Job ID = 6454716 SRX = SRX2541749 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:35:40 prefetch.2.10.7: 1) Downloading 'SRR5234223'... 2020-06-21T09:35:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:41:05 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:41:05 prefetch.2.10.7: 1) 'SRR5234223' was downloaded successfully Read 17755470 spots for SRR5234223/SRR5234223.sra Written 17755470 spots for SRR5234223/SRR5234223.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: 00:04:05 17755470 reads; of these: 17755470 (100.00%) were unpaired; of these: 6250684 (35.20%) aligned 0 times 8326457 (46.90%) aligned exactly 1 time 3178329 (17.90%) aligned >1 times 64.80% overall alignment rate Time searching: 00:04:05 Overall time: 00:04:05 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] 2019080 / 11504786 = 0.1755 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 18:49:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2541749/SRX2541749.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2541749/SRX2541749.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2541749/SRX2541749.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2541749/SRX2541749.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 18:49:30: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:49:30: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:49:36: 1000000 INFO @ Sun, 21 Jun 2020 18:49:42: 2000000 INFO @ Sun, 21 Jun 2020 18:49:47: 3000000 INFO @ Sun, 21 Jun 2020 18:49:53: 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 @ Sun, 21 Jun 2020 18:49:59: 5000000 INFO @ Sun, 21 Jun 2020 18:50:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2541749/SRX2541749.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2541749/SRX2541749.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2541749/SRX2541749.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2541749/SRX2541749.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 18:50:00: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:50:00: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:50:04: 6000000 INFO @ Sun, 21 Jun 2020 18:50:06: 1000000 INFO @ Sun, 21 Jun 2020 18:50:10: 7000000 INFO @ Sun, 21 Jun 2020 18:50:12: 2000000 INFO @ Sun, 21 Jun 2020 18:50:17: 8000000 INFO @ Sun, 21 Jun 2020 18:50:18: 3000000 INFO @ Sun, 21 Jun 2020 18:50:22: 9000000 INFO @ Sun, 21 Jun 2020 18:50:24: 4000000 INFO @ Sun, 21 Jun 2020 18:50:25: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:50:25: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:50:25: #1 total tags in treatment: 9485706 INFO @ Sun, 21 Jun 2020 18:50:25: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:50:25: #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 18:50:26: #1 tags after filtering in treatment: 9485706 INFO @ Sun, 21 Jun 2020 18:50:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:50:26: #1 finished! INFO @ Sun, 21 Jun 2020 18:50:26: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:50:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:50:27: #2 number of paired peaks: 1766 INFO @ Sun, 21 Jun 2020 18:50:27: start model_add_line... INFO @ Sun, 21 Jun 2020 18:50:27: start X-correlation... INFO @ Sun, 21 Jun 2020 18:50:27: end of X-cor INFO @ Sun, 21 Jun 2020 18:50:27: #2 finished! INFO @ Sun, 21 Jun 2020 18:50:27: #2 predicted fragment length is 165 bps INFO @ Sun, 21 Jun 2020 18:50:27: #2 alternative fragment length(s) may be 165 bps INFO @ Sun, 21 Jun 2020 18:50:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2541749/SRX2541749.05_model.r INFO @ Sun, 21 Jun 2020 18:50:27: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:50:27: #3 Pre-compute pvalue-qvalue table... 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 18:50:29: 5000000 INFO @ Sun, 21 Jun 2020 18:50:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2541749/SRX2541749.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2541749/SRX2541749.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2541749/SRX2541749.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2541749/SRX2541749.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 18:50:30: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:50:30: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:50:35: 6000000 INFO @ Sun, 21 Jun 2020 18:50:36: 1000000 INFO @ Sun, 21 Jun 2020 18:50:41: 7000000 INFO @ Sun, 21 Jun 2020 18:50:42: 2000000 INFO @ Sun, 21 Jun 2020 18:50:48: 8000000 INFO @ Sun, 21 Jun 2020 18:50:48: 3000000 INFO @ Sun, 21 Jun 2020 18:50:49: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:50:53: 9000000 INFO @ Sun, 21 Jun 2020 18:50:54: 4000000 INFO @ Sun, 21 Jun 2020 18:50:56: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:50:56: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:50:56: #1 total tags in treatment: 9485706 INFO @ Sun, 21 Jun 2020 18:50:56: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:50:56: #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 18:50:57: #1 tags after filtering in treatment: 9485706 INFO @ Sun, 21 Jun 2020 18:50:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:50:57: #1 finished! INFO @ Sun, 21 Jun 2020 18:50:57: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:50:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:50:58: #2 number of paired peaks: 1766 INFO @ Sun, 21 Jun 2020 18:50:58: start model_add_line... INFO @ Sun, 21 Jun 2020 18:50:58: start X-correlation... INFO @ Sun, 21 Jun 2020 18:50:58: end of X-cor INFO @ Sun, 21 Jun 2020 18:50:58: #2 finished! INFO @ Sun, 21 Jun 2020 18:50:58: #2 predicted fragment length is 165 bps INFO @ Sun, 21 Jun 2020 18:50:58: #2 alternative fragment length(s) may be 165 bps INFO @ Sun, 21 Jun 2020 18:50:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2541749/SRX2541749.10_model.r INFO @ Sun, 21 Jun 2020 18:50:58: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:50:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:50:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2541749/SRX2541749.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:50:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2541749/SRX2541749.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:50:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2541749/SRX2541749.05_summits.bed INFO @ Sun, 21 Jun 2020 18:50:59: Done! INFO @ Sun, 21 Jun 2020 18:51:00: 5000000 pass1 - making usageList (560 chroms): 1 millis pass2 - checking and writing primary data (4441 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:51:06: 6000000 INFO @ Sun, 21 Jun 2020 18:51:11: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:51:17: 8000000 INFO @ Sun, 21 Jun 2020 18:51:20: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:51:23: 9000000 INFO @ Sun, 21 Jun 2020 18:51:26: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:51:26: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:51:26: #1 total tags in treatment: 9485706 INFO @ Sun, 21 Jun 2020 18:51:26: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:51:26: #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 18:51:26: #1 tags after filtering in treatment: 9485706 INFO @ Sun, 21 Jun 2020 18:51:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:51:26: #1 finished! INFO @ Sun, 21 Jun 2020 18:51:26: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:51:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:51:27: #2 number of paired peaks: 1766 INFO @ Sun, 21 Jun 2020 18:51:27: start model_add_line... INFO @ Sun, 21 Jun 2020 18:51:27: start X-correlation... INFO @ Sun, 21 Jun 2020 18:51:27: end of X-cor INFO @ Sun, 21 Jun 2020 18:51:27: #2 finished! INFO @ Sun, 21 Jun 2020 18:51:27: #2 predicted fragment length is 165 bps INFO @ Sun, 21 Jun 2020 18:51:27: #2 alternative fragment length(s) may be 165 bps INFO @ Sun, 21 Jun 2020 18:51:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2541749/SRX2541749.20_model.r INFO @ Sun, 21 Jun 2020 18:51:27: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:51:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:51:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2541749/SRX2541749.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:51:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2541749/SRX2541749.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:51:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2541749/SRX2541749.10_summits.bed INFO @ Sun, 21 Jun 2020 18:51:31: Done! pass1 - making usageList (490 chroms): 1 millis pass2 - checking and writing primary data (3032 records, 4 fields): 16 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:51:49: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:52:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2541749/SRX2541749.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:52:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2541749/SRX2541749.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:52:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2541749/SRX2541749.20_summits.bed INFO @ Sun, 21 Jun 2020 18:52:00: Done! pass1 - making usageList (423 chroms): 1 millis pass2 - checking and writing primary data (1921 records, 4 fields): 13 millis CompletedMACS2peakCalling