Job ID = 6455649 SRX = SRX287957 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:30:51 prefetch.2.10.7: 1) Downloading 'SRR870146'... 2020-06-21T10:30:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:33:34 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:33:35 prefetch.2.10.7: 'SRR870146' is valid 2020-06-21T10:33:35 prefetch.2.10.7: 1) 'SRR870146' was downloaded successfully Read 13596200 spots for SRR870146/SRR870146.sra Written 13596200 spots for SRR870146/SRR870146.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: 00:03:45 13596200 reads; of these: 13596200 (100.00%) were unpaired; of these: 845518 (6.22%) aligned 0 times 9999865 (73.55%) aligned exactly 1 time 2750817 (20.23%) aligned >1 times 93.78% overall alignment rate Time searching: 00:03:45 Overall time: 00:03:45 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] 3151248 / 12750682 = 0.2471 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 19:41:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287957/SRX287957.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287957/SRX287957.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287957/SRX287957.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287957/SRX287957.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 19:41:28: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:41:28: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:41:33: 1000000 INFO @ Sun, 21 Jun 2020 19:41:38: 2000000 INFO @ Sun, 21 Jun 2020 19:41:43: 3000000 INFO @ Sun, 21 Jun 2020 19:41:48: 4000000 INFO @ Sun, 21 Jun 2020 19:41:53: 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 19:41:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287957/SRX287957.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287957/SRX287957.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287957/SRX287957.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287957/SRX287957.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 19:41:58: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:41:58: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:41:58: 6000000 INFO @ Sun, 21 Jun 2020 19:42:03: 1000000 INFO @ Sun, 21 Jun 2020 19:42:03: 7000000 INFO @ Sun, 21 Jun 2020 19:42:08: 2000000 INFO @ Sun, 21 Jun 2020 19:42:09: 8000000 INFO @ Sun, 21 Jun 2020 19:42:14: 3000000 INFO @ Sun, 21 Jun 2020 19:42:14: 9000000 INFO @ Sun, 21 Jun 2020 19:42:18: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:42:18: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:42:18: #1 total tags in treatment: 9599434 INFO @ Sun, 21 Jun 2020 19:42:18: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:42:18: #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 19:42:18: #1 tags after filtering in treatment: 9599434 INFO @ Sun, 21 Jun 2020 19:42:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:42:18: #1 finished! INFO @ Sun, 21 Jun 2020 19:42:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:42:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:42:19: 4000000 INFO @ Sun, 21 Jun 2020 19:42:19: #2 number of paired peaks: 2197 INFO @ Sun, 21 Jun 2020 19:42:19: start model_add_line... INFO @ Sun, 21 Jun 2020 19:42:19: start X-correlation... INFO @ Sun, 21 Jun 2020 19:42:19: end of X-cor INFO @ Sun, 21 Jun 2020 19:42:19: #2 finished! INFO @ Sun, 21 Jun 2020 19:42:19: #2 predicted fragment length is 419 bps INFO @ Sun, 21 Jun 2020 19:42:19: #2 alternative fragment length(s) may be 419 bps INFO @ Sun, 21 Jun 2020 19:42:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287957/SRX287957.05_model.r INFO @ Sun, 21 Jun 2020 19:42:19: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:42:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:42:24: 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 19:42:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287957/SRX287957.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287957/SRX287957.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287957/SRX287957.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287957/SRX287957.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 19:42:28: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:42:28: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:42:30: 6000000 INFO @ Sun, 21 Jun 2020 19:42:33: 1000000 INFO @ Sun, 21 Jun 2020 19:42:35: 7000000 INFO @ Sun, 21 Jun 2020 19:42:38: 2000000 INFO @ Sun, 21 Jun 2020 19:42:41: 8000000 INFO @ Sun, 21 Jun 2020 19:42:44: 3000000 INFO @ Sun, 21 Jun 2020 19:42:46: 9000000 INFO @ Sun, 21 Jun 2020 19:42:48: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:42:49: 4000000 INFO @ Sun, 21 Jun 2020 19:42:49: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:42:49: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:42:49: #1 total tags in treatment: 9599434 INFO @ Sun, 21 Jun 2020 19:42:49: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:42:49: #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 19:42:50: #1 tags after filtering in treatment: 9599434 INFO @ Sun, 21 Jun 2020 19:42:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:42:50: #1 finished! INFO @ Sun, 21 Jun 2020 19:42:50: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:42:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:42:51: #2 number of paired peaks: 2197 INFO @ Sun, 21 Jun 2020 19:42:51: start model_add_line... INFO @ Sun, 21 Jun 2020 19:42:51: start X-correlation... INFO @ Sun, 21 Jun 2020 19:42:51: end of X-cor INFO @ Sun, 21 Jun 2020 19:42:51: #2 finished! INFO @ Sun, 21 Jun 2020 19:42:51: #2 predicted fragment length is 419 bps INFO @ Sun, 21 Jun 2020 19:42:51: #2 alternative fragment length(s) may be 419 bps INFO @ Sun, 21 Jun 2020 19:42:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287957/SRX287957.10_model.r INFO @ Sun, 21 Jun 2020 19:42:51: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:42:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:42:54: 5000000 INFO @ Sun, 21 Jun 2020 19:42:59: 6000000 INFO @ Sun, 21 Jun 2020 19:43:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287957/SRX287957.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:43:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287957/SRX287957.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:43:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287957/SRX287957.05_summits.bed INFO @ Sun, 21 Jun 2020 19:43:01: Done! pass1 - making usageList (562 chroms): 1 millis pass2 - checking and writing primary data (5391 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:43:04: 7000000 INFO @ Sun, 21 Jun 2020 19:43:10: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:43:15: 9000000 INFO @ Sun, 21 Jun 2020 19:43:18: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:43:18: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:43:18: #1 total tags in treatment: 9599434 INFO @ Sun, 21 Jun 2020 19:43:18: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:43:18: #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 19:43:18: #1 tags after filtering in treatment: 9599434 INFO @ Sun, 21 Jun 2020 19:43:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:43:18: #1 finished! INFO @ Sun, 21 Jun 2020 19:43:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:43:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:43:19: #2 number of paired peaks: 2197 INFO @ Sun, 21 Jun 2020 19:43:19: start model_add_line... INFO @ Sun, 21 Jun 2020 19:43:19: start X-correlation... INFO @ Sun, 21 Jun 2020 19:43:19: end of X-cor INFO @ Sun, 21 Jun 2020 19:43:19: #2 finished! INFO @ Sun, 21 Jun 2020 19:43:19: #2 predicted fragment length is 419 bps INFO @ Sun, 21 Jun 2020 19:43:19: #2 alternative fragment length(s) may be 419 bps INFO @ Sun, 21 Jun 2020 19:43:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287957/SRX287957.20_model.r INFO @ Sun, 21 Jun 2020 19:43:19: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:43:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:43:20: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:43:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287957/SRX287957.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:43:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287957/SRX287957.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:43:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287957/SRX287957.10_summits.bed INFO @ Sun, 21 Jun 2020 19:43:33: Done! pass1 - making usageList (492 chroms): 2 millis pass2 - checking and writing primary data (4132 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:43:48: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:44:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287957/SRX287957.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:44:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287957/SRX287957.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:44:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287957/SRX287957.20_summits.bed INFO @ Sun, 21 Jun 2020 19:44:00: Done! pass1 - making usageList (427 chroms): 1 millis pass2 - checking and writing primary data (2893 records, 4 fields): 15 millis CompletedMACS2peakCalling