Job ID = 6454883 SRX = SRX2592471 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:48:55 prefetch.2.10.7: 1) Downloading 'SRR5289748'... 2020-06-21T09:48:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:50:52 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:50:52 prefetch.2.10.7: 1) 'SRR5289748' was downloaded successfully Read 16958488 spots for SRR5289748/SRR5289748.sra Written 16958488 spots for SRR5289748/SRR5289748.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: 00:03:46 16958488 reads; of these: 16958488 (100.00%) were unpaired; of these: 3477122 (20.50%) aligned 0 times 10910927 (64.34%) aligned exactly 1 time 2570439 (15.16%) aligned >1 times 79.50% overall alignment rate Time searching: 00:03:46 Overall time: 00:03:46 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] 4540804 / 13481366 = 0.3368 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 18:59:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592471/SRX2592471.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592471/SRX2592471.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592471/SRX2592471.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592471/SRX2592471.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 18:59:21: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:59:21: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:59:28: 1000000 INFO @ Sun, 21 Jun 2020 18:59:35: 2000000 INFO @ Sun, 21 Jun 2020 18:59:41: 3000000 INFO @ Sun, 21 Jun 2020 18:59:48: 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 18:59:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592471/SRX2592471.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592471/SRX2592471.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592471/SRX2592471.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592471/SRX2592471.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 18:59:51: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:59:51: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:59:55: 5000000 INFO @ Sun, 21 Jun 2020 18:59:58: 1000000 INFO @ Sun, 21 Jun 2020 19:00:02: 6000000 INFO @ Sun, 21 Jun 2020 19:00:04: 2000000 INFO @ Sun, 21 Jun 2020 19:00:09: 7000000 INFO @ Sun, 21 Jun 2020 19:00:10: 3000000 INFO @ Sun, 21 Jun 2020 19:00:16: 8000000 INFO @ Sun, 21 Jun 2020 19:00:16: 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 19:00:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592471/SRX2592471.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592471/SRX2592471.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592471/SRX2592471.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592471/SRX2592471.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 19:00:21: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:00:21: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:00:23: 5000000 INFO @ Sun, 21 Jun 2020 19:00:23: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:00:23: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:00:23: #1 total tags in treatment: 8940562 INFO @ Sun, 21 Jun 2020 19:00:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:00:23: #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 19:00:23: #1 tags after filtering in treatment: 8940322 INFO @ Sun, 21 Jun 2020 19:00:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:00:23: #1 finished! INFO @ Sun, 21 Jun 2020 19:00:23: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:00:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:00:25: #2 number of paired peaks: 8924 INFO @ Sun, 21 Jun 2020 19:00:25: start model_add_line... INFO @ Sun, 21 Jun 2020 19:00:25: start X-correlation... INFO @ Sun, 21 Jun 2020 19:00:25: end of X-cor INFO @ Sun, 21 Jun 2020 19:00:25: #2 finished! INFO @ Sun, 21 Jun 2020 19:00:25: #2 predicted fragment length is 225 bps INFO @ Sun, 21 Jun 2020 19:00:25: #2 alternative fragment length(s) may be 225 bps INFO @ Sun, 21 Jun 2020 19:00:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592471/SRX2592471.05_model.r INFO @ Sun, 21 Jun 2020 19:00:25: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:00:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:00:28: 1000000 INFO @ Sun, 21 Jun 2020 19:00:29: 6000000 INFO @ Sun, 21 Jun 2020 19:00:34: 2000000 INFO @ Sun, 21 Jun 2020 19:00:35: 7000000 INFO @ Sun, 21 Jun 2020 19:00:41: 3000000 INFO @ Sun, 21 Jun 2020 19:00:41: 8000000 INFO @ Sun, 21 Jun 2020 19:00:47: 4000000 INFO @ Sun, 21 Jun 2020 19:00:47: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:00:47: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:00:47: #1 total tags in treatment: 8940562 INFO @ Sun, 21 Jun 2020 19:00:47: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:00:47: #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 19:00:47: #1 tags after filtering in treatment: 8940322 INFO @ Sun, 21 Jun 2020 19:00:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:00:47: #1 finished! INFO @ Sun, 21 Jun 2020 19:00:47: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:00:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:00:48: #2 number of paired peaks: 8924 INFO @ Sun, 21 Jun 2020 19:00:48: start model_add_line... INFO @ Sun, 21 Jun 2020 19:00:48: start X-correlation... INFO @ Sun, 21 Jun 2020 19:00:48: end of X-cor INFO @ Sun, 21 Jun 2020 19:00:48: #2 finished! INFO @ Sun, 21 Jun 2020 19:00:48: #2 predicted fragment length is 225 bps INFO @ Sun, 21 Jun 2020 19:00:48: #2 alternative fragment length(s) may be 225 bps INFO @ Sun, 21 Jun 2020 19:00:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592471/SRX2592471.10_model.r INFO @ Sun, 21 Jun 2020 19:00:48: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:00:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:00:52: 5000000 INFO @ Sun, 21 Jun 2020 19:00:58: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:00:58: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:01:03: 7000000 INFO @ Sun, 21 Jun 2020 19:01:09: 8000000 INFO @ Sun, 21 Jun 2020 19:01:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592471/SRX2592471.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:01:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592471/SRX2592471.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:01:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592471/SRX2592471.05_summits.bed INFO @ Sun, 21 Jun 2020 19:01:11: Done! pass1 - making usageList (161 chroms): 2 millis pass2 - checking and writing primary data (8590 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:01:15: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:01:15: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:01:15: #1 total tags in treatment: 8940562 INFO @ Sun, 21 Jun 2020 19:01:15: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:01:15: #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 19:01:15: #1 tags after filtering in treatment: 8940322 INFO @ Sun, 21 Jun 2020 19:01:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:01:15: #1 finished! INFO @ Sun, 21 Jun 2020 19:01:15: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:01:15: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:01:16: #2 number of paired peaks: 8924 INFO @ Sun, 21 Jun 2020 19:01:16: start model_add_line... INFO @ Sun, 21 Jun 2020 19:01:16: start X-correlation... INFO @ Sun, 21 Jun 2020 19:01:16: end of X-cor INFO @ Sun, 21 Jun 2020 19:01:16: #2 finished! INFO @ Sun, 21 Jun 2020 19:01:16: #2 predicted fragment length is 225 bps INFO @ Sun, 21 Jun 2020 19:01:16: #2 alternative fragment length(s) may be 225 bps INFO @ Sun, 21 Jun 2020 19:01:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592471/SRX2592471.20_model.r INFO @ Sun, 21 Jun 2020 19:01:16: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:01:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:01:21: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:01:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592471/SRX2592471.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:01:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592471/SRX2592471.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:01:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592471/SRX2592471.10_summits.bed INFO @ Sun, 21 Jun 2020 19:01:34: Done! pass1 - making usageList (133 chroms): 2 millis pass2 - checking and writing primary data (7133 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:01:48: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:02:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592471/SRX2592471.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:02:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592471/SRX2592471.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:02:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592471/SRX2592471.20_summits.bed INFO @ Sun, 21 Jun 2020 19:02:01: Done! pass1 - making usageList (104 chroms): 1 millis pass2 - checking and writing primary data (5598 records, 4 fields): 11 millis CompletedMACS2peakCalling