Job ID = 6498057 SRX = SRX297099 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T22:57:12 prefetch.2.10.7: 1) Downloading 'SRR886300'... 2020-06-25T22:57:12 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T23:00:07 prefetch.2.10.7: HTTPS download succeed 2020-06-25T23:00:07 prefetch.2.10.7: 1) 'SRR886300' was downloaded successfully Read 30098109 spots for SRR886300/SRR886300.sra Written 30098109 spots for SRR886300/SRR886300.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: 00:16:17 30098109 reads; of these: 30098109 (100.00%) were unpaired; of these: 2023184 (6.72%) aligned 0 times 13503988 (44.87%) aligned exactly 1 time 14570937 (48.41%) aligned >1 times 93.28% overall alignment rate Time searching: 00:16:17 Overall time: 00:16:17 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 16557039 / 28074925 = 0.5897 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 @ Fri, 26 Jun 2020 08:24:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX297099/SRX297099.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX297099/SRX297099.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX297099/SRX297099.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX297099/SRX297099.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 @ Fri, 26 Jun 2020 08:24:08: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:24:08: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:24:15: 1000000 INFO @ Fri, 26 Jun 2020 08:24:22: 2000000 INFO @ Fri, 26 Jun 2020 08:24:29: 3000000 INFO @ Fri, 26 Jun 2020 08:24:35: 4000000 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 @ Fri, 26 Jun 2020 08:24:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX297099/SRX297099.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX297099/SRX297099.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX297099/SRX297099.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX297099/SRX297099.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 @ Fri, 26 Jun 2020 08:24:39: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:24:39: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:24:41: 5000000 INFO @ Fri, 26 Jun 2020 08:24:44: 1000000 INFO @ Fri, 26 Jun 2020 08:24:48: 6000000 INFO @ Fri, 26 Jun 2020 08:24:50: 2000000 INFO @ Fri, 26 Jun 2020 08:24:54: 7000000 INFO @ Fri, 26 Jun 2020 08:24:55: 3000000 INFO @ Fri, 26 Jun 2020 08:25:00: 8000000 INFO @ Fri, 26 Jun 2020 08:25:01: 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 @ Fri, 26 Jun 2020 08:25:06: 9000000 INFO @ Fri, 26 Jun 2020 08:25:06: 5000000 INFO @ Fri, 26 Jun 2020 08:25:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX297099/SRX297099.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX297099/SRX297099.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX297099/SRX297099.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX297099/SRX297099.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 @ Fri, 26 Jun 2020 08:25:08: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:25:08: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:25:12: 6000000 INFO @ Fri, 26 Jun 2020 08:25:13: 10000000 INFO @ Fri, 26 Jun 2020 08:25:14: 1000000 INFO @ Fri, 26 Jun 2020 08:25:18: 7000000 INFO @ Fri, 26 Jun 2020 08:25:19: 11000000 INFO @ Fri, 26 Jun 2020 08:25:21: 2000000 INFO @ Fri, 26 Jun 2020 08:25:23: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:25:23: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:25:23: #1 total tags in treatment: 11517886 INFO @ Fri, 26 Jun 2020 08:25:23: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:25:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 08:25:23: #1 tags after filtering in treatment: 11517886 INFO @ Fri, 26 Jun 2020 08:25:23: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:25:23: #1 finished! INFO @ Fri, 26 Jun 2020 08:25:23: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:25:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:25:23: 8000000 INFO @ Fri, 26 Jun 2020 08:25:24: #2 number of paired peaks: 1966 INFO @ Fri, 26 Jun 2020 08:25:24: start model_add_line... INFO @ Fri, 26 Jun 2020 08:25:24: start X-correlation... INFO @ Fri, 26 Jun 2020 08:25:24: end of X-cor INFO @ Fri, 26 Jun 2020 08:25:24: #2 finished! INFO @ Fri, 26 Jun 2020 08:25:24: #2 predicted fragment length is 115 bps INFO @ Fri, 26 Jun 2020 08:25:24: #2 alternative fragment length(s) may be 115 bps INFO @ Fri, 26 Jun 2020 08:25:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX297099/SRX297099.05_model.r INFO @ Fri, 26 Jun 2020 08:25:24: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:25:24: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:25:27: 3000000 INFO @ Fri, 26 Jun 2020 08:25:29: 9000000 INFO @ Fri, 26 Jun 2020 08:25:34: 4000000 INFO @ Fri, 26 Jun 2020 08:25:34: 10000000 INFO @ Fri, 26 Jun 2020 08:25:40: 11000000 INFO @ Fri, 26 Jun 2020 08:25:40: 5000000 INFO @ Fri, 26 Jun 2020 08:25:43: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:25:43: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:25:43: #1 total tags in treatment: 11517886 INFO @ Fri, 26 Jun 2020 08:25:43: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:25:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 08:25:43: #1 tags after filtering in treatment: 11517886 INFO @ Fri, 26 Jun 2020 08:25:43: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:25:43: #1 finished! INFO @ Fri, 26 Jun 2020 08:25:43: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:25:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:25:44: #2 number of paired peaks: 1966 INFO @ Fri, 26 Jun 2020 08:25:44: start model_add_line... INFO @ Fri, 26 Jun 2020 08:25:44: start X-correlation... INFO @ Fri, 26 Jun 2020 08:25:44: end of X-cor INFO @ Fri, 26 Jun 2020 08:25:44: #2 finished! INFO @ Fri, 26 Jun 2020 08:25:44: #2 predicted fragment length is 115 bps INFO @ Fri, 26 Jun 2020 08:25:44: #2 alternative fragment length(s) may be 115 bps INFO @ Fri, 26 Jun 2020 08:25:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX297099/SRX297099.10_model.r INFO @ Fri, 26 Jun 2020 08:25:44: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:25:44: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:25:47: 6000000 INFO @ Fri, 26 Jun 2020 08:25:52: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:25:53: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 08:26:00: 8000000 INFO @ Fri, 26 Jun 2020 08:26:06: 9000000 INFO @ Fri, 26 Jun 2020 08:26:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX297099/SRX297099.05_peaks.xls INFO @ Fri, 26 Jun 2020 08:26:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX297099/SRX297099.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:26:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX297099/SRX297099.05_summits.bed INFO @ Fri, 26 Jun 2020 08:26:08: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (19658 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:26:11: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:26:13: 10000000 INFO @ Fri, 26 Jun 2020 08:26:20: 11000000 INFO @ Fri, 26 Jun 2020 08:26:23: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:26:23: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:26:23: #1 total tags in treatment: 11517886 INFO @ Fri, 26 Jun 2020 08:26:23: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:26:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 08:26:23: #1 tags after filtering in treatment: 11517886 INFO @ Fri, 26 Jun 2020 08:26:23: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:26:23: #1 finished! INFO @ Fri, 26 Jun 2020 08:26:23: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:26:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:26:24: #2 number of paired peaks: 1966 INFO @ Fri, 26 Jun 2020 08:26:24: start model_add_line... INFO @ Fri, 26 Jun 2020 08:26:24: start X-correlation... INFO @ Fri, 26 Jun 2020 08:26:24: end of X-cor INFO @ Fri, 26 Jun 2020 08:26:24: #2 finished! INFO @ Fri, 26 Jun 2020 08:26:24: #2 predicted fragment length is 115 bps INFO @ Fri, 26 Jun 2020 08:26:24: #2 alternative fragment length(s) may be 115 bps INFO @ Fri, 26 Jun 2020 08:26:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX297099/SRX297099.20_model.r INFO @ Fri, 26 Jun 2020 08:26:24: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:26:24: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 08:26:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX297099/SRX297099.10_peaks.xls INFO @ Fri, 26 Jun 2020 08:26:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX297099/SRX297099.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:26:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX297099/SRX297099.10_summits.bed INFO @ Fri, 26 Jun 2020 08:26:26: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (10843 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:26:54: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:27:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX297099/SRX297099.20_peaks.xls INFO @ Fri, 26 Jun 2020 08:27:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX297099/SRX297099.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:27:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX297099/SRX297099.20_summits.bed INFO @ Fri, 26 Jun 2020 08:27:08: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5034 records, 4 fields): 7 millis CompletedMACS2peakCalling