Job ID = 6457681 SRX = SRX467101 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:06:36 prefetch.2.10.7: 1) Downloading 'SRR1164525'... 2020-06-21T12:06:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:08:28 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:08:29 prefetch.2.10.7: 'SRR1164525' is valid 2020-06-21T12:08:29 prefetch.2.10.7: 1) 'SRR1164525' was downloaded successfully Read 13046410 spots for SRR1164525/SRR1164525.sra Written 13046410 spots for SRR1164525/SRR1164525.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: 00:03:26 13046410 reads; of these: 13046410 (100.00%) were unpaired; of these: 2334856 (17.90%) aligned 0 times 8502352 (65.17%) aligned exactly 1 time 2209202 (16.93%) aligned >1 times 82.10% overall alignment rate Time searching: 00:03:26 Overall time: 00:03:26 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] 1192546 / 10711554 = 0.1113 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 21:15:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX467101/SRX467101.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX467101/SRX467101.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX467101/SRX467101.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX467101/SRX467101.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 21:15:42: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:15:42: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:15:47: 1000000 INFO @ Sun, 21 Jun 2020 21:15:52: 2000000 INFO @ Sun, 21 Jun 2020 21:15:57: 3000000 INFO @ Sun, 21 Jun 2020 21:16:02: 4000000 INFO @ Sun, 21 Jun 2020 21:16:07: 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 21:16:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX467101/SRX467101.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX467101/SRX467101.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX467101/SRX467101.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX467101/SRX467101.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 21:16:12: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:16:12: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:16:12: 6000000 INFO @ Sun, 21 Jun 2020 21:16:17: 1000000 INFO @ Sun, 21 Jun 2020 21:16:17: 7000000 INFO @ Sun, 21 Jun 2020 21:16:22: 2000000 INFO @ Sun, 21 Jun 2020 21:16:23: 8000000 INFO @ Sun, 21 Jun 2020 21:16:28: 3000000 INFO @ Sun, 21 Jun 2020 21:16:28: 9000000 INFO @ Sun, 21 Jun 2020 21:16:31: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:16:31: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:16:31: #1 total tags in treatment: 9519008 INFO @ Sun, 21 Jun 2020 21:16:31: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:16:31: #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 21:16:32: #1 tags after filtering in treatment: 9519004 INFO @ Sun, 21 Jun 2020 21:16:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:16:32: #1 finished! INFO @ Sun, 21 Jun 2020 21:16:32: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:16:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:16:32: #2 number of paired peaks: 1368 INFO @ Sun, 21 Jun 2020 21:16:32: start model_add_line... INFO @ Sun, 21 Jun 2020 21:16:33: start X-correlation... INFO @ Sun, 21 Jun 2020 21:16:33: end of X-cor INFO @ Sun, 21 Jun 2020 21:16:33: #2 finished! INFO @ Sun, 21 Jun 2020 21:16:33: #2 predicted fragment length is 171 bps INFO @ Sun, 21 Jun 2020 21:16:33: #2 alternative fragment length(s) may be 171 bps INFO @ Sun, 21 Jun 2020 21:16:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX467101/SRX467101.05_model.r INFO @ Sun, 21 Jun 2020 21:16:33: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:16:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:16:33: 4000000 INFO @ Sun, 21 Jun 2020 21:16:38: 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 21:16:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX467101/SRX467101.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX467101/SRX467101.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX467101/SRX467101.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX467101/SRX467101.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 21:16:42: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:16:42: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:16:43: 6000000 INFO @ Sun, 21 Jun 2020 21:16:48: 1000000 INFO @ Sun, 21 Jun 2020 21:16:49: 7000000 INFO @ Sun, 21 Jun 2020 21:16:52: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:16:55: 2000000 INFO @ Sun, 21 Jun 2020 21:16:55: 8000000 INFO @ Sun, 21 Jun 2020 21:17:00: 9000000 INFO @ Sun, 21 Jun 2020 21:17:01: 3000000 INFO @ Sun, 21 Jun 2020 21:17:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX467101/SRX467101.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:17:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX467101/SRX467101.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:17:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX467101/SRX467101.05_summits.bed INFO @ Sun, 21 Jun 2020 21:17:03: Done! pass1 - making usageList (499 chroms): 1 millis pass2 - checking and writing primary data (5965 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:17:04: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:17:04: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:17:04: #1 total tags in treatment: 9519008 INFO @ Sun, 21 Jun 2020 21:17:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:17:04: #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 21:17:04: #1 tags after filtering in treatment: 9519004 INFO @ Sun, 21 Jun 2020 21:17:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:17:04: #1 finished! INFO @ Sun, 21 Jun 2020 21:17:04: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:17:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:17:05: #2 number of paired peaks: 1368 INFO @ Sun, 21 Jun 2020 21:17:05: start model_add_line... INFO @ Sun, 21 Jun 2020 21:17:05: start X-correlation... INFO @ Sun, 21 Jun 2020 21:17:05: end of X-cor INFO @ Sun, 21 Jun 2020 21:17:05: #2 finished! INFO @ Sun, 21 Jun 2020 21:17:05: #2 predicted fragment length is 171 bps INFO @ Sun, 21 Jun 2020 21:17:05: #2 alternative fragment length(s) may be 171 bps INFO @ Sun, 21 Jun 2020 21:17:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX467101/SRX467101.10_model.r INFO @ Sun, 21 Jun 2020 21:17:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:17:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:17:08: 4000000 INFO @ Sun, 21 Jun 2020 21:17:14: 5000000 INFO @ Sun, 21 Jun 2020 21:17:20: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:17:25: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:17:26: 7000000 INFO @ Sun, 21 Jun 2020 21:17:33: 8000000 INFO @ Sun, 21 Jun 2020 21:17:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX467101/SRX467101.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:17:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX467101/SRX467101.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:17:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX467101/SRX467101.10_summits.bed INFO @ Sun, 21 Jun 2020 21:17:36: Done! pass1 - making usageList (440 chroms): 2 millis pass2 - checking and writing primary data (4416 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:17:39: 9000000 INFO @ Sun, 21 Jun 2020 21:17:42: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:17:42: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:17:42: #1 total tags in treatment: 9519008 INFO @ Sun, 21 Jun 2020 21:17:42: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:17:42: #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 21:17:43: #1 tags after filtering in treatment: 9519004 INFO @ Sun, 21 Jun 2020 21:17:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:17:43: #1 finished! INFO @ Sun, 21 Jun 2020 21:17:43: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:17:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:17:43: #2 number of paired peaks: 1368 INFO @ Sun, 21 Jun 2020 21:17:43: start model_add_line... INFO @ Sun, 21 Jun 2020 21:17:43: start X-correlation... INFO @ Sun, 21 Jun 2020 21:17:43: end of X-cor INFO @ Sun, 21 Jun 2020 21:17:43: #2 finished! INFO @ Sun, 21 Jun 2020 21:17:43: #2 predicted fragment length is 171 bps INFO @ Sun, 21 Jun 2020 21:17:43: #2 alternative fragment length(s) may be 171 bps INFO @ Sun, 21 Jun 2020 21:17:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX467101/SRX467101.20_model.r INFO @ Sun, 21 Jun 2020 21:17:43: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:17:43: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:18:05: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:18:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX467101/SRX467101.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:18:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX467101/SRX467101.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:18:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX467101/SRX467101.20_summits.bed INFO @ Sun, 21 Jun 2020 21:18:15: Done! pass1 - making usageList (302 chroms): 1 millis pass2 - checking and writing primary data (2476 records, 4 fields): 11 millis CompletedMACS2peakCalling