Job ID = 6457998 SRX = SRX4933901 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:05:54 prefetch.2.10.7: 1) Downloading 'SRR8107292'... 2020-06-21T12:05:54 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:08:50 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:08:50 prefetch.2.10.7: 1) 'SRR8107292' was downloaded successfully Read 24717305 spots for SRR8107292/SRR8107292.sra Written 24717305 spots for SRR8107292/SRR8107292.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: 00:05:19 24717305 reads; of these: 24717305 (100.00%) were unpaired; of these: 3969139 (16.06%) aligned 0 times 18562751 (75.10%) aligned exactly 1 time 2185415 (8.84%) aligned >1 times 83.94% overall alignment rate Time searching: 00:05:19 Overall time: 00:05:19 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 12 files... [bam_rmdupse_core] 14610151 / 20748166 = 0.7042 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 21:21:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4933901/SRX4933901.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4933901/SRX4933901.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4933901/SRX4933901.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4933901/SRX4933901.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 21:21:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:21:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:21:12: 1000000 INFO @ Sun, 21 Jun 2020 21:21:18: 2000000 INFO @ Sun, 21 Jun 2020 21:21:24: 3000000 INFO @ Sun, 21 Jun 2020 21:21:30: 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 21:21:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4933901/SRX4933901.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4933901/SRX4933901.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4933901/SRX4933901.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4933901/SRX4933901.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 21:21:36: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:21:36: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:21:37: 5000000 INFO @ Sun, 21 Jun 2020 21:21:43: 1000000 INFO @ Sun, 21 Jun 2020 21:21:43: 6000000 INFO @ Sun, 21 Jun 2020 21:21:44: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:21:44: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:21:44: #1 total tags in treatment: 6138015 INFO @ Sun, 21 Jun 2020 21:21:44: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:21:44: #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 21:21:45: #1 tags after filtering in treatment: 6137879 INFO @ Sun, 21 Jun 2020 21:21:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:21:45: #1 finished! INFO @ Sun, 21 Jun 2020 21:21:45: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:21:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:21:46: #2 number of paired peaks: 6791 INFO @ Sun, 21 Jun 2020 21:21:46: start model_add_line... INFO @ Sun, 21 Jun 2020 21:21:46: start X-correlation... INFO @ Sun, 21 Jun 2020 21:21:46: end of X-cor INFO @ Sun, 21 Jun 2020 21:21:46: #2 finished! INFO @ Sun, 21 Jun 2020 21:21:46: #2 predicted fragment length is 141 bps INFO @ Sun, 21 Jun 2020 21:21:46: #2 alternative fragment length(s) may be 141 bps INFO @ Sun, 21 Jun 2020 21:21:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4933901/SRX4933901.05_model.r INFO @ Sun, 21 Jun 2020 21:21:46: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:21:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:21:49: 2000000 INFO @ Sun, 21 Jun 2020 21:21:54: 3000000 INFO @ Sun, 21 Jun 2020 21:22:00: 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 21:22:05: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:22:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4933901/SRX4933901.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4933901/SRX4933901.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4933901/SRX4933901.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4933901/SRX4933901.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 21:22:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:22:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:22:07: 5000000 INFO @ Sun, 21 Jun 2020 21:22:13: 1000000 INFO @ Sun, 21 Jun 2020 21:22:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4933901/SRX4933901.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:22:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4933901/SRX4933901.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:22:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4933901/SRX4933901.05_summits.bed INFO @ Sun, 21 Jun 2020 21:22:13: Done! pass1 - making usageList (434 chroms): 2 millis pass2 - checking and writing primary data (9309 records, 4 fields): 36 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:22:14: 6000000 INFO @ Sun, 21 Jun 2020 21:22:15: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:22:15: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:22:15: #1 total tags in treatment: 6138015 INFO @ Sun, 21 Jun 2020 21:22:15: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:22:15: #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 21:22:15: #1 tags after filtering in treatment: 6137879 INFO @ Sun, 21 Jun 2020 21:22:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:22:15: #1 finished! INFO @ Sun, 21 Jun 2020 21:22:15: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:22:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:22:16: #2 number of paired peaks: 6791 INFO @ Sun, 21 Jun 2020 21:22:16: start model_add_line... INFO @ Sun, 21 Jun 2020 21:22:16: start X-correlation... INFO @ Sun, 21 Jun 2020 21:22:16: end of X-cor INFO @ Sun, 21 Jun 2020 21:22:16: #2 finished! INFO @ Sun, 21 Jun 2020 21:22:16: #2 predicted fragment length is 141 bps INFO @ Sun, 21 Jun 2020 21:22:16: #2 alternative fragment length(s) may be 141 bps INFO @ Sun, 21 Jun 2020 21:22:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4933901/SRX4933901.10_model.r INFO @ Sun, 21 Jun 2020 21:22:16: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:22:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:22:19: 2000000 INFO @ Sun, 21 Jun 2020 21:22:25: 3000000 INFO @ Sun, 21 Jun 2020 21:22:30: 4000000 INFO @ Sun, 21 Jun 2020 21:22:35: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:22:37: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:22:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4933901/SRX4933901.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:22:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4933901/SRX4933901.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:22:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4933901/SRX4933901.10_summits.bed INFO @ Sun, 21 Jun 2020 21:22:43: Done! INFO @ Sun, 21 Jun 2020 21:22:43: 6000000 pass1 - making usageList (307 chroms): 1 millis pass2 - checking and writing primary data (4380 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:22:44: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:22:44: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:22:44: #1 total tags in treatment: 6138015 INFO @ Sun, 21 Jun 2020 21:22:44: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:22:44: #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 21:22:45: #1 tags after filtering in treatment: 6137879 INFO @ Sun, 21 Jun 2020 21:22:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:22:45: #1 finished! INFO @ Sun, 21 Jun 2020 21:22:45: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:22:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:22:46: #2 number of paired peaks: 6791 INFO @ Sun, 21 Jun 2020 21:22:46: start model_add_line... INFO @ Sun, 21 Jun 2020 21:22:46: start X-correlation... INFO @ Sun, 21 Jun 2020 21:22:46: end of X-cor INFO @ Sun, 21 Jun 2020 21:22:46: #2 finished! INFO @ Sun, 21 Jun 2020 21:22:46: #2 predicted fragment length is 141 bps INFO @ Sun, 21 Jun 2020 21:22:46: #2 alternative fragment length(s) may be 141 bps INFO @ Sun, 21 Jun 2020 21:22:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4933901/SRX4933901.20_model.r INFO @ Sun, 21 Jun 2020 21:22:46: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:22:46: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:23:04: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:23:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4933901/SRX4933901.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:23:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4933901/SRX4933901.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:23:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4933901/SRX4933901.20_summits.bed INFO @ Sun, 21 Jun 2020 21:23:12: Done! pass1 - making usageList (206 chroms): 2 millis pass2 - checking and writing primary data (1594 records, 4 fields): 14 millis CompletedMACS2peakCalling