Job ID = 6454033 SRX = SRX1794219 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:55:04 prefetch.2.10.7: 1) Downloading 'SRR3575252'... 2020-06-21T08:55:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:56:11 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:56:12 prefetch.2.10.7: 'SRR3575252' is valid 2020-06-21T08:56:12 prefetch.2.10.7: 1) 'SRR3575252' was downloaded successfully Read 8515402 spots for SRR3575252/SRR3575252.sra Written 8515402 spots for SRR3575252/SRR3575252.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: 00:02:09 8515402 reads; of these: 8515402 (100.00%) were unpaired; of these: 657554 (7.72%) aligned 0 times 6445951 (75.70%) aligned exactly 1 time 1411897 (16.58%) aligned >1 times 92.28% overall alignment rate Time searching: 00:02:09 Overall time: 00:02:09 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_rmdupse_core] 463728 / 7857848 = 0.0590 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 18:01:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1794219/SRX1794219.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1794219/SRX1794219.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1794219/SRX1794219.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1794219/SRX1794219.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 18:01:30: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:01:30: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:01:36: 1000000 INFO @ Sun, 21 Jun 2020 18:01:41: 2000000 INFO @ Sun, 21 Jun 2020 18:01:47: 3000000 INFO @ Sun, 21 Jun 2020 18:01:53: 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 18:01:59: 5000000 INFO @ Sun, 21 Jun 2020 18:02:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1794219/SRX1794219.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1794219/SRX1794219.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1794219/SRX1794219.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1794219/SRX1794219.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 18:02:00: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:02:00: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:02:05: 6000000 INFO @ Sun, 21 Jun 2020 18:02:07: 1000000 INFO @ Sun, 21 Jun 2020 18:02:11: 7000000 INFO @ Sun, 21 Jun 2020 18:02:14: 2000000 INFO @ Sun, 21 Jun 2020 18:02:14: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:02:14: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:02:14: #1 total tags in treatment: 7394120 INFO @ Sun, 21 Jun 2020 18:02:14: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:02:14: #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 18:02:14: #1 tags after filtering in treatment: 7393893 INFO @ Sun, 21 Jun 2020 18:02:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:02:14: #1 finished! INFO @ Sun, 21 Jun 2020 18:02:14: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:02:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:02:15: #2 number of paired peaks: 3152 INFO @ Sun, 21 Jun 2020 18:02:15: start model_add_line... INFO @ Sun, 21 Jun 2020 18:02:15: start X-correlation... INFO @ Sun, 21 Jun 2020 18:02:15: end of X-cor INFO @ Sun, 21 Jun 2020 18:02:15: #2 finished! INFO @ Sun, 21 Jun 2020 18:02:15: #2 predicted fragment length is 155 bps INFO @ Sun, 21 Jun 2020 18:02:15: #2 alternative fragment length(s) may be 4,155 bps INFO @ Sun, 21 Jun 2020 18:02:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1794219/SRX1794219.05_model.r INFO @ Sun, 21 Jun 2020 18:02:15: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:02:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:02:20: 3000000 INFO @ Sun, 21 Jun 2020 18:02:27: 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 18:02:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1794219/SRX1794219.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1794219/SRX1794219.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1794219/SRX1794219.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1794219/SRX1794219.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 18:02:30: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:02:30: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:02:33: 5000000 INFO @ Sun, 21 Jun 2020 18:02:36: 1000000 INFO @ Sun, 21 Jun 2020 18:02:36: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:02:40: 6000000 INFO @ Sun, 21 Jun 2020 18:02:42: 2000000 INFO @ Sun, 21 Jun 2020 18:02:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1794219/SRX1794219.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:02:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1794219/SRX1794219.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:02:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1794219/SRX1794219.05_summits.bed INFO @ Sun, 21 Jun 2020 18:02:47: Done! pass1 - making usageList (182 chroms): 2 millis pass2 - checking and writing primary data (4700 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:02:47: 7000000 INFO @ Sun, 21 Jun 2020 18:02:48: 3000000 INFO @ Sun, 21 Jun 2020 18:02:50: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:02:50: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:02:50: #1 total tags in treatment: 7394120 INFO @ Sun, 21 Jun 2020 18:02:50: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:02:50: #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 18:02:51: #1 tags after filtering in treatment: 7393893 INFO @ Sun, 21 Jun 2020 18:02:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:02:51: #1 finished! INFO @ Sun, 21 Jun 2020 18:02:51: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:02:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:02:52: #2 number of paired peaks: 3152 INFO @ Sun, 21 Jun 2020 18:02:52: start model_add_line... INFO @ Sun, 21 Jun 2020 18:02:52: start X-correlation... INFO @ Sun, 21 Jun 2020 18:02:52: end of X-cor INFO @ Sun, 21 Jun 2020 18:02:52: #2 finished! INFO @ Sun, 21 Jun 2020 18:02:52: #2 predicted fragment length is 155 bps INFO @ Sun, 21 Jun 2020 18:02:52: #2 alternative fragment length(s) may be 4,155 bps INFO @ Sun, 21 Jun 2020 18:02:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1794219/SRX1794219.10_model.r INFO @ Sun, 21 Jun 2020 18:02:52: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:02:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:02:54: 4000000 INFO @ Sun, 21 Jun 2020 18:03:00: 5000000 INFO @ Sun, 21 Jun 2020 18:03:06: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:03:12: 7000000 INFO @ Sun, 21 Jun 2020 18:03:13: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:03:14: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:03:14: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:03:14: #1 total tags in treatment: 7394120 INFO @ Sun, 21 Jun 2020 18:03:14: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:03:14: #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 18:03:14: #1 tags after filtering in treatment: 7393893 INFO @ Sun, 21 Jun 2020 18:03:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:03:14: #1 finished! INFO @ Sun, 21 Jun 2020 18:03:14: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:03:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:03:15: #2 number of paired peaks: 3152 INFO @ Sun, 21 Jun 2020 18:03:15: start model_add_line... INFO @ Sun, 21 Jun 2020 18:03:15: start X-correlation... INFO @ Sun, 21 Jun 2020 18:03:15: end of X-cor INFO @ Sun, 21 Jun 2020 18:03:15: #2 finished! INFO @ Sun, 21 Jun 2020 18:03:15: #2 predicted fragment length is 155 bps INFO @ Sun, 21 Jun 2020 18:03:15: #2 alternative fragment length(s) may be 4,155 bps INFO @ Sun, 21 Jun 2020 18:03:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1794219/SRX1794219.20_model.r INFO @ Sun, 21 Jun 2020 18:03:15: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:03:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:03:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1794219/SRX1794219.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:03:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1794219/SRX1794219.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:03:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1794219/SRX1794219.10_summits.bed INFO @ Sun, 21 Jun 2020 18:03:24: Done! pass1 - making usageList (122 chroms): 1 millis pass2 - checking and writing primary data (1305 records, 4 fields): 8 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:03:35: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:03:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1794219/SRX1794219.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:03:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1794219/SRX1794219.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:03:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1794219/SRX1794219.20_summits.bed INFO @ Sun, 21 Jun 2020 18:03:45: Done! pass1 - making usageList (86 chroms): 1 millis pass2 - checking and writing primary data (284 records, 4 fields): 8 millis CompletedMACS2peakCalling