Job ID = 6454219 SRX = SRX191912 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:52:19 prefetch.2.10.7: 1) Downloading 'SRR580342'... 2020-06-21T08:52:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:56:32 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:56:33 prefetch.2.10.7: 'SRR580342' is valid 2020-06-21T08:56:33 prefetch.2.10.7: 1) 'SRR580342' was downloaded successfully Read 12220759 spots for SRR580342/SRR580342.sra Written 12220759 spots for SRR580342/SRR580342.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: 00:01:48 12220759 reads; of these: 12220759 (100.00%) were unpaired; of these: 2880969 (23.57%) aligned 0 times 7938435 (64.96%) aligned exactly 1 time 1401355 (11.47%) aligned >1 times 76.43% overall alignment rate Time searching: 00:01:48 Overall time: 00:01:48 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] 3804197 / 9339790 = 0.4073 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 18:01:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX191912/SRX191912.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX191912/SRX191912.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX191912/SRX191912.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX191912/SRX191912.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 18:01:34: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:01:34: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:01:41: 1000000 INFO @ Sun, 21 Jun 2020 18:01:48: 2000000 INFO @ Sun, 21 Jun 2020 18:01:54: 3000000 INFO @ Sun, 21 Jun 2020 18:02:01: 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 18:02:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX191912/SRX191912.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX191912/SRX191912.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX191912/SRX191912.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX191912/SRX191912.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 18:02:04: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:02:04: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:02:08: 5000000 INFO @ Sun, 21 Jun 2020 18:02:12: 1000000 INFO @ Sun, 21 Jun 2020 18:02:12: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:02:12: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:02:12: #1 total tags in treatment: 5535593 INFO @ Sun, 21 Jun 2020 18:02:12: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:02:12: #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 18:02:12: #1 tags after filtering in treatment: 5535366 INFO @ Sun, 21 Jun 2020 18:02:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:02:12: #1 finished! INFO @ Sun, 21 Jun 2020 18:02:12: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:02:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:02:13: #2 number of paired peaks: 4484 INFO @ Sun, 21 Jun 2020 18:02:13: start model_add_line... INFO @ Sun, 21 Jun 2020 18:02:13: start X-correlation... INFO @ Sun, 21 Jun 2020 18:02:13: end of X-cor INFO @ Sun, 21 Jun 2020 18:02:13: #2 finished! INFO @ Sun, 21 Jun 2020 18:02:13: #2 predicted fragment length is 115 bps INFO @ Sun, 21 Jun 2020 18:02:13: #2 alternative fragment length(s) may be 115 bps INFO @ Sun, 21 Jun 2020 18:02:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX191912/SRX191912.05_model.r INFO @ Sun, 21 Jun 2020 18:02:13: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:02:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:02:18: 2000000 INFO @ Sun, 21 Jun 2020 18:02:25: 3000000 INFO @ Sun, 21 Jun 2020 18:02:27: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:02:32: 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 18:02:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX191912/SRX191912.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:02:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX191912/SRX191912.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:02:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX191912/SRX191912.05_summits.bed INFO @ Sun, 21 Jun 2020 18:02:34: Done! pass1 - making usageList (225 chroms): 2 millis pass2 - checking and writing primary data (8812 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:02:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX191912/SRX191912.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX191912/SRX191912.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX191912/SRX191912.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX191912/SRX191912.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 18:02:34: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:02:34: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:02:39: 5000000 INFO @ Sun, 21 Jun 2020 18:02:42: 1000000 INFO @ Sun, 21 Jun 2020 18:02:43: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:02:43: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:02:43: #1 total tags in treatment: 5535593 INFO @ Sun, 21 Jun 2020 18:02:43: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:02:43: #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 18:02:43: #1 tags after filtering in treatment: 5535366 INFO @ Sun, 21 Jun 2020 18:02:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:02:43: #1 finished! INFO @ Sun, 21 Jun 2020 18:02:43: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:02:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:02:44: #2 number of paired peaks: 4484 INFO @ Sun, 21 Jun 2020 18:02:44: start model_add_line... INFO @ Sun, 21 Jun 2020 18:02:44: start X-correlation... INFO @ Sun, 21 Jun 2020 18:02:44: end of X-cor INFO @ Sun, 21 Jun 2020 18:02:44: #2 finished! INFO @ Sun, 21 Jun 2020 18:02:44: #2 predicted fragment length is 115 bps INFO @ Sun, 21 Jun 2020 18:02:44: #2 alternative fragment length(s) may be 115 bps INFO @ Sun, 21 Jun 2020 18:02:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX191912/SRX191912.10_model.r INFO @ Sun, 21 Jun 2020 18:02:44: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:02:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:02:48: 2000000 INFO @ Sun, 21 Jun 2020 18:02:55: 3000000 INFO @ Sun, 21 Jun 2020 18:02:58: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:03:02: 4000000 INFO @ Sun, 21 Jun 2020 18:03:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX191912/SRX191912.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:03:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX191912/SRX191912.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:03:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX191912/SRX191912.10_summits.bed INFO @ Sun, 21 Jun 2020 18:03:05: Done! pass1 - making usageList (168 chroms): 2 millis pass2 - checking and writing primary data (6673 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:03:08: 5000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:03:12: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:03:12: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:03:12: #1 total tags in treatment: 5535593 INFO @ Sun, 21 Jun 2020 18:03:12: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:03:12: #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 18:03:12: #1 tags after filtering in treatment: 5535366 INFO @ Sun, 21 Jun 2020 18:03:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:03:12: #1 finished! INFO @ Sun, 21 Jun 2020 18:03:12: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:03:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:03:13: #2 number of paired peaks: 4484 INFO @ Sun, 21 Jun 2020 18:03:13: start model_add_line... INFO @ Sun, 21 Jun 2020 18:03:13: start X-correlation... INFO @ Sun, 21 Jun 2020 18:03:13: end of X-cor INFO @ Sun, 21 Jun 2020 18:03:13: #2 finished! INFO @ Sun, 21 Jun 2020 18:03:13: #2 predicted fragment length is 115 bps INFO @ Sun, 21 Jun 2020 18:03:13: #2 alternative fragment length(s) may be 115 bps INFO @ Sun, 21 Jun 2020 18:03:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX191912/SRX191912.20_model.r INFO @ Sun, 21 Jun 2020 18:03:13: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:03:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:03:26: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:03:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX191912/SRX191912.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:03:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX191912/SRX191912.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:03:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX191912/SRX191912.20_summits.bed INFO @ Sun, 21 Jun 2020 18:03:32: Done! pass1 - making usageList (125 chroms): 1 millis pass2 - checking and writing primary data (4664 records, 4 fields): 9 millis CompletedMACS2peakCalling