Job ID = 6457516 SRX = SRX4664667 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:42:10 prefetch.2.10.7: 1) Downloading 'SRR7813094'... 2020-06-21T11:42:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:46:04 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:46:04 prefetch.2.10.7: 1) 'SRR7813094' was downloaded successfully Read 30166481 spots for SRR7813094/SRR7813094.sra Written 30166481 spots for SRR7813094/SRR7813094.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: 00:09:09 30166481 reads; of these: 30166481 (100.00%) were unpaired; of these: 1188395 (3.94%) aligned 0 times 20005661 (66.32%) aligned exactly 1 time 8972425 (29.74%) aligned >1 times 96.06% overall alignment rate Time searching: 00:09:09 Overall time: 00:09:09 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 12 files... [bam_rmdupse_core] 9324770 / 28978086 = 0.3218 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 21:02:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4664667/SRX4664667.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4664667/SRX4664667.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4664667/SRX4664667.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4664667/SRX4664667.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 21:02:17: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:02:17: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:02:23: 1000000 INFO @ Sun, 21 Jun 2020 21:02:29: 2000000 INFO @ Sun, 21 Jun 2020 21:02:35: 3000000 INFO @ Sun, 21 Jun 2020 21:02:40: 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 21:02:46: 5000000 INFO @ Sun, 21 Jun 2020 21:02:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4664667/SRX4664667.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4664667/SRX4664667.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4664667/SRX4664667.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4664667/SRX4664667.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 21:02:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:02:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:02:52: 1000000 INFO @ Sun, 21 Jun 2020 21:02:52: 6000000 INFO @ Sun, 21 Jun 2020 21:02:57: 2000000 INFO @ Sun, 21 Jun 2020 21:02:59: 7000000 INFO @ Sun, 21 Jun 2020 21:03:03: 3000000 INFO @ Sun, 21 Jun 2020 21:03:05: 8000000 INFO @ Sun, 21 Jun 2020 21:03:08: 4000000 INFO @ Sun, 21 Jun 2020 21:03:11: 9000000 INFO @ Sun, 21 Jun 2020 21:03:13: 5000000 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 21:03:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4664667/SRX4664667.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4664667/SRX4664667.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4664667/SRX4664667.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4664667/SRX4664667.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 21:03:17: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:03:17: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:03:17: 10000000 INFO @ Sun, 21 Jun 2020 21:03:18: 6000000 INFO @ Sun, 21 Jun 2020 21:03:22: 1000000 INFO @ Sun, 21 Jun 2020 21:03:23: 11000000 INFO @ Sun, 21 Jun 2020 21:03:24: 7000000 INFO @ Sun, 21 Jun 2020 21:03:27: 2000000 INFO @ Sun, 21 Jun 2020 21:03:29: 8000000 INFO @ Sun, 21 Jun 2020 21:03:29: 12000000 INFO @ Sun, 21 Jun 2020 21:03:33: 3000000 INFO @ Sun, 21 Jun 2020 21:03:34: 9000000 INFO @ Sun, 21 Jun 2020 21:03:35: 13000000 INFO @ Sun, 21 Jun 2020 21:03:38: 4000000 INFO @ Sun, 21 Jun 2020 21:03:39: 10000000 INFO @ Sun, 21 Jun 2020 21:03:42: 14000000 INFO @ Sun, 21 Jun 2020 21:03:43: 5000000 INFO @ Sun, 21 Jun 2020 21:03:44: 11000000 INFO @ Sun, 21 Jun 2020 21:03:48: 15000000 INFO @ Sun, 21 Jun 2020 21:03:48: 6000000 INFO @ Sun, 21 Jun 2020 21:03:50: 12000000 INFO @ Sun, 21 Jun 2020 21:03:54: 7000000 INFO @ Sun, 21 Jun 2020 21:03:54: 16000000 INFO @ Sun, 21 Jun 2020 21:03:55: 13000000 INFO @ Sun, 21 Jun 2020 21:03:59: 8000000 INFO @ Sun, 21 Jun 2020 21:04:00: 14000000 INFO @ Sun, 21 Jun 2020 21:04:01: 17000000 INFO @ Sun, 21 Jun 2020 21:04:04: 9000000 INFO @ Sun, 21 Jun 2020 21:04:05: 15000000 INFO @ Sun, 21 Jun 2020 21:04:07: 18000000 INFO @ Sun, 21 Jun 2020 21:04:09: 10000000 INFO @ Sun, 21 Jun 2020 21:04:11: 16000000 INFO @ Sun, 21 Jun 2020 21:04:13: 19000000 INFO @ Sun, 21 Jun 2020 21:04:15: 11000000 INFO @ Sun, 21 Jun 2020 21:04:16: 17000000 INFO @ Sun, 21 Jun 2020 21:04:17: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:04:17: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:04:17: #1 total tags in treatment: 19653316 INFO @ Sun, 21 Jun 2020 21:04:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:04:17: #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 21:04:18: #1 tags after filtering in treatment: 19653238 INFO @ Sun, 21 Jun 2020 21:04:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:04:18: #1 finished! INFO @ Sun, 21 Jun 2020 21:04:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:04:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:04:19: #2 number of paired peaks: 1820 INFO @ Sun, 21 Jun 2020 21:04:19: start model_add_line... INFO @ Sun, 21 Jun 2020 21:04:20: start X-correlation... INFO @ Sun, 21 Jun 2020 21:04:20: end of X-cor INFO @ Sun, 21 Jun 2020 21:04:20: #2 finished! INFO @ Sun, 21 Jun 2020 21:04:20: #2 predicted fragment length is 174 bps INFO @ Sun, 21 Jun 2020 21:04:20: #2 alternative fragment length(s) may be 4,174 bps INFO @ Sun, 21 Jun 2020 21:04:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4664667/SRX4664667.05_model.r INFO @ Sun, 21 Jun 2020 21:04:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:04:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:04:20: 12000000 INFO @ Sun, 21 Jun 2020 21:04:21: 18000000 INFO @ Sun, 21 Jun 2020 21:04:25: 13000000 INFO @ Sun, 21 Jun 2020 21:04:26: 19000000 INFO @ Sun, 21 Jun 2020 21:04:30: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:04:30: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:04:30: #1 total tags in treatment: 19653316 INFO @ Sun, 21 Jun 2020 21:04:30: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:04:30: #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 21:04:30: 14000000 INFO @ Sun, 21 Jun 2020 21:04:30: #1 tags after filtering in treatment: 19653238 INFO @ Sun, 21 Jun 2020 21:04:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:04:30: #1 finished! INFO @ Sun, 21 Jun 2020 21:04:30: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:04:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:04:32: #2 number of paired peaks: 1820 INFO @ Sun, 21 Jun 2020 21:04:32: start model_add_line... INFO @ Sun, 21 Jun 2020 21:04:32: start X-correlation... INFO @ Sun, 21 Jun 2020 21:04:32: end of X-cor INFO @ Sun, 21 Jun 2020 21:04:32: #2 finished! INFO @ Sun, 21 Jun 2020 21:04:32: #2 predicted fragment length is 174 bps INFO @ Sun, 21 Jun 2020 21:04:32: #2 alternative fragment length(s) may be 4,174 bps INFO @ Sun, 21 Jun 2020 21:04:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4664667/SRX4664667.10_model.r INFO @ Sun, 21 Jun 2020 21:04:32: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:04:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:04:35: 15000000 INFO @ Sun, 21 Jun 2020 21:04:40: 16000000 INFO @ Sun, 21 Jun 2020 21:04:45: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:04:51: 18000000 INFO @ Sun, 21 Jun 2020 21:04:56: 19000000 INFO @ Sun, 21 Jun 2020 21:04:59: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:04:59: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:04:59: #1 total tags in treatment: 19653316 INFO @ Sun, 21 Jun 2020 21:04:59: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:04:59: #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 21:05:00: #1 tags after filtering in treatment: 19653238 INFO @ Sun, 21 Jun 2020 21:05:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:05:00: #1 finished! INFO @ Sun, 21 Jun 2020 21:05:00: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:05:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:05:01: #2 number of paired peaks: 1820 INFO @ Sun, 21 Jun 2020 21:05:01: start model_add_line... INFO @ Sun, 21 Jun 2020 21:05:01: start X-correlation... INFO @ Sun, 21 Jun 2020 21:05:01: end of X-cor INFO @ Sun, 21 Jun 2020 21:05:01: #2 finished! INFO @ Sun, 21 Jun 2020 21:05:01: #2 predicted fragment length is 174 bps INFO @ Sun, 21 Jun 2020 21:05:01: #2 alternative fragment length(s) may be 4,174 bps INFO @ Sun, 21 Jun 2020 21:05:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4664667/SRX4664667.20_model.r INFO @ Sun, 21 Jun 2020 21:05:01: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:05:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:05:06: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:05:18: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:05:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4664667/SRX4664667.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:05:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4664667/SRX4664667.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:05:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4664667/SRX4664667.05_summits.bed INFO @ Sun, 21 Jun 2020 21:05:26: Done! pass1 - making usageList (697 chroms): 1 millis pass2 - checking and writing primary data (5601 records, 4 fields): 24 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:05:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4664667/SRX4664667.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:05:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4664667/SRX4664667.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:05:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4664667/SRX4664667.10_summits.bed INFO @ Sun, 21 Jun 2020 21:05:38: Done! pass1 - making usageList (595 chroms): 1 millis pass2 - checking and writing primary data (3653 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:05:46: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:06:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4664667/SRX4664667.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:06:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4664667/SRX4664667.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:06:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4664667/SRX4664667.20_summits.bed INFO @ Sun, 21 Jun 2020 21:06:06: Done! pass1 - making usageList (488 chroms): 1 millis pass2 - checking and writing primary data (2134 records, 4 fields): 17 millis CompletedMACS2peakCalling