Job ID = 6453611 SRX = SRX1299937 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:29:28 prefetch.2.10.7: 1) Downloading 'SRR2546856'... 2020-06-21T08:29:28 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:33:08 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:33:08 prefetch.2.10.7: 1) 'SRR2546856' was downloaded successfully Read 16265894 spots for SRR2546856/SRR2546856.sra Written 16265894 spots for SRR2546856/SRR2546856.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: 00:03:18 16265894 reads; of these: 16265894 (100.00%) were unpaired; of these: 5710797 (35.11%) aligned 0 times 8344506 (51.30%) aligned exactly 1 time 2210591 (13.59%) aligned >1 times 64.89% overall alignment rate Time searching: 00:03:18 Overall time: 00:03:18 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] 3643821 / 10555097 = 0.3452 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 17:40:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1299937/SRX1299937.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1299937/SRX1299937.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1299937/SRX1299937.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1299937/SRX1299937.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 17:40:14: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:40:14: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:40:20: 1000000 INFO @ Sun, 21 Jun 2020 17:40:26: 2000000 INFO @ Sun, 21 Jun 2020 17:40:33: 3000000 INFO @ Sun, 21 Jun 2020 17:40:39: 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 17:40:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1299937/SRX1299937.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1299937/SRX1299937.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1299937/SRX1299937.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1299937/SRX1299937.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 17:40:44: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:40:44: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:40:45: 5000000 INFO @ Sun, 21 Jun 2020 17:40:51: 1000000 INFO @ Sun, 21 Jun 2020 17:40:53: 6000000 INFO @ Sun, 21 Jun 2020 17:40:59: 2000000 INFO @ Sun, 21 Jun 2020 17:40:59: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:40:59: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:40:59: #1 total tags in treatment: 6911276 INFO @ Sun, 21 Jun 2020 17:40:59: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:40:59: #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 17:41:00: #1 tags after filtering in treatment: 6911069 INFO @ Sun, 21 Jun 2020 17:41:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:41:00: #1 finished! INFO @ Sun, 21 Jun 2020 17:41:00: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:41:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:41:00: #2 number of paired peaks: 6738 INFO @ Sun, 21 Jun 2020 17:41:00: start model_add_line... INFO @ Sun, 21 Jun 2020 17:41:01: start X-correlation... INFO @ Sun, 21 Jun 2020 17:41:01: end of X-cor INFO @ Sun, 21 Jun 2020 17:41:01: #2 finished! INFO @ Sun, 21 Jun 2020 17:41:01: #2 predicted fragment length is 158 bps INFO @ Sun, 21 Jun 2020 17:41:01: #2 alternative fragment length(s) may be 4,158 bps INFO @ Sun, 21 Jun 2020 17:41:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1299937/SRX1299937.05_model.r INFO @ Sun, 21 Jun 2020 17:41:01: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:41:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:41:05: 3000000 INFO @ Sun, 21 Jun 2020 17:41:12: 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 17:41:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1299937/SRX1299937.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1299937/SRX1299937.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1299937/SRX1299937.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1299937/SRX1299937.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 17:41:14: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:41:14: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:41:19: 5000000 INFO @ Sun, 21 Jun 2020 17:41:22: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:41:22: 1000000 INFO @ Sun, 21 Jun 2020 17:41:26: 6000000 INFO @ Sun, 21 Jun 2020 17:41:29: 2000000 INFO @ Sun, 21 Jun 2020 17:41:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1299937/SRX1299937.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:41:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1299937/SRX1299937.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:41:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1299937/SRX1299937.05_summits.bed INFO @ Sun, 21 Jun 2020 17:41:32: Done! pass1 - making usageList (257 chroms): 2 millis pass2 - checking and writing primary data (5340 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:41:33: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:41:33: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:41:33: #1 total tags in treatment: 6911276 INFO @ Sun, 21 Jun 2020 17:41:33: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:41:33: #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 17:41:33: #1 tags after filtering in treatment: 6911069 INFO @ Sun, 21 Jun 2020 17:41:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:41:33: #1 finished! INFO @ Sun, 21 Jun 2020 17:41:33: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:41:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:41:34: #2 number of paired peaks: 6738 INFO @ Sun, 21 Jun 2020 17:41:34: start model_add_line... INFO @ Sun, 21 Jun 2020 17:41:34: start X-correlation... INFO @ Sun, 21 Jun 2020 17:41:34: end of X-cor INFO @ Sun, 21 Jun 2020 17:41:34: #2 finished! INFO @ Sun, 21 Jun 2020 17:41:34: #2 predicted fragment length is 158 bps INFO @ Sun, 21 Jun 2020 17:41:34: #2 alternative fragment length(s) may be 4,158 bps INFO @ Sun, 21 Jun 2020 17:41:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1299937/SRX1299937.10_model.r INFO @ Sun, 21 Jun 2020 17:41:34: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:41:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:41:36: 3000000 INFO @ Sun, 21 Jun 2020 17:41:43: 4000000 INFO @ Sun, 21 Jun 2020 17:41:49: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:41:55: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:41:56: 6000000 INFO @ Sun, 21 Jun 2020 17:42:02: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:42:02: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:42:02: #1 total tags in treatment: 6911276 INFO @ Sun, 21 Jun 2020 17:42:02: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:42:02: #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 17:42:03: #1 tags after filtering in treatment: 6911069 INFO @ Sun, 21 Jun 2020 17:42:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:42:03: #1 finished! INFO @ Sun, 21 Jun 2020 17:42:03: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:42:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:42:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1299937/SRX1299937.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:42:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1299937/SRX1299937.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:42:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1299937/SRX1299937.10_summits.bed INFO @ Sun, 21 Jun 2020 17:42:04: Done! INFO @ Sun, 21 Jun 2020 17:42:04: #2 number of paired peaks: 6738 INFO @ Sun, 21 Jun 2020 17:42:04: start model_add_line... INFO @ Sun, 21 Jun 2020 17:42:04: start X-correlation... INFO @ Sun, 21 Jun 2020 17:42:04: end of X-cor INFO @ Sun, 21 Jun 2020 17:42:04: #2 finished! INFO @ Sun, 21 Jun 2020 17:42:04: #2 predicted fragment length is 158 bps INFO @ Sun, 21 Jun 2020 17:42:04: #2 alternative fragment length(s) may be 4,158 bps INFO @ Sun, 21 Jun 2020 17:42:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1299937/SRX1299937.20_model.r INFO @ Sun, 21 Jun 2020 17:42:04: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:42:04: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (190 chroms): 2 millis pass2 - checking and writing primary data (2893 records, 4 fields): 10 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:42:25: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:42:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1299937/SRX1299937.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:42:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1299937/SRX1299937.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:42:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1299937/SRX1299937.20_summits.bed INFO @ Sun, 21 Jun 2020 17:42:35: Done! pass1 - making usageList (139 chroms): 1 millis pass2 - checking and writing primary data (1244 records, 4 fields): 6 millis CompletedMACS2peakCalling