Job ID = 6454402 SRX = SRX2033488 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:09:09 prefetch.2.10.7: 1) Downloading 'SRR4042503'... 2020-06-21T09:09:09 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:10:12 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:10:13 prefetch.2.10.7: 'SRR4042503' is valid 2020-06-21T09:10:13 prefetch.2.10.7: 1) 'SRR4042503' was downloaded successfully 2020-06-21T09:10:13 prefetch.2.10.7: 'SRR4042503' has 0 unresolved dependencies Read 6637677 spots for SRR4042503/SRR4042503.sra Written 6637677 spots for SRR4042503/SRR4042503.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: 00:01:18 6637677 reads; of these: 6637677 (100.00%) were unpaired; of these: 323422 (4.87%) aligned 0 times 5391417 (81.22%) aligned exactly 1 time 922838 (13.90%) aligned >1 times 95.13% overall alignment rate Time searching: 00:01:18 Overall time: 00:01:18 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] 1255603 / 6314255 = 0.1989 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 18:13:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2033488/SRX2033488.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2033488/SRX2033488.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2033488/SRX2033488.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2033488/SRX2033488.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 18:13:55: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:13:55: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:14:00: 1000000 INFO @ Sun, 21 Jun 2020 18:14:06: 2000000 INFO @ Sun, 21 Jun 2020 18:14:12: 3000000 INFO @ Sun, 21 Jun 2020 18:14:17: 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 18:14:23: 5000000 INFO @ Sun, 21 Jun 2020 18:14:24: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:14:24: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:14:24: #1 total tags in treatment: 5058652 INFO @ Sun, 21 Jun 2020 18:14:24: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:14:24: #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 18:14:24: #1 tags after filtering in treatment: 5058386 INFO @ Sun, 21 Jun 2020 18:14:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:14:24: #1 finished! INFO @ Sun, 21 Jun 2020 18:14:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:14:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:14:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2033488/SRX2033488.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2033488/SRX2033488.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2033488/SRX2033488.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2033488/SRX2033488.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 18:14:25: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:14:25: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:14:25: #2 number of paired peaks: 7654 INFO @ Sun, 21 Jun 2020 18:14:25: start model_add_line... INFO @ Sun, 21 Jun 2020 18:14:25: start X-correlation... INFO @ Sun, 21 Jun 2020 18:14:25: end of X-cor INFO @ Sun, 21 Jun 2020 18:14:25: #2 finished! INFO @ Sun, 21 Jun 2020 18:14:25: #2 predicted fragment length is 155 bps INFO @ Sun, 21 Jun 2020 18:14:25: #2 alternative fragment length(s) may be 155 bps INFO @ Sun, 21 Jun 2020 18:14:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2033488/SRX2033488.05_model.r INFO @ Sun, 21 Jun 2020 18:14:25: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:14:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:14:30: 1000000 INFO @ Sun, 21 Jun 2020 18:14:36: 2000000 INFO @ Sun, 21 Jun 2020 18:14:39: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:14:42: 3000000 INFO @ Sun, 21 Jun 2020 18:14:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2033488/SRX2033488.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:14:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2033488/SRX2033488.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:14:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2033488/SRX2033488.05_summits.bed INFO @ Sun, 21 Jun 2020 18:14:45: Done! pass1 - making usageList (158 chroms): 2 millis pass2 - checking and writing primary data (9629 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:14:48: 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 18:14:54: 5000000 INFO @ Sun, 21 Jun 2020 18:14:54: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:14:54: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:14:54: #1 total tags in treatment: 5058652 INFO @ Sun, 21 Jun 2020 18:14:54: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:14:54: #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 18:14:54: #1 tags after filtering in treatment: 5058386 INFO @ Sun, 21 Jun 2020 18:14:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:14:54: #1 finished! INFO @ Sun, 21 Jun 2020 18:14:54: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:14:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:14:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2033488/SRX2033488.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2033488/SRX2033488.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2033488/SRX2033488.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2033488/SRX2033488.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 18:14:55: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:14:55: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:14:55: #2 number of paired peaks: 7654 INFO @ Sun, 21 Jun 2020 18:14:55: start model_add_line... INFO @ Sun, 21 Jun 2020 18:14:55: start X-correlation... INFO @ Sun, 21 Jun 2020 18:14:55: end of X-cor INFO @ Sun, 21 Jun 2020 18:14:55: #2 finished! INFO @ Sun, 21 Jun 2020 18:14:55: #2 predicted fragment length is 155 bps INFO @ Sun, 21 Jun 2020 18:14:55: #2 alternative fragment length(s) may be 155 bps INFO @ Sun, 21 Jun 2020 18:14:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2033488/SRX2033488.10_model.r INFO @ Sun, 21 Jun 2020 18:14:55: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:14:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:15:01: 1000000 INFO @ Sun, 21 Jun 2020 18:15:06: 2000000 INFO @ Sun, 21 Jun 2020 18:15:10: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:15:12: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:15:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2033488/SRX2033488.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:15:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2033488/SRX2033488.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:15:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2033488/SRX2033488.10_summits.bed INFO @ Sun, 21 Jun 2020 18:15:17: Done! pass1 - making usageList (130 chroms): 2 millis pass2 - checking and writing primary data (7675 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:15:18: 4000000 INFO @ Sun, 21 Jun 2020 18:15:25: 5000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:15:25: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:15:25: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:15:25: #1 total tags in treatment: 5058652 INFO @ Sun, 21 Jun 2020 18:15:25: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:15:25: #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 18:15:25: #1 tags after filtering in treatment: 5058386 INFO @ Sun, 21 Jun 2020 18:15:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:15:25: #1 finished! INFO @ Sun, 21 Jun 2020 18:15:25: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:15:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:15:26: #2 number of paired peaks: 7654 INFO @ Sun, 21 Jun 2020 18:15:26: start model_add_line... INFO @ Sun, 21 Jun 2020 18:15:26: start X-correlation... INFO @ Sun, 21 Jun 2020 18:15:26: end of X-cor INFO @ Sun, 21 Jun 2020 18:15:26: #2 finished! INFO @ Sun, 21 Jun 2020 18:15:26: #2 predicted fragment length is 155 bps INFO @ Sun, 21 Jun 2020 18:15:26: #2 alternative fragment length(s) may be 155 bps INFO @ Sun, 21 Jun 2020 18:15:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2033488/SRX2033488.20_model.r INFO @ Sun, 21 Jun 2020 18:15:26: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:15:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:15:40: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:15:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2033488/SRX2033488.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:15:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2033488/SRX2033488.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:15:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2033488/SRX2033488.20_summits.bed INFO @ Sun, 21 Jun 2020 18:15:47: Done! pass1 - making usageList (93 chroms): 2 millis pass2 - checking and writing primary data (5407 records, 4 fields): 9 millis CompletedMACS2peakCalling