Job ID = 6528395 SRX = SRX5717033 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T14:59:59 prefetch.2.10.7: 1) Downloading 'SRR8936393'... 2020-06-29T14:59:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T15:02:44 prefetch.2.10.7: HTTPS download succeed 2020-06-29T15:02:44 prefetch.2.10.7: 1) 'SRR8936393' was downloaded successfully Read 25658952 spots for SRR8936393/SRR8936393.sra Written 25658952 spots for SRR8936393/SRR8936393.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: 00:06:31 25658952 reads; of these: 25658952 (100.00%) were unpaired; of these: 2873014 (11.20%) aligned 0 times 17749006 (69.17%) aligned exactly 1 time 5036932 (19.63%) aligned >1 times 88.80% overall alignment rate Time searching: 00:06:31 Overall time: 00:06:31 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] 8209795 / 22785938 = 0.3603 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, 30 Jun 2020 00:23:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5717033/SRX5717033.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5717033/SRX5717033.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5717033/SRX5717033.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5717033/SRX5717033.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 @ Tue, 30 Jun 2020 00:23:51: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:23:51: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:23:56: 1000000 INFO @ Tue, 30 Jun 2020 00:24:00: 2000000 INFO @ Tue, 30 Jun 2020 00:24:05: 3000000 INFO @ Tue, 30 Jun 2020 00:24:10: 4000000 INFO @ Tue, 30 Jun 2020 00:24:14: 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, 30 Jun 2020 00:24:19: 6000000 INFO @ Tue, 30 Jun 2020 00:24:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5717033/SRX5717033.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5717033/SRX5717033.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5717033/SRX5717033.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5717033/SRX5717033.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 @ Tue, 30 Jun 2020 00:24:21: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:24:21: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:24:24: 7000000 INFO @ Tue, 30 Jun 2020 00:24:26: 1000000 INFO @ Tue, 30 Jun 2020 00:24:29: 8000000 INFO @ Tue, 30 Jun 2020 00:24:31: 2000000 INFO @ Tue, 30 Jun 2020 00:24:34: 9000000 INFO @ Tue, 30 Jun 2020 00:24:37: 3000000 INFO @ Tue, 30 Jun 2020 00:24:40: 10000000 INFO @ Tue, 30 Jun 2020 00:24:42: 4000000 INFO @ Tue, 30 Jun 2020 00:24:45: 11000000 INFO @ Tue, 30 Jun 2020 00:24:48: 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 @ Tue, 30 Jun 2020 00:24:50: 12000000 INFO @ Tue, 30 Jun 2020 00:24:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5717033/SRX5717033.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5717033/SRX5717033.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5717033/SRX5717033.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5717033/SRX5717033.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 @ Tue, 30 Jun 2020 00:24:51: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:24:51: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:24:53: 6000000 INFO @ Tue, 30 Jun 2020 00:24:55: 13000000 INFO @ Tue, 30 Jun 2020 00:24:57: 1000000 INFO @ Tue, 30 Jun 2020 00:24:59: 7000000 INFO @ Tue, 30 Jun 2020 00:25:00: 14000000 INFO @ Tue, 30 Jun 2020 00:25:03: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:25:03: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:25:03: #1 total tags in treatment: 14576143 INFO @ Tue, 30 Jun 2020 00:25:03: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:25:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 00:25:03: #1 tags after filtering in treatment: 14576143 INFO @ Tue, 30 Jun 2020 00:25:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 00:25:03: #1 finished! INFO @ Tue, 30 Jun 2020 00:25:03: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:25:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:25:03: 2000000 INFO @ Tue, 30 Jun 2020 00:25:04: 8000000 INFO @ Tue, 30 Jun 2020 00:25:04: #2 number of paired peaks: 1897 INFO @ Tue, 30 Jun 2020 00:25:04: start model_add_line... INFO @ Tue, 30 Jun 2020 00:25:04: start X-correlation... INFO @ Tue, 30 Jun 2020 00:25:04: end of X-cor INFO @ Tue, 30 Jun 2020 00:25:04: #2 finished! INFO @ Tue, 30 Jun 2020 00:25:04: #2 predicted fragment length is 167 bps INFO @ Tue, 30 Jun 2020 00:25:04: #2 alternative fragment length(s) may be 61,79,90,121,137,167,189,195,234,289,498,528,570,592 bps INFO @ Tue, 30 Jun 2020 00:25:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5717033/SRX5717033.05_model.r INFO @ Tue, 30 Jun 2020 00:25:05: #3 Call peaks... INFO @ Tue, 30 Jun 2020 00:25:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 00:25:09: 9000000 INFO @ Tue, 30 Jun 2020 00:25:09: 3000000 INFO @ Tue, 30 Jun 2020 00:25:14: 10000000 INFO @ Tue, 30 Jun 2020 00:25:15: 4000000 INFO @ Tue, 30 Jun 2020 00:25:19: 11000000 INFO @ Tue, 30 Jun 2020 00:25:22: 5000000 INFO @ Tue, 30 Jun 2020 00:25:25: 12000000 INFO @ Tue, 30 Jun 2020 00:25:28: 6000000 INFO @ Tue, 30 Jun 2020 00:25:30: 13000000 INFO @ Tue, 30 Jun 2020 00:25:34: 7000000 INFO @ Tue, 30 Jun 2020 00:25:35: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 00:25:36: 14000000 INFO @ Tue, 30 Jun 2020 00:25:39: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:25:39: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:25:39: #1 total tags in treatment: 14576143 INFO @ Tue, 30 Jun 2020 00:25:39: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:25:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 00:25:40: #1 tags after filtering in treatment: 14576143 INFO @ Tue, 30 Jun 2020 00:25:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 00:25:40: #1 finished! INFO @ Tue, 30 Jun 2020 00:25:40: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:25:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:25:40: 8000000 INFO @ Tue, 30 Jun 2020 00:25:41: #2 number of paired peaks: 1897 INFO @ Tue, 30 Jun 2020 00:25:41: start model_add_line... INFO @ Tue, 30 Jun 2020 00:25:41: start X-correlation... INFO @ Tue, 30 Jun 2020 00:25:41: end of X-cor INFO @ Tue, 30 Jun 2020 00:25:41: #2 finished! INFO @ Tue, 30 Jun 2020 00:25:41: #2 predicted fragment length is 167 bps INFO @ Tue, 30 Jun 2020 00:25:41: #2 alternative fragment length(s) may be 61,79,90,121,137,167,189,195,234,289,498,528,570,592 bps INFO @ Tue, 30 Jun 2020 00:25:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5717033/SRX5717033.10_model.r INFO @ Tue, 30 Jun 2020 00:25:41: #3 Call peaks... INFO @ Tue, 30 Jun 2020 00:25:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 00:25:45: 9000000 INFO @ Tue, 30 Jun 2020 00:25:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5717033/SRX5717033.05_peaks.xls INFO @ Tue, 30 Jun 2020 00:25:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5717033/SRX5717033.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:25:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5717033/SRX5717033.05_summits.bed INFO @ Tue, 30 Jun 2020 00:25:50: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3030 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 00:25:51: 10000000 INFO @ Tue, 30 Jun 2020 00:25:57: 11000000 INFO @ Tue, 30 Jun 2020 00:26:03: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 00:26:09: 13000000 INFO @ Tue, 30 Jun 2020 00:26:12: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 00:26:15: 14000000 INFO @ Tue, 30 Jun 2020 00:26:18: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:26:18: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:26:18: #1 total tags in treatment: 14576143 INFO @ Tue, 30 Jun 2020 00:26:18: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:26:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 00:26:18: #1 tags after filtering in treatment: 14576143 INFO @ Tue, 30 Jun 2020 00:26:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 00:26:18: #1 finished! INFO @ Tue, 30 Jun 2020 00:26:18: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:26:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:26:20: #2 number of paired peaks: 1897 INFO @ Tue, 30 Jun 2020 00:26:20: start model_add_line... INFO @ Tue, 30 Jun 2020 00:26:20: start X-correlation... INFO @ Tue, 30 Jun 2020 00:26:20: end of X-cor INFO @ Tue, 30 Jun 2020 00:26:20: #2 finished! INFO @ Tue, 30 Jun 2020 00:26:20: #2 predicted fragment length is 167 bps INFO @ Tue, 30 Jun 2020 00:26:20: #2 alternative fragment length(s) may be 61,79,90,121,137,167,189,195,234,289,498,528,570,592 bps INFO @ Tue, 30 Jun 2020 00:26:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5717033/SRX5717033.20_model.r INFO @ Tue, 30 Jun 2020 00:26:20: #3 Call peaks... INFO @ Tue, 30 Jun 2020 00:26:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 00:26:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5717033/SRX5717033.10_peaks.xls INFO @ Tue, 30 Jun 2020 00:26:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5717033/SRX5717033.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:26:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5717033/SRX5717033.10_summits.bed INFO @ Tue, 30 Jun 2020 00:26:26: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1271 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 00:26:52: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 00:27:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5717033/SRX5717033.20_peaks.xls INFO @ Tue, 30 Jun 2020 00:27:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5717033/SRX5717033.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:27:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5717033/SRX5717033.20_summits.bed INFO @ Tue, 30 Jun 2020 00:27:06: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (566 records, 4 fields): 2 millis CompletedMACS2peakCalling