Job ID = 6498307 SRX = SRX467118 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T23:18:07 prefetch.2.10.7: 1) Downloading 'SRR1164542'... 2020-06-25T23:18:07 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T23:20:36 prefetch.2.10.7: HTTPS download succeed 2020-06-25T23:20:37 prefetch.2.10.7: 'SRR1164542' is valid 2020-06-25T23:20:37 prefetch.2.10.7: 1) 'SRR1164542' was downloaded successfully Read 14747011 spots for SRR1164542/SRR1164542.sra Written 14747011 spots for SRR1164542/SRR1164542.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: 00:04:28 14747011 reads; of these: 14747011 (100.00%) were unpaired; of these: 892625 (6.05%) aligned 0 times 10980950 (74.46%) aligned exactly 1 time 2873436 (19.48%) aligned >1 times 93.95% overall alignment rate Time searching: 00:04:28 Overall time: 00:04:28 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 8 files... [bam_rmdupse_core] 2000854 / 13854386 = 0.1444 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 08:30:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467118/SRX467118.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467118/SRX467118.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467118/SRX467118.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467118/SRX467118.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 08:30:01: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:30:01: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:30:08: 1000000 INFO @ Fri, 26 Jun 2020 08:30:14: 2000000 INFO @ Fri, 26 Jun 2020 08:30:21: 3000000 INFO @ Fri, 26 Jun 2020 08:30:27: 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 08:30:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467118/SRX467118.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467118/SRX467118.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467118/SRX467118.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467118/SRX467118.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 08:30:31: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:30:31: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:30:34: 5000000 INFO @ Fri, 26 Jun 2020 08:30:38: 1000000 INFO @ Fri, 26 Jun 2020 08:30:41: 6000000 INFO @ Fri, 26 Jun 2020 08:30:45: 2000000 INFO @ Fri, 26 Jun 2020 08:30:47: 7000000 INFO @ Fri, 26 Jun 2020 08:30:51: 3000000 INFO @ Fri, 26 Jun 2020 08:30:54: 8000000 INFO @ Fri, 26 Jun 2020 08:30:58: 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 08:31:01: 9000000 INFO @ Fri, 26 Jun 2020 08:31:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467118/SRX467118.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467118/SRX467118.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467118/SRX467118.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467118/SRX467118.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 08:31:02: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:31:02: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:31:05: 5000000 INFO @ Fri, 26 Jun 2020 08:31:08: 10000000 INFO @ Fri, 26 Jun 2020 08:31:08: 1000000 INFO @ Fri, 26 Jun 2020 08:31:11: 6000000 INFO @ Fri, 26 Jun 2020 08:31:14: 2000000 INFO @ Fri, 26 Jun 2020 08:31:14: 11000000 INFO @ Fri, 26 Jun 2020 08:31:18: 7000000 INFO @ Fri, 26 Jun 2020 08:31:20: 3000000 INFO @ Fri, 26 Jun 2020 08:31:20: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:31:20: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:31:20: #1 total tags in treatment: 11853532 INFO @ Fri, 26 Jun 2020 08:31:20: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:31:20: #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 08:31:21: #1 tags after filtering in treatment: 11853532 INFO @ Fri, 26 Jun 2020 08:31:21: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:31:21: #1 finished! INFO @ Fri, 26 Jun 2020 08:31:21: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:31:21: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:31:22: #2 number of paired peaks: 6658 INFO @ Fri, 26 Jun 2020 08:31:22: start model_add_line... INFO @ Fri, 26 Jun 2020 08:31:22: start X-correlation... INFO @ Fri, 26 Jun 2020 08:31:22: end of X-cor INFO @ Fri, 26 Jun 2020 08:31:22: #2 finished! INFO @ Fri, 26 Jun 2020 08:31:22: #2 predicted fragment length is 213 bps INFO @ Fri, 26 Jun 2020 08:31:22: #2 alternative fragment length(s) may be 213 bps INFO @ Fri, 26 Jun 2020 08:31:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX467118/SRX467118.05_model.r INFO @ Fri, 26 Jun 2020 08:31:22: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:31:22: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:31:24: 8000000 INFO @ Fri, 26 Jun 2020 08:31:26: 4000000 INFO @ Fri, 26 Jun 2020 08:31:31: 9000000 INFO @ Fri, 26 Jun 2020 08:31:32: 5000000 INFO @ Fri, 26 Jun 2020 08:31:37: 6000000 INFO @ Fri, 26 Jun 2020 08:31:38: 10000000 INFO @ Fri, 26 Jun 2020 08:31:43: 7000000 INFO @ Fri, 26 Jun 2020 08:31:45: 11000000 INFO @ Fri, 26 Jun 2020 08:31:49: 8000000 INFO @ Fri, 26 Jun 2020 08:31:51: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:31:51: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:31:51: #1 total tags in treatment: 11853532 INFO @ Fri, 26 Jun 2020 08:31:51: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:31:51: #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 08:31:52: #1 tags after filtering in treatment: 11853532 INFO @ Fri, 26 Jun 2020 08:31:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:31:52: #1 finished! INFO @ Fri, 26 Jun 2020 08:31:52: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:31:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:31:53: #2 number of paired peaks: 6658 INFO @ Fri, 26 Jun 2020 08:31:53: start model_add_line... INFO @ Fri, 26 Jun 2020 08:31:53: start X-correlation... INFO @ Fri, 26 Jun 2020 08:31:53: end of X-cor INFO @ Fri, 26 Jun 2020 08:31:53: #2 finished! INFO @ Fri, 26 Jun 2020 08:31:53: #2 predicted fragment length is 213 bps INFO @ Fri, 26 Jun 2020 08:31:53: #2 alternative fragment length(s) may be 213 bps INFO @ Fri, 26 Jun 2020 08:31:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX467118/SRX467118.10_model.r INFO @ Fri, 26 Jun 2020 08:31:53: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:31:53: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:31:55: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 08:31:59: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:32:01: 10000000 INFO @ Fri, 26 Jun 2020 08:32:07: 11000000 INFO @ Fri, 26 Jun 2020 08:32:12: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:32:12: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:32:12: #1 total tags in treatment: 11853532 INFO @ Fri, 26 Jun 2020 08:32:12: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:32:12: #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 08:32:12: #1 tags after filtering in treatment: 11853532 INFO @ Fri, 26 Jun 2020 08:32:12: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:32:12: #1 finished! INFO @ Fri, 26 Jun 2020 08:32:12: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:32:12: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:32:13: #2 number of paired peaks: 6658 INFO @ Fri, 26 Jun 2020 08:32:13: start model_add_line... INFO @ Fri, 26 Jun 2020 08:32:14: start X-correlation... INFO @ Fri, 26 Jun 2020 08:32:14: end of X-cor INFO @ Fri, 26 Jun 2020 08:32:14: #2 finished! INFO @ Fri, 26 Jun 2020 08:32:14: #2 predicted fragment length is 213 bps INFO @ Fri, 26 Jun 2020 08:32:14: #2 alternative fragment length(s) may be 213 bps INFO @ Fri, 26 Jun 2020 08:32:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX467118/SRX467118.20_model.r INFO @ Fri, 26 Jun 2020 08:32:14: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:32:14: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:32:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX467118/SRX467118.05_peaks.xls INFO @ Fri, 26 Jun 2020 08:32:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX467118/SRX467118.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:32:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX467118/SRX467118.05_summits.bed INFO @ Fri, 26 Jun 2020 08:32:15: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7695 records, 4 fields): 10 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 08:32:31: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:32:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX467118/SRX467118.10_peaks.xls INFO @ Fri, 26 Jun 2020 08:32:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX467118/SRX467118.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:32:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX467118/SRX467118.10_summits.bed INFO @ Fri, 26 Jun 2020 08:32:47: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (6305 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:32:51: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:33:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX467118/SRX467118.20_peaks.xls INFO @ Fri, 26 Jun 2020 08:33:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX467118/SRX467118.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:33:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX467118/SRX467118.20_summits.bed INFO @ Fri, 26 Jun 2020 08:33:08: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4715 records, 4 fields): 7 millis CompletedMACS2peakCalling