were unpaired; of these: 152775 (0.80%) aligned 0 times 17318992 (90.23%) aligned exactly 1 time 1722571 (8.97%) aligned >1 times 99.20% overall alignment rate Time searching: 00:06:08 Overall time: 00:06:08 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] 3065408 / 19041563 = 0.1610 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 09:49:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5985674/SRX5985674.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5985674/SRX5985674.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5985674/SRX5985674.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5985674/SRX5985674.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 09:49:12: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:49:12: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:49:20: 1000000 INFO @ Tue, 16 Jun 2020 09:49:29: 2000000 INFO @ Tue, 16 Jun 2020 09:49:37: 3000000 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 09:49:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5985674/SRX5985674.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5985674/SRX5985674.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5985674/SRX5985674.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5985674/SRX5985674.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 09:49:42: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:49:42: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:49:46: 4000000 INFO @ Tue, 16 Jun 2020 09:49:51: 1000000 INFO @ Tue, 16 Jun 2020 09:49:54: 5000000 INFO @ Tue, 16 Jun 2020 09:49:59: 2000000 INFO @ Tue, 16 Jun 2020 09:50:03: 6000000 INFO @ Tue, 16 Jun 2020 09:50:08: 3000000 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 09:50:12: 7000000 INFO @ Tue, 16 Jun 2020 09:50:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5985674/SRX5985674.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5985674/SRX5985674.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5985674/SRX5985674.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5985674/SRX5985674.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 09:50:12: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:50:12: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:50:17: 4000000 INFO @ Tue, 16 Jun 2020 09:50:19: 1000000 INFO @ Tue, 16 Jun 2020 09:50:20: 8000000 INFO @ Tue, 16 Jun 2020 09:50:25: 5000000 INFO @ Tue, 16 Jun 2020 09:50:27: 2000000 INFO @ Tue, 16 Jun 2020 09:50:28: 9000000 INFO @ Tue, 16 Jun 2020 09:50:34: 6000000 INFO @ Tue, 16 Jun 2020 09:50:34: 3000000 INFO @ Tue, 16 Jun 2020 09:50:37: 10000000 INFO @ Tue, 16 Jun 2020 09:50:42: 4000000 INFO @ Tue, 16 Jun 2020 09:50:42: 7000000 INFO @ Tue, 16 Jun 2020 09:50:46: 11000000 INFO @ Tue, 16 Jun 2020 09:50:49: 5000000 INFO @ Tue, 16 Jun 2020 09:50:51: 8000000 INFO @ Tue, 16 Jun 2020 09:50:55: 12000000 INFO @ Tue, 16 Jun 2020 09:50:56: 6000000 INFO @ Tue, 16 Jun 2020 09:51:00: 9000000 INFO @ Tue, 16 Jun 2020 09:51:03: 13000000 INFO @ Tue, 16 Jun 2020 09:51:04: 7000000 INFO @ Tue, 16 Jun 2020 09:51:08: 10000000 INFO @ Tue, 16 Jun 2020 09:51:11: 8000000 INFO @ Tue, 16 Jun 2020 09:51:12: 14000000 INFO @ Tue, 16 Jun 2020 09:51:16: 11000000 INFO @ Tue, 16 Jun 2020 09:51:18: 9000000 INFO @ Tue, 16 Jun 2020 09:51:21: 15000000 INFO @ Tue, 16 Jun 2020 09:51:25: 12000000 INFO @ Tue, 16 Jun 2020 09:51:26: 10000000 INFO @ Tue, 16 Jun 2020 09:51:31: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:51:31: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:51:31: #1 total tags in treatment: 15976155 INFO @ Tue, 16 Jun 2020 09:51:31: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:51:31: #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 09:51:31: #1 tags after filtering in treatment: 15976155 INFO @ Tue, 16 Jun 2020 09:51:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:51:31: #1 finished! INFO @ Tue, 16 Jun 2020 09:51:31: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:51:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:51:32: #2 number of paired peaks: 1256 INFO @ Tue, 16 Jun 2020 09:51:32: start model_add_line... INFO @ Tue, 16 Jun 2020 09:51:32: start X-correlation... INFO @ Tue, 16 Jun 2020 09:51:32: end of X-cor INFO @ Tue, 16 Jun 2020 09:51:32: #2 finished! INFO @ Tue, 16 Jun 2020 09:51:32: #2 predicted fragment length is 204 bps INFO @ Tue, 16 Jun 2020 09:51:32: #2 alternative fragment length(s) may be 2,181,204,206 bps INFO @ Tue, 16 Jun 2020 09:51:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5985674/SRX5985674.05_model.r INFO @ Tue, 16 Jun 2020 09:51:32: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:51:32: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:51:33: 13000000 INFO @ Tue, 16 Jun 2020 09:51:33: 11000000 INFO @ Tue, 16 Jun 2020 09:51:41: 12000000 INFO @ Tue, 16 Jun 2020 09:51:41: 14000000 INFO @ Tue, 16 Jun 2020 09:51:48: 13000000 INFO @ Tue, 16 Jun 2020 09:51:50: 15000000 INFO @ Tue, 16 Jun 2020 09:51:56: 14000000 INFO @ Tue, 16 Jun 2020 09:51:58: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:51:58: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:51:58: #1 total tags in treatment: 15976155 INFO @ Tue, 16 Jun 2020 09:51:58: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:51:58: #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 09:51:58: #1 tags after filtering in treatment: 15976155 INFO @ Tue, 16 Jun 2020 09:51:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:51:58: #1 finished! INFO @ Tue, 16 Jun 2020 09:51:58: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:51:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:51:59: #2 number of paired peaks: 1256 INFO @ Tue, 16 Jun 2020 09:51:59: start model_add_line... INFO @ Tue, 16 Jun 2020 09:51:59: start X-correlation... INFO @ Tue, 16 Jun 2020 09:51:59: end of X-cor INFO @ Tue, 16 Jun 2020 09:51:59: #2 finished! INFO @ Tue, 16 Jun 2020 09:51:59: #2 predicted fragment length is 204 bps INFO @ Tue, 16 Jun 2020 09:51:59: #2 alternative fragment length(s) may be 2,181,204,206 bps INFO @ Tue, 16 Jun 2020 09:51:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5985674/SRX5985674.10_model.r INFO @ Tue, 16 Jun 2020 09:51:59: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:51:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:52:03: 15000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:52:10: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:52:10: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:52:10: #1 total tags in treatment: 15976155 INFO @ Tue, 16 Jun 2020 09:52:10: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:52:10: #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 09:52:11: #1 tags after filtering in treatment: 15976155 INFO @ Tue, 16 Jun 2020 09:52:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:52:11: #1 finished! INFO @ Tue, 16 Jun 2020 09:52:11: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:52:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:52:12: #2 number of paired peaks: 1256 INFO @ Tue, 16 Jun 2020 09:52:12: start model_add_line... INFO @ Tue, 16 Jun 2020 09:52:12: start X-correlation... INFO @ Tue, 16 Jun 2020 09:52:12: end of X-cor INFO @ Tue, 16 Jun 2020 09:52:12: #2 finished! INFO @ Tue, 16 Jun 2020 09:52:12: #2 predicted fragment length is 204 bps INFO @ Tue, 16 Jun 2020 09:52:12: #2 alternative fragment length(s) may be 2,181,204,206 bps INFO @ Tue, 16 Jun 2020 09:52:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5985674/SRX5985674.20_model.r INFO @ Tue, 16 Jun 2020 09:52:12: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:52:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:52:13: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:52:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5985674/SRX5985674.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:52:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5985674/SRX5985674.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:52:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5985674/SRX5985674.05_summits.bed INFO @ Tue, 16 Jun 2020 09:52:30: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (6681 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:52:40: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:52:52: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:52:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5985674/SRX5985674.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:52:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5985674/SRX5985674.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:52:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5985674/SRX5985674.10_summits.bed INFO @ Tue, 16 Jun 2020 09:52:57: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3384 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:53:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5985674/SRX5985674.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:53:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5985674/SRX5985674.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:53:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5985674/SRX5985674.20_summits.bed INFO @ Tue, 16 Jun 2020 09:53:08: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (1010 records, 4 fields): 3 millis CompletedMACS2peakCalling