Job ID = 6454094 SRX = SRX181436 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:03:34 prefetch.2.10.7: 1) Downloading 'SRR548173'... 2020-06-21T09:03:34 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:06:19 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:06:19 prefetch.2.10.7: 1) 'SRR548173' was downloaded successfully Read 31443972 spots for SRR548173/SRR548173.sra Written 31443972 spots for SRR548173/SRR548173.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: 00:06:28 31443972 reads; of these: 31443972 (100.00%) were unpaired; of these: 2072580 (6.59%) aligned 0 times 25013507 (79.55%) aligned exactly 1 time 4357885 (13.86%) aligned >1 times 93.41% overall alignment rate Time searching: 00:06:28 Overall time: 00:06:28 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] 17047145 / 29371392 = 0.5804 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 18:19:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX181436/SRX181436.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX181436/SRX181436.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX181436/SRX181436.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX181436/SRX181436.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 18:19:05: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:19:05: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:19:10: 1000000 INFO @ Sun, 21 Jun 2020 18:19:15: 2000000 INFO @ Sun, 21 Jun 2020 18:19:20: 3000000 INFO @ Sun, 21 Jun 2020 18:19:25: 4000000 INFO @ Sun, 21 Jun 2020 18:19:30: 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 18:19:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX181436/SRX181436.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX181436/SRX181436.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX181436/SRX181436.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX181436/SRX181436.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 18:19:35: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:19:35: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:19:35: 6000000 INFO @ Sun, 21 Jun 2020 18:19:41: 7000000 INFO @ Sun, 21 Jun 2020 18:19:42: 1000000 INFO @ Sun, 21 Jun 2020 18:19:47: 8000000 INFO @ Sun, 21 Jun 2020 18:19:48: 2000000 INFO @ Sun, 21 Jun 2020 18:19:52: 9000000 INFO @ Sun, 21 Jun 2020 18:19:55: 3000000 INFO @ Sun, 21 Jun 2020 18:19:58: 10000000 INFO @ Sun, 21 Jun 2020 18:20:02: 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 18:20:04: 11000000 INFO @ Sun, 21 Jun 2020 18:20:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX181436/SRX181436.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX181436/SRX181436.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX181436/SRX181436.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX181436/SRX181436.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 18:20:05: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:20:05: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:20:09: 5000000 INFO @ Sun, 21 Jun 2020 18:20:10: 12000000 INFO @ Sun, 21 Jun 2020 18:20:11: 1000000 INFO @ Sun, 21 Jun 2020 18:20:12: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:20:12: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:20:12: #1 total tags in treatment: 12324247 INFO @ Sun, 21 Jun 2020 18:20:12: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:20:12: #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 18:20:13: #1 tags after filtering in treatment: 12324236 INFO @ Sun, 21 Jun 2020 18:20:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:20:13: #1 finished! INFO @ Sun, 21 Jun 2020 18:20:13: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:20:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:20:14: #2 number of paired peaks: 1492 INFO @ Sun, 21 Jun 2020 18:20:14: start model_add_line... INFO @ Sun, 21 Jun 2020 18:20:14: start X-correlation... INFO @ Sun, 21 Jun 2020 18:20:14: end of X-cor INFO @ Sun, 21 Jun 2020 18:20:14: #2 finished! INFO @ Sun, 21 Jun 2020 18:20:14: #2 predicted fragment length is 85 bps INFO @ Sun, 21 Jun 2020 18:20:14: #2 alternative fragment length(s) may be 4,82,85 bps INFO @ Sun, 21 Jun 2020 18:20:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX181436/SRX181436.05_model.r INFO @ Sun, 21 Jun 2020 18:20:14: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:20:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:20:15: 6000000 INFO @ Sun, 21 Jun 2020 18:20:17: 2000000 INFO @ Sun, 21 Jun 2020 18:20:22: 7000000 INFO @ Sun, 21 Jun 2020 18:20:23: 3000000 INFO @ Sun, 21 Jun 2020 18:20:29: 4000000 INFO @ Sun, 21 Jun 2020 18:20:29: 8000000 INFO @ Sun, 21 Jun 2020 18:20:35: 5000000 INFO @ Sun, 21 Jun 2020 18:20:36: 9000000 INFO @ Sun, 21 Jun 2020 18:20:39: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:20:41: 6000000 INFO @ Sun, 21 Jun 2020 18:20:43: 10000000 INFO @ Sun, 21 Jun 2020 18:20:47: 7000000 INFO @ Sun, 21 Jun 2020 18:20:49: 11000000 INFO @ Sun, 21 Jun 2020 18:20:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX181436/SRX181436.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:20:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX181436/SRX181436.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:20:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX181436/SRX181436.05_summits.bed INFO @ Sun, 21 Jun 2020 18:20:52: Done! pass1 - making usageList (509 chroms): 2 millis pass2 - checking and writing primary data (7428 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:20:53: 8000000 INFO @ Sun, 21 Jun 2020 18:20:56: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:20:58: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:20:58: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:20:58: #1 total tags in treatment: 12324247 INFO @ Sun, 21 Jun 2020 18:20:58: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:20:58: #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 18:20:59: 9000000 INFO @ Sun, 21 Jun 2020 18:20:59: #1 tags after filtering in treatment: 12324236 INFO @ Sun, 21 Jun 2020 18:20:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:20:59: #1 finished! INFO @ Sun, 21 Jun 2020 18:20:59: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:20:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:21:00: #2 number of paired peaks: 1492 INFO @ Sun, 21 Jun 2020 18:21:00: start model_add_line... INFO @ Sun, 21 Jun 2020 18:21:00: start X-correlation... INFO @ Sun, 21 Jun 2020 18:21:00: end of X-cor INFO @ Sun, 21 Jun 2020 18:21:00: #2 finished! INFO @ Sun, 21 Jun 2020 18:21:00: #2 predicted fragment length is 85 bps INFO @ Sun, 21 Jun 2020 18:21:00: #2 alternative fragment length(s) may be 4,82,85 bps INFO @ Sun, 21 Jun 2020 18:21:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX181436/SRX181436.10_model.r INFO @ Sun, 21 Jun 2020 18:21:00: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:21:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:21:05: 10000000 INFO @ Sun, 21 Jun 2020 18:21:10: 11000000 INFO @ Sun, 21 Jun 2020 18:21:15: 12000000 INFO @ Sun, 21 Jun 2020 18:21:17: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:21:17: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:21:17: #1 total tags in treatment: 12324247 INFO @ Sun, 21 Jun 2020 18:21:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:21:17: #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 18:21:17: #1 tags after filtering in treatment: 12324236 INFO @ Sun, 21 Jun 2020 18:21:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:21:17: #1 finished! INFO @ Sun, 21 Jun 2020 18:21:17: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:21:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:21:18: #2 number of paired peaks: 1492 INFO @ Sun, 21 Jun 2020 18:21:18: start model_add_line... INFO @ Sun, 21 Jun 2020 18:21:18: start X-correlation... INFO @ Sun, 21 Jun 2020 18:21:18: end of X-cor INFO @ Sun, 21 Jun 2020 18:21:18: #2 finished! INFO @ Sun, 21 Jun 2020 18:21:18: #2 predicted fragment length is 85 bps INFO @ Sun, 21 Jun 2020 18:21:18: #2 alternative fragment length(s) may be 4,82,85 bps INFO @ Sun, 21 Jun 2020 18:21:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX181436/SRX181436.20_model.r INFO @ Sun, 21 Jun 2020 18:21:18: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:21:18: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:21:27: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:21:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX181436/SRX181436.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:21:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX181436/SRX181436.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:21:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX181436/SRX181436.10_summits.bed INFO @ Sun, 21 Jun 2020 18:21:41: Done! pass1 - making usageList (473 chroms): 1 millis pass2 - checking and writing primary data (3491 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:21:44: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:21:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX181436/SRX181436.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:21:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX181436/SRX181436.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:21:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX181436/SRX181436.20_summits.bed INFO @ Sun, 21 Jun 2020 18:21:58: Done! pass1 - making usageList (426 chroms): 1 millis pass2 - checking and writing primary data (1480 records, 4 fields): 15 millis CompletedMACS2peakCalling