Job ID = 6367750 SRX = SRX4082364 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:36:14 prefetch.2.10.7: 1) Downloading 'SRR7164182'... 2020-06-15T23:36:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:42:51 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:42:51 prefetch.2.10.7: 1) 'SRR7164182' was downloaded successfully Read 32928597 spots for SRR7164182/SRR7164182.sra Written 32928597 spots for SRR7164182/SRR7164182.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: 00:07:11 32928597 reads; of these: 32928597 (100.00%) were unpaired; of these: 843211 (2.56%) aligned 0 times 29024489 (88.14%) aligned exactly 1 time 3060897 (9.30%) aligned >1 times 97.44% overall alignment rate Time searching: 00:07:11 Overall time: 00:07:11 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] 10908826 / 32085386 = 0.3400 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 09:00:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082364/SRX4082364.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082364/SRX4082364.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082364/SRX4082364.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082364/SRX4082364.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 09:00:13: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:00:13: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:00:20: 1000000 INFO @ Tue, 16 Jun 2020 09:00:28: 2000000 INFO @ Tue, 16 Jun 2020 09:00:36: 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 09:00:44: 4000000 INFO @ Tue, 16 Jun 2020 09:00:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082364/SRX4082364.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082364/SRX4082364.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082364/SRX4082364.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082364/SRX4082364.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 09:00:44: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:00:44: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:00:51: 1000000 INFO @ Tue, 16 Jun 2020 09:00:52: 5000000 INFO @ Tue, 16 Jun 2020 09:00:59: 2000000 INFO @ Tue, 16 Jun 2020 09:01:00: 6000000 INFO @ Tue, 16 Jun 2020 09:01:06: 3000000 INFO @ Tue, 16 Jun 2020 09:01:08: 7000000 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 09:01:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082364/SRX4082364.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082364/SRX4082364.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082364/SRX4082364.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082364/SRX4082364.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 09:01:13: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:01:13: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:01:14: 4000000 INFO @ Tue, 16 Jun 2020 09:01:16: 8000000 INFO @ Tue, 16 Jun 2020 09:01:20: 1000000 INFO @ Tue, 16 Jun 2020 09:01:21: 5000000 INFO @ Tue, 16 Jun 2020 09:01:24: 9000000 INFO @ Tue, 16 Jun 2020 09:01:28: 2000000 INFO @ Tue, 16 Jun 2020 09:01:29: 6000000 INFO @ Tue, 16 Jun 2020 09:01:32: 10000000 INFO @ Tue, 16 Jun 2020 09:01:36: 3000000 INFO @ Tue, 16 Jun 2020 09:01:37: 7000000 INFO @ Tue, 16 Jun 2020 09:01:40: 11000000 INFO @ Tue, 16 Jun 2020 09:01:43: 4000000 INFO @ Tue, 16 Jun 2020 09:01:44: 8000000 INFO @ Tue, 16 Jun 2020 09:01:48: 12000000 INFO @ Tue, 16 Jun 2020 09:01:51: 5000000 INFO @ Tue, 16 Jun 2020 09:01:52: 9000000 INFO @ Tue, 16 Jun 2020 09:01:57: 13000000 INFO @ Tue, 16 Jun 2020 09:01:59: 6000000 INFO @ Tue, 16 Jun 2020 09:01:59: 10000000 INFO @ Tue, 16 Jun 2020 09:02:05: 14000000 INFO @ Tue, 16 Jun 2020 09:02:06: 7000000 INFO @ Tue, 16 Jun 2020 09:02:07: 11000000 INFO @ Tue, 16 Jun 2020 09:02:13: 15000000 INFO @ Tue, 16 Jun 2020 09:02:14: 8000000 INFO @ Tue, 16 Jun 2020 09:02:15: 12000000 INFO @ Tue, 16 Jun 2020 09:02:21: 16000000 INFO @ Tue, 16 Jun 2020 09:02:21: 9000000 INFO @ Tue, 16 Jun 2020 09:02:22: 13000000 INFO @ Tue, 16 Jun 2020 09:02:29: 10000000 INFO @ Tue, 16 Jun 2020 09:02:29: 17000000 INFO @ Tue, 16 Jun 2020 09:02:30: 14000000 INFO @ Tue, 16 Jun 2020 09:02:37: 11000000 INFO @ Tue, 16 Jun 2020 09:02:37: 18000000 INFO @ Tue, 16 Jun 2020 09:02:38: 15000000 INFO @ Tue, 16 Jun 2020 09:02:44: 12000000 INFO @ Tue, 16 Jun 2020 09:02:46: 16000000 INFO @ Tue, 16 Jun 2020 09:02:46: 19000000 INFO @ Tue, 16 Jun 2020 09:02:52: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:02:53: 17000000 INFO @ Tue, 16 Jun 2020 09:02:54: 20000000 INFO @ Tue, 16 Jun 2020 09:03:00: 14000000 INFO @ Tue, 16 Jun 2020 09:03:01: 18000000 INFO @ Tue, 16 Jun 2020 09:03:02: 21000000 INFO @ Tue, 16 Jun 2020 09:03:03: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:03:03: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:03:03: #1 total tags in treatment: 21176560 INFO @ Tue, 16 Jun 2020 09:03:03: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:03:03: #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 09:03:04: #1 tags after filtering in treatment: 21176560 INFO @ Tue, 16 Jun 2020 09:03:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:03:04: #1 finished! INFO @ Tue, 16 Jun 2020 09:03:04: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:03:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:03:06: #2 number of paired peaks: 1778 INFO @ Tue, 16 Jun 2020 09:03:06: start model_add_line... INFO @ Tue, 16 Jun 2020 09:03:06: start X-correlation... INFO @ Tue, 16 Jun 2020 09:03:06: end of X-cor INFO @ Tue, 16 Jun 2020 09:03:06: #2 finished! INFO @ Tue, 16 Jun 2020 09:03:06: #2 predicted fragment length is 105 bps INFO @ Tue, 16 Jun 2020 09:03:06: #2 alternative fragment length(s) may be 2,84,105,119 bps INFO @ Tue, 16 Jun 2020 09:03:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082364/SRX4082364.05_model.r INFO @ Tue, 16 Jun 2020 09:03:06: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:03:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:03:07: 15000000 INFO @ Tue, 16 Jun 2020 09:03:08: 19000000 INFO @ Tue, 16 Jun 2020 09:03:14: 16000000 INFO @ Tue, 16 Jun 2020 09:03:15: 20000000 INFO @ Tue, 16 Jun 2020 09:03:21: 17000000 INFO @ Tue, 16 Jun 2020 09:03:22: 21000000 INFO @ Tue, 16 Jun 2020 09:03:23: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:03:23: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:03:23: #1 total tags in treatment: 21176560 INFO @ Tue, 16 Jun 2020 09:03:23: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:03:23: #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 09:03:24: #1 tags after filtering in treatment: 21176560 INFO @ Tue, 16 Jun 2020 09:03:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:03:24: #1 finished! INFO @ Tue, 16 Jun 2020 09:03:24: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:03:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:03:26: #2 number of paired peaks: 1778 INFO @ Tue, 16 Jun 2020 09:03:26: start model_add_line... INFO @ Tue, 16 Jun 2020 09:03:26: start X-correlation... INFO @ Tue, 16 Jun 2020 09:03:26: end of X-cor INFO @ Tue, 16 Jun 2020 09:03:26: #2 finished! INFO @ Tue, 16 Jun 2020 09:03:26: #2 predicted fragment length is 105 bps INFO @ Tue, 16 Jun 2020 09:03:26: #2 alternative fragment length(s) may be 2,84,105,119 bps INFO @ Tue, 16 Jun 2020 09:03:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082364/SRX4082364.10_model.r INFO @ Tue, 16 Jun 2020 09:03:26: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:03:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:03:28: 18000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:03:34: 19000000 INFO @ Tue, 16 Jun 2020 09:03:41: 20000000 INFO @ Tue, 16 Jun 2020 09:03:47: 21000000 INFO @ Tue, 16 Jun 2020 09:03:49: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:03:49: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:03:49: #1 total tags in treatment: 21176560 INFO @ Tue, 16 Jun 2020 09:03:49: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:03:49: #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 09:03:49: #1 tags after filtering in treatment: 21176560 INFO @ Tue, 16 Jun 2020 09:03:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:03:49: #1 finished! INFO @ Tue, 16 Jun 2020 09:03:49: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:03:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:03:51: #2 number of paired peaks: 1778 INFO @ Tue, 16 Jun 2020 09:03:51: start model_add_line... INFO @ Tue, 16 Jun 2020 09:03:51: start X-correlation... INFO @ Tue, 16 Jun 2020 09:03:51: end of X-cor INFO @ Tue, 16 Jun 2020 09:03:51: #2 finished! INFO @ Tue, 16 Jun 2020 09:03:51: #2 predicted fragment length is 105 bps INFO @ Tue, 16 Jun 2020 09:03:51: #2 alternative fragment length(s) may be 2,84,105,119 bps INFO @ Tue, 16 Jun 2020 09:03:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082364/SRX4082364.20_model.r INFO @ Tue, 16 Jun 2020 09:03:51: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:03:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:03:51: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:04:11: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:04:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082364/SRX4082364.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:04:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082364/SRX4082364.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:04:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082364/SRX4082364.05_summits.bed INFO @ Tue, 16 Jun 2020 09:04:13: Done! pass1 - making usageList (6 chroms): 3 millis pass2 - checking and writing primary data (13430 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:04:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082364/SRX4082364.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:04:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082364/SRX4082364.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:04:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082364/SRX4082364.10_summits.bed INFO @ Tue, 16 Jun 2020 09:04:32: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (8364 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:04:35: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:04:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082364/SRX4082364.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:04:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082364/SRX4082364.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:04:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082364/SRX4082364.20_summits.bed INFO @ Tue, 16 Jun 2020 09:04:56: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2834 records, 4 fields): 4 millis CompletedMACS2peakCalling