Job ID = 6455494 SRX = SRX287831 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:17:36 prefetch.2.10.7: 1) Downloading 'SRR870020'... 2020-06-21T10:17:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:20:20 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:20:21 prefetch.2.10.7: 'SRR870020' is valid 2020-06-21T10:20:21 prefetch.2.10.7: 1) 'SRR870020' was downloaded successfully Read 14733908 spots for SRR870020/SRR870020.sra Written 14733908 spots for SRR870020/SRR870020.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: 00:03:09 14733908 reads; of these: 14733908 (100.00%) were unpaired; of these: 630019 (4.28%) aligned 0 times 12950266 (87.89%) aligned exactly 1 time 1153623 (7.83%) aligned >1 times 95.72% overall alignment rate Time searching: 00:03:09 Overall time: 00:03:09 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] 1858117 / 14103889 = 0.1317 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 19:27:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287831/SRX287831.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287831/SRX287831.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287831/SRX287831.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287831/SRX287831.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 19:27:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:27:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:28:02: 1000000 INFO @ Sun, 21 Jun 2020 19:28:07: 2000000 INFO @ Sun, 21 Jun 2020 19:28:13: 3000000 INFO @ Sun, 21 Jun 2020 19:28:18: 4000000 INFO @ Sun, 21 Jun 2020 19:28:23: 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 19:28:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287831/SRX287831.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287831/SRX287831.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287831/SRX287831.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287831/SRX287831.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 19:28:27: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:28:27: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:28:28: 6000000 INFO @ Sun, 21 Jun 2020 19:28:32: 1000000 INFO @ Sun, 21 Jun 2020 19:28:34: 7000000 INFO @ Sun, 21 Jun 2020 19:28:38: 2000000 INFO @ Sun, 21 Jun 2020 19:28:40: 8000000 INFO @ Sun, 21 Jun 2020 19:28:44: 3000000 INFO @ Sun, 21 Jun 2020 19:28:47: 9000000 INFO @ Sun, 21 Jun 2020 19:28:50: 4000000 INFO @ Sun, 21 Jun 2020 19:28:53: 10000000 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 19:28:56: 5000000 INFO @ Sun, 21 Jun 2020 19:28:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287831/SRX287831.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287831/SRX287831.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287831/SRX287831.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287831/SRX287831.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 19:28:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:28:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:28:59: 11000000 INFO @ Sun, 21 Jun 2020 19:29:02: 6000000 INFO @ Sun, 21 Jun 2020 19:29:03: 1000000 INFO @ Sun, 21 Jun 2020 19:29:05: 12000000 INFO @ Sun, 21 Jun 2020 19:29:07: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:29:07: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:29:07: #1 total tags in treatment: 12245772 INFO @ Sun, 21 Jun 2020 19:29:07: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:29:07: #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 19:29:07: #1 tags after filtering in treatment: 12245725 INFO @ Sun, 21 Jun 2020 19:29:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:29:07: #1 finished! INFO @ Sun, 21 Jun 2020 19:29:07: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:29:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:29:08: 7000000 INFO @ Sun, 21 Jun 2020 19:29:09: #2 number of paired peaks: 7705 INFO @ Sun, 21 Jun 2020 19:29:09: start model_add_line... INFO @ Sun, 21 Jun 2020 19:29:09: 2000000 INFO @ Sun, 21 Jun 2020 19:29:09: start X-correlation... INFO @ Sun, 21 Jun 2020 19:29:09: end of X-cor INFO @ Sun, 21 Jun 2020 19:29:09: #2 finished! INFO @ Sun, 21 Jun 2020 19:29:09: #2 predicted fragment length is 209 bps INFO @ Sun, 21 Jun 2020 19:29:09: #2 alternative fragment length(s) may be 209 bps INFO @ Sun, 21 Jun 2020 19:29:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287831/SRX287831.05_model.r INFO @ Sun, 21 Jun 2020 19:29:09: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:29:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:29:14: 8000000 INFO @ Sun, 21 Jun 2020 19:29:15: 3000000 INFO @ Sun, 21 Jun 2020 19:29:20: 9000000 INFO @ Sun, 21 Jun 2020 19:29:21: 4000000 INFO @ Sun, 21 Jun 2020 19:29:26: 10000000 INFO @ Sun, 21 Jun 2020 19:29:26: 5000000 INFO @ Sun, 21 Jun 2020 19:29:32: 6000000 INFO @ Sun, 21 Jun 2020 19:29:32: 11000000 INFO @ Sun, 21 Jun 2020 19:29:38: 7000000 INFO @ Sun, 21 Jun 2020 19:29:38: 12000000 INFO @ Sun, 21 Jun 2020 19:29:40: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:29:40: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:29:40: #1 total tags in treatment: 12245772 INFO @ Sun, 21 Jun 2020 19:29:40: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:29:40: #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 19:29:41: #1 tags after filtering in treatment: 12245725 INFO @ Sun, 21 Jun 2020 19:29:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:29:41: #1 finished! INFO @ Sun, 21 Jun 2020 19:29:41: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:29:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:29:41: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:29:42: #2 number of paired peaks: 7705 INFO @ Sun, 21 Jun 2020 19:29:42: start model_add_line... INFO @ Sun, 21 Jun 2020 19:29:42: start X-correlation... INFO @ Sun, 21 Jun 2020 19:29:42: end of X-cor INFO @ Sun, 21 Jun 2020 19:29:42: #2 finished! INFO @ Sun, 21 Jun 2020 19:29:42: #2 predicted fragment length is 209 bps INFO @ Sun, 21 Jun 2020 19:29:42: #2 alternative fragment length(s) may be 209 bps INFO @ Sun, 21 Jun 2020 19:29:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287831/SRX287831.10_model.r INFO @ Sun, 21 Jun 2020 19:29:42: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:29:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:29:44: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:29:49: 9000000 INFO @ Sun, 21 Jun 2020 19:29:55: 10000000 INFO @ Sun, 21 Jun 2020 19:29:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287831/SRX287831.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:29:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287831/SRX287831.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:29:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287831/SRX287831.05_summits.bed INFO @ Sun, 21 Jun 2020 19:29:58: Done! INFO @ Sun, 21 Jun 2020 19:30:00: 11000000 pass1 - making usageList (95 chroms): 2 millis pass2 - checking and writing primary data (8804 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:30:06: 12000000 INFO @ Sun, 21 Jun 2020 19:30:07: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:30:07: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:30:07: #1 total tags in treatment: 12245772 INFO @ Sun, 21 Jun 2020 19:30:07: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:30:07: #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 19:30:08: #1 tags after filtering in treatment: 12245725 INFO @ Sun, 21 Jun 2020 19:30:08: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:30:08: #1 finished! INFO @ Sun, 21 Jun 2020 19:30:08: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:30:08: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:30:09: #2 number of paired peaks: 7705 INFO @ Sun, 21 Jun 2020 19:30:09: start model_add_line... INFO @ Sun, 21 Jun 2020 19:30:09: start X-correlation... INFO @ Sun, 21 Jun 2020 19:30:09: end of X-cor INFO @ Sun, 21 Jun 2020 19:30:09: #2 finished! INFO @ Sun, 21 Jun 2020 19:30:09: #2 predicted fragment length is 209 bps INFO @ Sun, 21 Jun 2020 19:30:09: #2 alternative fragment length(s) may be 209 bps INFO @ Sun, 21 Jun 2020 19:30:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287831/SRX287831.20_model.r INFO @ Sun, 21 Jun 2020 19:30:09: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:30:09: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:30:13: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:30:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287831/SRX287831.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:30:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287831/SRX287831.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:30:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287831/SRX287831.10_summits.bed INFO @ Sun, 21 Jun 2020 19:30:28: Done! pass1 - making usageList (67 chroms): 2 millis pass2 - checking and writing primary data (7007 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:30:40: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:30:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287831/SRX287831.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:30:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287831/SRX287831.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:30:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287831/SRX287831.20_summits.bed INFO @ Sun, 21 Jun 2020 19:30:55: Done! pass1 - making usageList (49 chroms): 1 millis pass2 - checking and writing primary data (4650 records, 4 fields): 7 millis CompletedMACS2peakCalling