Job ID = 6453267 SRX = SRX110781 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:26:27 prefetch.2.10.7: 1) Downloading 'SRR388363'... 2020-06-21T08:26:27 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:29:49 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:29:50 prefetch.2.10.7: 'SRR388363' is valid 2020-06-21T08:29:50 prefetch.2.10.7: 1) 'SRR388363' was downloaded successfully Read 40013592 spots for SRR388363/SRR388363.sra Written 40013592 spots for SRR388363/SRR388363.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: 00:12:10 40013592 reads; of these: 40013592 (100.00%) were unpaired; of these: 6016161 (15.04%) aligned 0 times 16796084 (41.98%) aligned exactly 1 time 17201347 (42.99%) aligned >1 times 84.96% overall alignment rate Time searching: 00:12:10 Overall time: 00:12:10 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] 14181134 / 33997431 = 0.4171 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 17:48:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX110781/SRX110781.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX110781/SRX110781.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX110781/SRX110781.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX110781/SRX110781.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 17:48:28: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:48:28: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:48:33: 1000000 INFO @ Sun, 21 Jun 2020 17:48:37: 2000000 INFO @ Sun, 21 Jun 2020 17:48:41: 3000000 INFO @ Sun, 21 Jun 2020 17:48:45: 4000000 INFO @ Sun, 21 Jun 2020 17:48:49: 5000000 INFO @ Sun, 21 Jun 2020 17:48:53: 6000000 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 17:48:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX110781/SRX110781.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX110781/SRX110781.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX110781/SRX110781.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX110781/SRX110781.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 17:48:56: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:48:56: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:48:57: 7000000 INFO @ Sun, 21 Jun 2020 17:49:00: 1000000 INFO @ Sun, 21 Jun 2020 17:49:01: 8000000 INFO @ Sun, 21 Jun 2020 17:49:05: 2000000 INFO @ Sun, 21 Jun 2020 17:49:05: 9000000 INFO @ Sun, 21 Jun 2020 17:49:09: 10000000 INFO @ Sun, 21 Jun 2020 17:49:09: 3000000 INFO @ Sun, 21 Jun 2020 17:49:14: 11000000 INFO @ Sun, 21 Jun 2020 17:49:14: 4000000 INFO @ Sun, 21 Jun 2020 17:49:18: 12000000 INFO @ Sun, 21 Jun 2020 17:49:19: 5000000 INFO @ Sun, 21 Jun 2020 17:49:22: 13000000 INFO @ Sun, 21 Jun 2020 17:49:23: 6000000 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 17:49:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX110781/SRX110781.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX110781/SRX110781.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX110781/SRX110781.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX110781/SRX110781.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 17:49:26: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:49:26: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:49:26: 14000000 INFO @ Sun, 21 Jun 2020 17:49:28: 7000000 INFO @ Sun, 21 Jun 2020 17:49:30: 1000000 INFO @ Sun, 21 Jun 2020 17:49:30: 15000000 INFO @ Sun, 21 Jun 2020 17:49:32: 8000000 INFO @ Sun, 21 Jun 2020 17:49:35: 2000000 INFO @ Sun, 21 Jun 2020 17:49:35: 16000000 INFO @ Sun, 21 Jun 2020 17:49:37: 9000000 INFO @ Sun, 21 Jun 2020 17:49:39: 17000000 INFO @ Sun, 21 Jun 2020 17:49:39: 3000000 INFO @ Sun, 21 Jun 2020 17:49:42: 10000000 INFO @ Sun, 21 Jun 2020 17:49:43: 18000000 INFO @ Sun, 21 Jun 2020 17:49:44: 4000000 INFO @ Sun, 21 Jun 2020 17:49:46: 11000000 INFO @ Sun, 21 Jun 2020 17:49:48: 19000000 INFO @ Sun, 21 Jun 2020 17:49:49: 5000000 INFO @ Sun, 21 Jun 2020 17:49:51: 12000000 INFO @ Sun, 21 Jun 2020 17:49:51: #1 tag size is determined as 18 bps INFO @ Sun, 21 Jun 2020 17:49:51: #1 tag size = 18 INFO @ Sun, 21 Jun 2020 17:49:51: #1 total tags in treatment: 19816297 INFO @ Sun, 21 Jun 2020 17:49:51: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:49:51: #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 17:49:52: #1 tags after filtering in treatment: 19816297 INFO @ Sun, 21 Jun 2020 17:49:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:49:52: #1 finished! INFO @ Sun, 21 Jun 2020 17:49:52: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:49:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:49:53: #2 number of paired peaks: 1311 INFO @ Sun, 21 Jun 2020 17:49:53: start model_add_line... INFO @ Sun, 21 Jun 2020 17:49:53: 6000000 INFO @ Sun, 21 Jun 2020 17:49:53: start X-correlation... INFO @ Sun, 21 Jun 2020 17:49:53: end of X-cor INFO @ Sun, 21 Jun 2020 17:49:53: #2 finished! INFO @ Sun, 21 Jun 2020 17:49:53: #2 predicted fragment length is 286 bps INFO @ Sun, 21 Jun 2020 17:49:53: #2 alternative fragment length(s) may be 3,273,275,286 bps INFO @ Sun, 21 Jun 2020 17:49:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX110781/SRX110781.05_model.r INFO @ Sun, 21 Jun 2020 17:49:53: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:49:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:49:55: 13000000 INFO @ Sun, 21 Jun 2020 17:49:58: 7000000 INFO @ Sun, 21 Jun 2020 17:50:00: 14000000 INFO @ Sun, 21 Jun 2020 17:50:03: 8000000 INFO @ Sun, 21 Jun 2020 17:50:04: 15000000 INFO @ Sun, 21 Jun 2020 17:50:07: 9000000 INFO @ Sun, 21 Jun 2020 17:50:09: 16000000 INFO @ Sun, 21 Jun 2020 17:50:12: 10000000 INFO @ Sun, 21 Jun 2020 17:50:14: 17000000 INFO @ Sun, 21 Jun 2020 17:50:16: 11000000 INFO @ Sun, 21 Jun 2020 17:50:18: 18000000 INFO @ Sun, 21 Jun 2020 17:50:21: 12000000 INFO @ Sun, 21 Jun 2020 17:50:23: 19000000 INFO @ Sun, 21 Jun 2020 17:50:25: 13000000 INFO @ Sun, 21 Jun 2020 17:50:27: #1 tag size is determined as 18 bps INFO @ Sun, 21 Jun 2020 17:50:27: #1 tag size = 18 INFO @ Sun, 21 Jun 2020 17:50:27: #1 total tags in treatment: 19816297 INFO @ Sun, 21 Jun 2020 17:50:27: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:50:27: #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 17:50:27: #1 tags after filtering in treatment: 19816297 INFO @ Sun, 21 Jun 2020 17:50:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:50:27: #1 finished! INFO @ Sun, 21 Jun 2020 17:50:27: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:50:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:50:29: #2 number of paired peaks: 1311 INFO @ Sun, 21 Jun 2020 17:50:29: start model_add_line... INFO @ Sun, 21 Jun 2020 17:50:29: start X-correlation... INFO @ Sun, 21 Jun 2020 17:50:29: end of X-cor INFO @ Sun, 21 Jun 2020 17:50:29: #2 finished! INFO @ Sun, 21 Jun 2020 17:50:29: #2 predicted fragment length is 286 bps INFO @ Sun, 21 Jun 2020 17:50:29: #2 alternative fragment length(s) may be 3,273,275,286 bps INFO @ Sun, 21 Jun 2020 17:50:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX110781/SRX110781.10_model.r INFO @ Sun, 21 Jun 2020 17:50:29: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:50:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:50:30: 14000000 INFO @ Sun, 21 Jun 2020 17:50:34: 15000000 INFO @ Sun, 21 Jun 2020 17:50:39: 16000000 INFO @ Sun, 21 Jun 2020 17:50:41: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:50:44: 17000000 INFO @ Sun, 21 Jun 2020 17:50:48: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:50:53: 19000000 INFO @ Sun, 21 Jun 2020 17:50:56: #1 tag size is determined as 18 bps INFO @ Sun, 21 Jun 2020 17:50:56: #1 tag size = 18 INFO @ Sun, 21 Jun 2020 17:50:56: #1 total tags in treatment: 19816297 INFO @ Sun, 21 Jun 2020 17:50:56: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:50:56: #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 17:50:57: #1 tags after filtering in treatment: 19816297 INFO @ Sun, 21 Jun 2020 17:50:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:50:57: #1 finished! INFO @ Sun, 21 Jun 2020 17:50:57: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:50:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:50:58: #2 number of paired peaks: 1311 INFO @ Sun, 21 Jun 2020 17:50:58: start model_add_line... INFO @ Sun, 21 Jun 2020 17:50:59: start X-correlation... INFO @ Sun, 21 Jun 2020 17:50:59: end of X-cor INFO @ Sun, 21 Jun 2020 17:50:59: #2 finished! INFO @ Sun, 21 Jun 2020 17:50:59: #2 predicted fragment length is 286 bps INFO @ Sun, 21 Jun 2020 17:50:59: #2 alternative fragment length(s) may be 3,273,275,286 bps INFO @ Sun, 21 Jun 2020 17:50:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX110781/SRX110781.20_model.r INFO @ Sun, 21 Jun 2020 17:50:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:50:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:51:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX110781/SRX110781.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:51:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX110781/SRX110781.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:51:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX110781/SRX110781.05_summits.bed INFO @ Sun, 21 Jun 2020 17:51:01: Done! pass1 - making usageList (585 chroms): 1 millis pass2 - checking and writing primary data (1847 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:51:17: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:51:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX110781/SRX110781.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:51:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX110781/SRX110781.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:51:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX110781/SRX110781.10_summits.bed INFO @ Sun, 21 Jun 2020 17:51:36: Done! pass1 - making usageList (531 chroms): 1 millis pass2 - checking and writing primary data (1167 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:51:46: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:52:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX110781/SRX110781.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:52:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX110781/SRX110781.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:52:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX110781/SRX110781.20_summits.bed INFO @ Sun, 21 Jun 2020 17:52:06: Done! pass1 - making usageList (446 chroms): 1 millis pass2 - checking and writing primary data (694 records, 4 fields): 13 millis CompletedMACS2peakCalling