Job ID = 6454154 SRX = SRX1840073 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:02:19 prefetch.2.10.7: 1) Downloading 'SRR3661299'... 2020-06-21T09:02:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:11:16 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:11:16 prefetch.2.10.7: 1) 'SRR3661299' was downloaded successfully Read 29339865 spots for SRR3661299/SRR3661299.sra Written 29339865 spots for SRR3661299/SRR3661299.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: 00:15:08 29339865 reads; of these: 29339865 (100.00%) were unpaired; of these: 1939860 (6.61%) aligned 0 times 22980887 (78.33%) aligned exactly 1 time 4419118 (15.06%) aligned >1 times 93.39% overall alignment rate Time searching: 00:15:08 Overall time: 00:15:08 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] 5834694 / 27400005 = 0.2129 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 18:41:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1840073/SRX1840073.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1840073/SRX1840073.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1840073/SRX1840073.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1840073/SRX1840073.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 18:41:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:41:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:41:24: 1000000 INFO @ Sun, 21 Jun 2020 18:41:32: 2000000 INFO @ Sun, 21 Jun 2020 18:41:40: 3000000 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 18:41:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1840073/SRX1840073.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1840073/SRX1840073.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1840073/SRX1840073.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1840073/SRX1840073.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 18:41:46: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:41:46: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:41:48: 4000000 INFO @ Sun, 21 Jun 2020 18:41:54: 1000000 INFO @ Sun, 21 Jun 2020 18:41:57: 5000000 INFO @ Sun, 21 Jun 2020 18:42:02: 2000000 INFO @ Sun, 21 Jun 2020 18:42:06: 6000000 INFO @ Sun, 21 Jun 2020 18:42:10: 3000000 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 18:42:14: 7000000 INFO @ Sun, 21 Jun 2020 18:42:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1840073/SRX1840073.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1840073/SRX1840073.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1840073/SRX1840073.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1840073/SRX1840073.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 18:42:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:42:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:42:18: 4000000 INFO @ Sun, 21 Jun 2020 18:42:23: 8000000 INFO @ Sun, 21 Jun 2020 18:42:24: 1000000 INFO @ Sun, 21 Jun 2020 18:42:26: 5000000 INFO @ Sun, 21 Jun 2020 18:42:32: 2000000 INFO @ Sun, 21 Jun 2020 18:42:32: 9000000 INFO @ Sun, 21 Jun 2020 18:42:34: 6000000 INFO @ Sun, 21 Jun 2020 18:42:40: 3000000 INFO @ Sun, 21 Jun 2020 18:42:41: 10000000 INFO @ Sun, 21 Jun 2020 18:42:43: 7000000 INFO @ Sun, 21 Jun 2020 18:42:48: 4000000 INFO @ Sun, 21 Jun 2020 18:42:49: 11000000 INFO @ Sun, 21 Jun 2020 18:42:51: 8000000 INFO @ Sun, 21 Jun 2020 18:42:56: 5000000 INFO @ Sun, 21 Jun 2020 18:42:58: 12000000 INFO @ Sun, 21 Jun 2020 18:42:59: 9000000 INFO @ Sun, 21 Jun 2020 18:43:04: 6000000 INFO @ Sun, 21 Jun 2020 18:43:07: 13000000 INFO @ Sun, 21 Jun 2020 18:43:07: 10000000 INFO @ Sun, 21 Jun 2020 18:43:12: 7000000 INFO @ Sun, 21 Jun 2020 18:43:15: 11000000 INFO @ Sun, 21 Jun 2020 18:43:16: 14000000 INFO @ Sun, 21 Jun 2020 18:43:20: 8000000 INFO @ Sun, 21 Jun 2020 18:43:24: 12000000 INFO @ Sun, 21 Jun 2020 18:43:25: 15000000 INFO @ Sun, 21 Jun 2020 18:43:29: 9000000 INFO @ Sun, 21 Jun 2020 18:43:32: 13000000 INFO @ Sun, 21 Jun 2020 18:43:33: 16000000 INFO @ Sun, 21 Jun 2020 18:43:37: 10000000 INFO @ Sun, 21 Jun 2020 18:43:40: 14000000 INFO @ Sun, 21 Jun 2020 18:43:42: 17000000 INFO @ Sun, 21 Jun 2020 18:43:45: 11000000 INFO @ Sun, 21 Jun 2020 18:43:49: 15000000 INFO @ Sun, 21 Jun 2020 18:43:52: 18000000 INFO @ Sun, 21 Jun 2020 18:43:54: 12000000 INFO @ Sun, 21 Jun 2020 18:43:57: 16000000 INFO @ Sun, 21 Jun 2020 18:44:01: 19000000 INFO @ Sun, 21 Jun 2020 18:44:02: 13000000 INFO @ Sun, 21 Jun 2020 18:44:06: 17000000 INFO @ Sun, 21 Jun 2020 18:44:10: 20000000 INFO @ Sun, 21 Jun 2020 18:44:11: 14000000 INFO @ Sun, 21 Jun 2020 18:44:15: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:44:19: 21000000 INFO @ Sun, 21 Jun 2020 18:44:19: 15000000 INFO @ Sun, 21 Jun 2020 18:44:23: 19000000 INFO @ Sun, 21 Jun 2020 18:44:24: #1 tag size is determined as 101 bps INFO @ Sun, 21 Jun 2020 18:44:24: #1 tag size = 101 INFO @ Sun, 21 Jun 2020 18:44:24: #1 total tags in treatment: 21565311 INFO @ Sun, 21 Jun 2020 18:44:24: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:44:24: #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 18:44:25: #1 tags after filtering in treatment: 21565308 INFO @ Sun, 21 Jun 2020 18:44:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:44:25: #1 finished! INFO @ Sun, 21 Jun 2020 18:44:25: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:44:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:44:26: #2 number of paired peaks: 1616 INFO @ Sun, 21 Jun 2020 18:44:26: start model_add_line... INFO @ Sun, 21 Jun 2020 18:44:27: start X-correlation... INFO @ Sun, 21 Jun 2020 18:44:27: end of X-cor INFO @ Sun, 21 Jun 2020 18:44:27: #2 finished! INFO @ Sun, 21 Jun 2020 18:44:27: #2 predicted fragment length is 239 bps INFO @ Sun, 21 Jun 2020 18:44:27: #2 alternative fragment length(s) may be 239 bps INFO @ Sun, 21 Jun 2020 18:44:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1840073/SRX1840073.05_model.r INFO @ Sun, 21 Jun 2020 18:44:27: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:44:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:44:27: 16000000 INFO @ Sun, 21 Jun 2020 18:44:31: 20000000 INFO @ Sun, 21 Jun 2020 18:44:35: 17000000 INFO @ Sun, 21 Jun 2020 18:44:39: 21000000 INFO @ Sun, 21 Jun 2020 18:44:43: 18000000 INFO @ Sun, 21 Jun 2020 18:44:44: #1 tag size is determined as 101 bps INFO @ Sun, 21 Jun 2020 18:44:44: #1 tag size = 101 INFO @ Sun, 21 Jun 2020 18:44:44: #1 total tags in treatment: 21565311 INFO @ Sun, 21 Jun 2020 18:44:44: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:44:44: #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 18:44:44: #1 tags after filtering in treatment: 21565308 INFO @ Sun, 21 Jun 2020 18:44:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:44:44: #1 finished! INFO @ Sun, 21 Jun 2020 18:44:44: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:44:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:44:46: #2 number of paired peaks: 1616 INFO @ Sun, 21 Jun 2020 18:44:46: start model_add_line... INFO @ Sun, 21 Jun 2020 18:44:46: start X-correlation... INFO @ Sun, 21 Jun 2020 18:44:46: end of X-cor INFO @ Sun, 21 Jun 2020 18:44:46: #2 finished! INFO @ Sun, 21 Jun 2020 18:44:46: #2 predicted fragment length is 239 bps INFO @ Sun, 21 Jun 2020 18:44:46: #2 alternative fragment length(s) may be 239 bps INFO @ Sun, 21 Jun 2020 18:44:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1840073/SRX1840073.10_model.r INFO @ Sun, 21 Jun 2020 18:44:46: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:44:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:44:51: 19000000 INFO @ Sun, 21 Jun 2020 18:44:58: 20000000 INFO @ Sun, 21 Jun 2020 18:45:06: 21000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:45:10: #1 tag size is determined as 101 bps INFO @ Sun, 21 Jun 2020 18:45:10: #1 tag size = 101 INFO @ Sun, 21 Jun 2020 18:45:10: #1 total tags in treatment: 21565311 INFO @ Sun, 21 Jun 2020 18:45:10: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:45:10: #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 18:45:11: #1 tags after filtering in treatment: 21565308 INFO @ Sun, 21 Jun 2020 18:45:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:45:11: #1 finished! INFO @ Sun, 21 Jun 2020 18:45:11: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:45:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:45:13: #2 number of paired peaks: 1616 INFO @ Sun, 21 Jun 2020 18:45:13: start model_add_line... INFO @ Sun, 21 Jun 2020 18:45:13: start X-correlation... INFO @ Sun, 21 Jun 2020 18:45:13: end of X-cor INFO @ Sun, 21 Jun 2020 18:45:13: #2 finished! INFO @ Sun, 21 Jun 2020 18:45:13: #2 predicted fragment length is 239 bps INFO @ Sun, 21 Jun 2020 18:45:13: #2 alternative fragment length(s) may be 239 bps INFO @ Sun, 21 Jun 2020 18:45:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1840073/SRX1840073.20_model.r INFO @ Sun, 21 Jun 2020 18:45:13: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:45:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:45:20: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:45:42: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:45:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1840073/SRX1840073.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:45:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1840073/SRX1840073.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:45:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1840073/SRX1840073.05_summits.bed INFO @ Sun, 21 Jun 2020 18:45:45: Done! pass1 - making usageList (580 chroms): 2 millis pass2 - checking and writing primary data (11825 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:46:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1840073/SRX1840073.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:46:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1840073/SRX1840073.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:46:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1840073/SRX1840073.10_summits.bed INFO @ Sun, 21 Jun 2020 18:46:06: Done! pass1 - making usageList (485 chroms): 2 millis pass2 - checking and writing primary data (9115 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:46:09: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:46:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1840073/SRX1840073.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:46:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1840073/SRX1840073.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:46:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1840073/SRX1840073.20_summits.bed INFO @ Sun, 21 Jun 2020 18:46:35: Done! pass1 - making usageList (370 chroms): 2 millis pass2 - checking and writing primary data (6332 records, 4 fields): 18 millis CompletedMACS2peakCalling