Job ID = 6458243 SRX = SRX5011010 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:20:22 prefetch.2.10.7: 1) Downloading 'SRR8191459'... 2020-06-21T12:20:22 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:21:59 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:22:00 prefetch.2.10.7: 'SRR8191459' is valid 2020-06-21T12:22:00 prefetch.2.10.7: 1) 'SRR8191459' was downloaded successfully 2020-06-21T12:22:00 prefetch.2.10.7: 'SRR8191459' has 0 unresolved dependencies Read 17095829 spots for SRR8191459/SRR8191459.sra Written 17095829 spots for SRR8191459/SRR8191459.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: 00:03:56 17095829 reads; of these: 17095829 (100.00%) were unpaired; of these: 2419142 (14.15%) aligned 0 times 11508484 (67.32%) aligned exactly 1 time 3168203 (18.53%) aligned >1 times 85.85% overall alignment rate Time searching: 00:03:56 Overall time: 00:03:56 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] 6231394 / 14676687 = 0.4246 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 21:29:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011010/SRX5011010.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011010/SRX5011010.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011010/SRX5011010.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011010/SRX5011010.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 21:29:35: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:29:35: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:29:40: 1000000 INFO @ Sun, 21 Jun 2020 21:29:45: 2000000 INFO @ Sun, 21 Jun 2020 21:29:51: 3000000 INFO @ Sun, 21 Jun 2020 21:29:56: 4000000 INFO @ Sun, 21 Jun 2020 21:30:01: 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 21:30:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011010/SRX5011010.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011010/SRX5011010.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011010/SRX5011010.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011010/SRX5011010.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 21:30:05: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:30:05: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:30:06: 6000000 INFO @ Sun, 21 Jun 2020 21:30:11: 1000000 INFO @ Sun, 21 Jun 2020 21:30:12: 7000000 INFO @ Sun, 21 Jun 2020 21:30:17: 2000000 INFO @ Sun, 21 Jun 2020 21:30:18: 8000000 INFO @ Sun, 21 Jun 2020 21:30:21: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:30:21: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:30:21: #1 total tags in treatment: 8445293 INFO @ Sun, 21 Jun 2020 21:30:21: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:30:21: #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 21:30:21: #1 tags after filtering in treatment: 8445189 INFO @ Sun, 21 Jun 2020 21:30:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:30:21: #1 finished! INFO @ Sun, 21 Jun 2020 21:30:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:30:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:30:22: #2 number of paired peaks: 2316 INFO @ Sun, 21 Jun 2020 21:30:22: start model_add_line... INFO @ Sun, 21 Jun 2020 21:30:22: start X-correlation... INFO @ Sun, 21 Jun 2020 21:30:22: end of X-cor INFO @ Sun, 21 Jun 2020 21:30:22: #2 finished! INFO @ Sun, 21 Jun 2020 21:30:22: #2 predicted fragment length is 196 bps INFO @ Sun, 21 Jun 2020 21:30:22: #2 alternative fragment length(s) may be 196 bps INFO @ Sun, 21 Jun 2020 21:30:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011010/SRX5011010.05_model.r INFO @ Sun, 21 Jun 2020 21:30:22: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:30:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:30:23: 3000000 INFO @ Sun, 21 Jun 2020 21:30:28: 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 @ Sun, 21 Jun 2020 21:30:34: 5000000 INFO @ Sun, 21 Jun 2020 21:30:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011010/SRX5011010.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011010/SRX5011010.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011010/SRX5011010.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011010/SRX5011010.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 21:30:35: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:30:35: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:30:40: 6000000 INFO @ Sun, 21 Jun 2020 21:30:41: 1000000 INFO @ Sun, 21 Jun 2020 21:30:44: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:30:46: 7000000 INFO @ Sun, 21 Jun 2020 21:30:47: 2000000 INFO @ Sun, 21 Jun 2020 21:30:52: 8000000 INFO @ Sun, 21 Jun 2020 21:30:52: 3000000 INFO @ Sun, 21 Jun 2020 21:30:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011010/SRX5011010.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:30:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011010/SRX5011010.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:30:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011010/SRX5011010.05_summits.bed INFO @ Sun, 21 Jun 2020 21:30:54: Done! INFO @ Sun, 21 Jun 2020 21:30:55: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:30:55: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:30:55: #1 total tags in treatment: 8445293 INFO @ Sun, 21 Jun 2020 21:30:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:30:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) pass1 - making usageList (643 chroms): 2 millis pass2 - checking and writing primary data (8975 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:30:55: #1 tags after filtering in treatment: 8445189 INFO @ Sun, 21 Jun 2020 21:30:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:30:55: #1 finished! INFO @ Sun, 21 Jun 2020 21:30:55: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:30:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:30:56: #2 number of paired peaks: 2316 INFO @ Sun, 21 Jun 2020 21:30:56: start model_add_line... INFO @ Sun, 21 Jun 2020 21:30:56: start X-correlation... INFO @ Sun, 21 Jun 2020 21:30:56: end of X-cor INFO @ Sun, 21 Jun 2020 21:30:56: #2 finished! INFO @ Sun, 21 Jun 2020 21:30:56: #2 predicted fragment length is 196 bps INFO @ Sun, 21 Jun 2020 21:30:56: #2 alternative fragment length(s) may be 196 bps INFO @ Sun, 21 Jun 2020 21:30:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011010/SRX5011010.10_model.r INFO @ Sun, 21 Jun 2020 21:30:56: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:30:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:30:58: 4000000 INFO @ Sun, 21 Jun 2020 21:31:04: 5000000 INFO @ Sun, 21 Jun 2020 21:31:09: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:31:15: 7000000 INFO @ Sun, 21 Jun 2020 21:31:18: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:31:21: 8000000 INFO @ Sun, 21 Jun 2020 21:31:23: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:31:23: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:31:23: #1 total tags in treatment: 8445293 INFO @ Sun, 21 Jun 2020 21:31:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:31:23: #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 21:31:24: #1 tags after filtering in treatment: 8445189 INFO @ Sun, 21 Jun 2020 21:31:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:31:24: #1 finished! INFO @ Sun, 21 Jun 2020 21:31:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:31:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:31:25: #2 number of paired peaks: 2316 INFO @ Sun, 21 Jun 2020 21:31:25: start model_add_line... INFO @ Sun, 21 Jun 2020 21:31:25: start X-correlation... INFO @ Sun, 21 Jun 2020 21:31:25: end of X-cor INFO @ Sun, 21 Jun 2020 21:31:25: #2 finished! INFO @ Sun, 21 Jun 2020 21:31:25: #2 predicted fragment length is 196 bps INFO @ Sun, 21 Jun 2020 21:31:25: #2 alternative fragment length(s) may be 196 bps INFO @ Sun, 21 Jun 2020 21:31:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011010/SRX5011010.20_model.r INFO @ Sun, 21 Jun 2020 21:31:25: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:31:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:31:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011010/SRX5011010.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:31:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011010/SRX5011010.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:31:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011010/SRX5011010.10_summits.bed INFO @ Sun, 21 Jun 2020 21:31:28: Done! pass1 - making usageList (459 chroms): 2 millis pass2 - checking and writing primary data (5455 records, 4 fields): 18 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:31:47: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:31:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011010/SRX5011010.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:31:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011010/SRX5011010.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:31:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011010/SRX5011010.20_summits.bed INFO @ Sun, 21 Jun 2020 21:31:58: Done! pass1 - making usageList (208 chroms): 1 millis pass2 - checking and writing primary data (2541 records, 4 fields): 10 millis CompletedMACS2peakCalling