Job ID = 6367749 SRX = SRX4082363 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:51:03 prefetch.2.10.7: 1) Downloading 'SRR7164181'... 2020-06-15T23:51:03 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:52:55 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:52:56 prefetch.2.10.7: 'SRR7164181' is valid 2020-06-15T23:52:56 prefetch.2.10.7: 1) 'SRR7164181' was downloaded successfully 2020-06-15T23:52:56 prefetch.2.10.7: 'SRR7164181' has 0 unresolved dependencies Read 18559199 spots for SRR7164181/SRR7164181.sra Written 18559199 spots for SRR7164181/SRR7164181.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: 00:04:01 18559199 reads; of these: 18559199 (100.00%) were unpaired; of these: 248994 (1.34%) aligned 0 times 16386853 (88.30%) aligned exactly 1 time 1923352 (10.36%) aligned >1 times 98.66% overall alignment rate Time searching: 00:04:01 Overall time: 00:04:01 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] 3475211 / 18310205 = 0.1898 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 09:04:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082363/SRX4082363.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082363/SRX4082363.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082363/SRX4082363.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082363/SRX4082363.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 09:04:22: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:04:22: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:04:27: 1000000 INFO @ Tue, 16 Jun 2020 09:04:33: 2000000 INFO @ Tue, 16 Jun 2020 09:04:38: 3000000 INFO @ Tue, 16 Jun 2020 09:04:43: 4000000 INFO @ Tue, 16 Jun 2020 09:04:49: 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 09:04:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082363/SRX4082363.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082363/SRX4082363.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082363/SRX4082363.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082363/SRX4082363.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 09:04:52: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:04:52: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:04:55: 6000000 INFO @ Tue, 16 Jun 2020 09:04:58: 1000000 INFO @ Tue, 16 Jun 2020 09:05:01: 7000000 INFO @ Tue, 16 Jun 2020 09:05:04: 2000000 INFO @ Tue, 16 Jun 2020 09:05:07: 8000000 INFO @ Tue, 16 Jun 2020 09:05:10: 3000000 INFO @ Tue, 16 Jun 2020 09:05:13: 9000000 INFO @ Tue, 16 Jun 2020 09:05:17: 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 09:05:19: 10000000 INFO @ Tue, 16 Jun 2020 09:05:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082363/SRX4082363.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082363/SRX4082363.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082363/SRX4082363.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082363/SRX4082363.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 09:05:22: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:05:22: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:05:23: 5000000 INFO @ Tue, 16 Jun 2020 09:05:26: 11000000 INFO @ Tue, 16 Jun 2020 09:05:28: 1000000 INFO @ Tue, 16 Jun 2020 09:05:30: 6000000 INFO @ Tue, 16 Jun 2020 09:05:32: 12000000 INFO @ Tue, 16 Jun 2020 09:05:35: 2000000 INFO @ Tue, 16 Jun 2020 09:05:37: 7000000 INFO @ Tue, 16 Jun 2020 09:05:39: 13000000 INFO @ Tue, 16 Jun 2020 09:05:42: 3000000 INFO @ Tue, 16 Jun 2020 09:05:43: 8000000 INFO @ Tue, 16 Jun 2020 09:05:46: 14000000 INFO @ Tue, 16 Jun 2020 09:05:49: 4000000 INFO @ Tue, 16 Jun 2020 09:05:50: 9000000 INFO @ Tue, 16 Jun 2020 09:05:51: #1 tag size is determined as 49 bps INFO @ Tue, 16 Jun 2020 09:05:51: #1 tag size = 49 INFO @ Tue, 16 Jun 2020 09:05:51: #1 total tags in treatment: 14834994 INFO @ Tue, 16 Jun 2020 09:05:51: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:05:51: #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 09:05:51: #1 tags after filtering in treatment: 14834994 INFO @ Tue, 16 Jun 2020 09:05:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:05:51: #1 finished! INFO @ Tue, 16 Jun 2020 09:05:51: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:05:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:05:53: #2 number of paired peaks: 2535 INFO @ Tue, 16 Jun 2020 09:05:53: start model_add_line... INFO @ Tue, 16 Jun 2020 09:05:53: start X-correlation... INFO @ Tue, 16 Jun 2020 09:05:53: end of X-cor INFO @ Tue, 16 Jun 2020 09:05:53: #2 finished! INFO @ Tue, 16 Jun 2020 09:05:53: #2 predicted fragment length is 157 bps INFO @ Tue, 16 Jun 2020 09:05:53: #2 alternative fragment length(s) may be 3,157 bps INFO @ Tue, 16 Jun 2020 09:05:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082363/SRX4082363.05_model.r INFO @ Tue, 16 Jun 2020 09:05:53: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:05:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:05:56: 5000000 INFO @ Tue, 16 Jun 2020 09:05:56: 10000000 INFO @ Tue, 16 Jun 2020 09:06:02: 11000000 INFO @ Tue, 16 Jun 2020 09:06:02: 6000000 INFO @ Tue, 16 Jun 2020 09:06:08: 12000000 INFO @ Tue, 16 Jun 2020 09:06:09: 7000000 INFO @ Tue, 16 Jun 2020 09:06:15: 13000000 INFO @ Tue, 16 Jun 2020 09:06:15: 8000000 INFO @ Tue, 16 Jun 2020 09:06:22: 14000000 INFO @ Tue, 16 Jun 2020 09:06:22: 9000000 INFO @ Tue, 16 Jun 2020 09:06:27: #1 tag size is determined as 49 bps INFO @ Tue, 16 Jun 2020 09:06:27: #1 tag size = 49 INFO @ Tue, 16 Jun 2020 09:06:27: #1 total tags in treatment: 14834994 INFO @ Tue, 16 Jun 2020 09:06:27: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:06:27: #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 09:06:27: #1 tags after filtering in treatment: 14834994 INFO @ Tue, 16 Jun 2020 09:06:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:06:27: #1 finished! INFO @ Tue, 16 Jun 2020 09:06:27: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:06:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:06:28: 10000000 INFO @ Tue, 16 Jun 2020 09:06:29: #2 number of paired peaks: 2535 INFO @ Tue, 16 Jun 2020 09:06:29: start model_add_line... INFO @ Tue, 16 Jun 2020 09:06:29: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:06:29: start X-correlation... INFO @ Tue, 16 Jun 2020 09:06:29: end of X-cor INFO @ Tue, 16 Jun 2020 09:06:29: #2 finished! INFO @ Tue, 16 Jun 2020 09:06:29: #2 predicted fragment length is 157 bps INFO @ Tue, 16 Jun 2020 09:06:29: #2 alternative fragment length(s) may be 3,157 bps INFO @ Tue, 16 Jun 2020 09:06:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082363/SRX4082363.10_model.r INFO @ Tue, 16 Jun 2020 09:06:29: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:06:29: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:06:34: 11000000 INFO @ Tue, 16 Jun 2020 09:06:40: 12000000 INFO @ Tue, 16 Jun 2020 09:06:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082363/SRX4082363.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:06:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082363/SRX4082363.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:06:45: 13000000 INFO @ Tue, 16 Jun 2020 09:06:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082363/SRX4082363.05_summits.bed INFO @ Tue, 16 Jun 2020 09:06:45: Done! pass1 - making usageList (6 chroms): 3 millis pass2 - checking and writing primary data (10537 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:06:51: 14000000 INFO @ Tue, 16 Jun 2020 09:06:55: #1 tag size is determined as 49 bps INFO @ Tue, 16 Jun 2020 09:06:55: #1 tag size = 49 INFO @ Tue, 16 Jun 2020 09:06:55: #1 total tags in treatment: 14834994 INFO @ Tue, 16 Jun 2020 09:06:55: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:06:55: #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 09:06:56: #1 tags after filtering in treatment: 14834994 INFO @ Tue, 16 Jun 2020 09:06:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:06:56: #1 finished! INFO @ Tue, 16 Jun 2020 09:06:56: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:06:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:06:57: #2 number of paired peaks: 2535 INFO @ Tue, 16 Jun 2020 09:06:57: start model_add_line... INFO @ Tue, 16 Jun 2020 09:06:57: start X-correlation... INFO @ Tue, 16 Jun 2020 09:06:57: end of X-cor INFO @ Tue, 16 Jun 2020 09:06:57: #2 finished! INFO @ Tue, 16 Jun 2020 09:06:57: #2 predicted fragment length is 157 bps INFO @ Tue, 16 Jun 2020 09:06:57: #2 alternative fragment length(s) may be 3,157 bps INFO @ Tue, 16 Jun 2020 09:06:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082363/SRX4082363.20_model.r INFO @ Tue, 16 Jun 2020 09:06:57: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:06:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:07:04: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:07:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082363/SRX4082363.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:07:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082363/SRX4082363.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:07:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082363/SRX4082363.10_summits.bed INFO @ Tue, 16 Jun 2020 09:07:20: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (6903 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:07:32: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:07:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082363/SRX4082363.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:07:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082363/SRX4082363.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:07:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082363/SRX4082363.20_summits.bed INFO @ Tue, 16 Jun 2020 09:07:48: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2815 records, 4 fields): 4 millis CompletedMACS2peakCalling