Job ID = 6458298 SRX = SRX5011054 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:26:22 prefetch.2.10.7: 1) Downloading 'SRR8191503'... 2020-06-21T12:26:22 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:29:07 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:29:08 prefetch.2.10.7: 'SRR8191503' is valid 2020-06-21T12:29:08 prefetch.2.10.7: 1) 'SRR8191503' was downloaded successfully 2020-06-21T12:29:08 prefetch.2.10.7: 'SRR8191503' has 0 unresolved dependencies Read 32955638 spots for SRR8191503/SRR8191503.sra Written 32955638 spots for SRR8191503/SRR8191503.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: 00:06:14 32955638 reads; of these: 32955638 (100.00%) were unpaired; of these: 13598772 (41.26%) aligned 0 times 15031985 (45.61%) aligned exactly 1 time 4324881 (13.12%) aligned >1 times 58.74% overall alignment rate Time searching: 00:06:14 Overall time: 00:06:14 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 11628924 / 19356866 = 0.6008 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 @ Sun, 21 Jun 2020 21:40:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011054/SRX5011054.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011054/SRX5011054.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011054/SRX5011054.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011054/SRX5011054.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 21:40:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:40:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:40:15: 1000000 INFO @ Sun, 21 Jun 2020 21:40:20: 2000000 INFO @ Sun, 21 Jun 2020 21:40:25: 3000000 INFO @ Sun, 21 Jun 2020 21:40:30: 4000000 INFO @ Sun, 21 Jun 2020 21:40:36: 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 @ Sun, 21 Jun 2020 21:40:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011054/SRX5011054.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011054/SRX5011054.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011054/SRX5011054.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011054/SRX5011054.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 21:40:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:40:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:40:41: 6000000 INFO @ Sun, 21 Jun 2020 21:40:45: 1000000 INFO @ Sun, 21 Jun 2020 21:40:47: 7000000 INFO @ Sun, 21 Jun 2020 21:40:51: 2000000 INFO @ Sun, 21 Jun 2020 21:40:51: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:40:51: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:40:51: #1 total tags in treatment: 7727942 INFO @ Sun, 21 Jun 2020 21:40:51: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:40:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 21:40:52: #1 tags after filtering in treatment: 7727842 INFO @ Sun, 21 Jun 2020 21:40:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:40:52: #1 finished! INFO @ Sun, 21 Jun 2020 21:40:52: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:40:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:40:52: #2 number of paired peaks: 3875 INFO @ Sun, 21 Jun 2020 21:40:52: start model_add_line... INFO @ Sun, 21 Jun 2020 21:40:52: start X-correlation... INFO @ Sun, 21 Jun 2020 21:40:52: end of X-cor INFO @ Sun, 21 Jun 2020 21:40:52: #2 finished! INFO @ Sun, 21 Jun 2020 21:40:52: #2 predicted fragment length is 172 bps INFO @ Sun, 21 Jun 2020 21:40:52: #2 alternative fragment length(s) may be 172 bps INFO @ Sun, 21 Jun 2020 21:40:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011054/SRX5011054.05_model.r INFO @ Sun, 21 Jun 2020 21:40:52: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:40:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:40:56: 3000000 INFO @ Sun, 21 Jun 2020 21:41:02: 4000000 INFO @ Sun, 21 Jun 2020 21:41:07: 5000000 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 @ Sun, 21 Jun 2020 21:41:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011054/SRX5011054.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011054/SRX5011054.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011054/SRX5011054.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011054/SRX5011054.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 21:41:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:41:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:41:12: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:41:13: 6000000 INFO @ Sun, 21 Jun 2020 21:41:17: 1000000 INFO @ Sun, 21 Jun 2020 21:41:19: 7000000 INFO @ Sun, 21 Jun 2020 21:41:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011054/SRX5011054.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:41:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011054/SRX5011054.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:41:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011054/SRX5011054.05_summits.bed INFO @ Sun, 21 Jun 2020 21:41:22: Done! pass1 - making usageList (731 chroms): 2 millis pass2 - checking and writing primary data (6969 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:41:24: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:41:24: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:41:24: #1 total tags in treatment: 7727942 INFO @ Sun, 21 Jun 2020 21:41:24: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:41:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 21:41:24: #1 tags after filtering in treatment: 7727842 INFO @ Sun, 21 Jun 2020 21:41:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:41:24: #1 finished! INFO @ Sun, 21 Jun 2020 21:41:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:41:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:41:25: 2000000 INFO @ Sun, 21 Jun 2020 21:41:25: #2 number of paired peaks: 3875 INFO @ Sun, 21 Jun 2020 21:41:25: start model_add_line... INFO @ Sun, 21 Jun 2020 21:41:25: start X-correlation... INFO @ Sun, 21 Jun 2020 21:41:25: end of X-cor INFO @ Sun, 21 Jun 2020 21:41:25: #2 finished! INFO @ Sun, 21 Jun 2020 21:41:25: #2 predicted fragment length is 172 bps INFO @ Sun, 21 Jun 2020 21:41:25: #2 alternative fragment length(s) may be 172 bps INFO @ Sun, 21 Jun 2020 21:41:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011054/SRX5011054.10_model.r INFO @ Sun, 21 Jun 2020 21:41:25: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:41:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:41:32: 3000000 INFO @ Sun, 21 Jun 2020 21:41:38: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:41:45: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:41:45: 5000000 INFO @ Sun, 21 Jun 2020 21:41:52: 6000000 INFO @ Sun, 21 Jun 2020 21:41:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011054/SRX5011054.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:41:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011054/SRX5011054.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:41:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011054/SRX5011054.10_summits.bed INFO @ Sun, 21 Jun 2020 21:41:54: Done! pass1 - making usageList (635 chroms): 2 millis pass2 - checking and writing primary data (4778 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:41:59: 7000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:42:04: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:42:04: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:42:04: #1 total tags in treatment: 7727942 INFO @ Sun, 21 Jun 2020 21:42:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:42:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 21:42:05: #1 tags after filtering in treatment: 7727842 INFO @ Sun, 21 Jun 2020 21:42:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:42:05: #1 finished! INFO @ Sun, 21 Jun 2020 21:42:05: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:42:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:42:05: #2 number of paired peaks: 3875 INFO @ Sun, 21 Jun 2020 21:42:05: start model_add_line... INFO @ Sun, 21 Jun 2020 21:42:05: start X-correlation... INFO @ Sun, 21 Jun 2020 21:42:05: end of X-cor INFO @ Sun, 21 Jun 2020 21:42:05: #2 finished! INFO @ Sun, 21 Jun 2020 21:42:05: #2 predicted fragment length is 172 bps INFO @ Sun, 21 Jun 2020 21:42:05: #2 alternative fragment length(s) may be 172 bps INFO @ Sun, 21 Jun 2020 21:42:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011054/SRX5011054.20_model.r INFO @ Sun, 21 Jun 2020 21:42:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:42:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:42:25: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:42:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011054/SRX5011054.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:42:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011054/SRX5011054.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:42:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011054/SRX5011054.20_summits.bed INFO @ Sun, 21 Jun 2020 21:42:34: Done! pass1 - making usageList (472 chroms): 1 millis pass2 - checking and writing primary data (2855 records, 4 fields): 16 millis CompletedMACS2peakCalling