Job ID = 6457797 SRX = SRX4798833 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:57:03 prefetch.2.10.7: 1) Downloading 'SRR7965236'... 2020-06-21T11:57:03 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:58:10 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:58:11 prefetch.2.10.7: 'SRR7965236' is valid 2020-06-21T11:58:11 prefetch.2.10.7: 1) 'SRR7965236' was downloaded successfully Read 6367813 spots for SRR7965236/SRR7965236.sra Written 6367813 spots for SRR7965236/SRR7965236.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: 00:01:26 6367813 reads; of these: 6367813 (100.00%) were unpaired; of these: 744940 (11.70%) aligned 0 times 4765717 (74.84%) aligned exactly 1 time 857156 (13.46%) aligned >1 times 88.30% overall alignment rate Time searching: 00:01:26 Overall time: 00:01:26 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_rmdupse_core] 760707 / 5622873 = 0.1353 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 21:01:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4798833/SRX4798833.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4798833/SRX4798833.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4798833/SRX4798833.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4798833/SRX4798833.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 21:01:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:01:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:01:58: 1000000 INFO @ Sun, 21 Jun 2020 21:02:04: 2000000 INFO @ Sun, 21 Jun 2020 21:02:10: 3000000 INFO @ Sun, 21 Jun 2020 21:02:16: 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 21:02:21: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:02:21: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:02:21: #1 total tags in treatment: 4862166 INFO @ Sun, 21 Jun 2020 21:02:21: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:02:21: #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 21:02:22: #1 tags after filtering in treatment: 4862002 INFO @ Sun, 21 Jun 2020 21:02:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:02:22: #1 finished! INFO @ Sun, 21 Jun 2020 21:02:22: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:02:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:02:22: #2 number of paired peaks: 2070 INFO @ Sun, 21 Jun 2020 21:02:22: start model_add_line... INFO @ Sun, 21 Jun 2020 21:02:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4798833/SRX4798833.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4798833/SRX4798833.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4798833/SRX4798833.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4798833/SRX4798833.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 21:02:22: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:02:22: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:02:22: start X-correlation... INFO @ Sun, 21 Jun 2020 21:02:22: end of X-cor INFO @ Sun, 21 Jun 2020 21:02:22: #2 finished! INFO @ Sun, 21 Jun 2020 21:02:22: #2 predicted fragment length is 178 bps INFO @ Sun, 21 Jun 2020 21:02:22: #2 alternative fragment length(s) may be 178 bps INFO @ Sun, 21 Jun 2020 21:02:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4798833/SRX4798833.05_model.r INFO @ Sun, 21 Jun 2020 21:02:22: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:02:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:02:29: 1000000 INFO @ Sun, 21 Jun 2020 21:02:35: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:02:36: 2000000 INFO @ Sun, 21 Jun 2020 21:02:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4798833/SRX4798833.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:02:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4798833/SRX4798833.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:02:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4798833/SRX4798833.05_summits.bed INFO @ Sun, 21 Jun 2020 21:02:41: Done! pass1 - making usageList (266 chroms): 2 millis pass2 - checking and writing primary data (2297 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:02:43: 3000000 INFO @ Sun, 21 Jun 2020 21:02:50: 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 21:02:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4798833/SRX4798833.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4798833/SRX4798833.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4798833/SRX4798833.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4798833/SRX4798833.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 21:02:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:02:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:02:57: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:02:57: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:02:57: #1 total tags in treatment: 4862166 INFO @ Sun, 21 Jun 2020 21:02:57: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:02:57: #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 21:02:58: #1 tags after filtering in treatment: 4862002 INFO @ Sun, 21 Jun 2020 21:02:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:02:58: #1 finished! INFO @ Sun, 21 Jun 2020 21:02:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:02:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:02:58: #2 number of paired peaks: 2070 INFO @ Sun, 21 Jun 2020 21:02:58: start model_add_line... INFO @ Sun, 21 Jun 2020 21:02:58: start X-correlation... INFO @ Sun, 21 Jun 2020 21:02:58: end of X-cor INFO @ Sun, 21 Jun 2020 21:02:58: #2 finished! INFO @ Sun, 21 Jun 2020 21:02:58: #2 predicted fragment length is 178 bps INFO @ Sun, 21 Jun 2020 21:02:58: #2 alternative fragment length(s) may be 178 bps INFO @ Sun, 21 Jun 2020 21:02:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4798833/SRX4798833.10_model.r INFO @ Sun, 21 Jun 2020 21:02:58: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:02:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:02:59: 1000000 INFO @ Sun, 21 Jun 2020 21:03:06: 2000000 INFO @ Sun, 21 Jun 2020 21:03:11: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:03:13: 3000000 INFO @ Sun, 21 Jun 2020 21:03:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4798833/SRX4798833.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:03:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4798833/SRX4798833.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:03:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4798833/SRX4798833.10_summits.bed INFO @ Sun, 21 Jun 2020 21:03:17: Done! pass1 - making usageList (129 chroms): 1 millis pass2 - checking and writing primary data (595 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:03:19: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:03:25: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:03:25: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:03:25: #1 total tags in treatment: 4862166 INFO @ Sun, 21 Jun 2020 21:03:25: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:03:25: #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 21:03:25: #1 tags after filtering in treatment: 4862002 INFO @ Sun, 21 Jun 2020 21:03:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:03:25: #1 finished! INFO @ Sun, 21 Jun 2020 21:03:25: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:03:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:03:26: #2 number of paired peaks: 2070 INFO @ Sun, 21 Jun 2020 21:03:26: start model_add_line... INFO @ Sun, 21 Jun 2020 21:03:26: start X-correlation... INFO @ Sun, 21 Jun 2020 21:03:26: end of X-cor INFO @ Sun, 21 Jun 2020 21:03:26: #2 finished! INFO @ Sun, 21 Jun 2020 21:03:26: #2 predicted fragment length is 178 bps INFO @ Sun, 21 Jun 2020 21:03:26: #2 alternative fragment length(s) may be 178 bps INFO @ Sun, 21 Jun 2020 21:03:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4798833/SRX4798833.20_model.r INFO @ Sun, 21 Jun 2020 21:03:26: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:03:26: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:03:38: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:03:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4798833/SRX4798833.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:03:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4798833/SRX4798833.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:03:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4798833/SRX4798833.20_summits.bed INFO @ Sun, 21 Jun 2020 21:03:45: Done! pass1 - making usageList (57 chroms): 1 millis pass2 - checking and writing primary data (144 records, 4 fields): 4 millis CompletedMACS2peakCalling