Job ID = 6454403 SRX = SRX2033489 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:30:59 prefetch.2.10.7: 1) Downloading 'SRR4042504'... 2020-06-21T09:30:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:33:12 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:33:13 prefetch.2.10.7: 'SRR4042504' is valid 2020-06-21T09:33:13 prefetch.2.10.7: 1) 'SRR4042504' was downloaded successfully 2020-06-21T09:33:13 prefetch.2.10.7: 'SRR4042504' has 0 unresolved dependencies Read 10706947 spots for SRR4042504/SRR4042504.sra Written 10706947 spots for SRR4042504/SRR4042504.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: 00:02:35 10706947 reads; of these: 10706947 (100.00%) were unpaired; of these: 807039 (7.54%) aligned 0 times 7495743 (70.01%) aligned exactly 1 time 2404165 (22.45%) aligned >1 times 92.46% overall alignment rate Time searching: 00:02:35 Overall time: 00:02:35 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] 4036051 / 9899908 = 0.4077 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 18:38:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2033489/SRX2033489.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2033489/SRX2033489.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2033489/SRX2033489.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2033489/SRX2033489.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 18:38:59: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:38:59: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:39:04: 1000000 INFO @ Sun, 21 Jun 2020 18:39:08: 2000000 INFO @ Sun, 21 Jun 2020 18:39:13: 3000000 INFO @ Sun, 21 Jun 2020 18:39:19: 4000000 INFO @ Sun, 21 Jun 2020 18:39:25: 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 18:39:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2033489/SRX2033489.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2033489/SRX2033489.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2033489/SRX2033489.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2033489/SRX2033489.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 18:39:29: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:39:29: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:39:30: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:39:30: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:39:30: #1 total tags in treatment: 5863857 INFO @ Sun, 21 Jun 2020 18:39:30: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:39:30: #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 18:39:30: #1 tags after filtering in treatment: 5863687 INFO @ Sun, 21 Jun 2020 18:39:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:39:30: #1 finished! INFO @ Sun, 21 Jun 2020 18:39:30: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:39:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:39:31: #2 number of paired peaks: 5071 INFO @ Sun, 21 Jun 2020 18:39:31: start model_add_line... INFO @ Sun, 21 Jun 2020 18:39:31: start X-correlation... INFO @ Sun, 21 Jun 2020 18:39:31: end of X-cor INFO @ Sun, 21 Jun 2020 18:39:31: #2 finished! INFO @ Sun, 21 Jun 2020 18:39:31: #2 predicted fragment length is 153 bps INFO @ Sun, 21 Jun 2020 18:39:31: #2 alternative fragment length(s) may be 153 bps INFO @ Sun, 21 Jun 2020 18:39:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2033489/SRX2033489.05_model.r INFO @ Sun, 21 Jun 2020 18:39:31: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:39:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:39:34: 1000000 INFO @ Sun, 21 Jun 2020 18:39:40: 2000000 INFO @ Sun, 21 Jun 2020 18:39:45: 3000000 INFO @ Sun, 21 Jun 2020 18:39:46: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:39:50: 4000000 INFO @ Sun, 21 Jun 2020 18:39:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2033489/SRX2033489.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:39:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2033489/SRX2033489.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:39:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2033489/SRX2033489.05_summits.bed INFO @ Sun, 21 Jun 2020 18:39:53: Done! pass1 - making usageList (294 chroms): 2 millis pass2 - checking and writing primary data (10076 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:39:55: 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 18:39:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2033489/SRX2033489.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2033489/SRX2033489.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2033489/SRX2033489.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2033489/SRX2033489.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 18:39:59: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:39:59: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:39:59: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:39:59: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:39:59: #1 total tags in treatment: 5863857 INFO @ Sun, 21 Jun 2020 18:39:59: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:39:59: #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 18:40:00: #1 tags after filtering in treatment: 5863687 INFO @ Sun, 21 Jun 2020 18:40:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:40:00: #1 finished! INFO @ Sun, 21 Jun 2020 18:40:00: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:40:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:40:00: #2 number of paired peaks: 5071 INFO @ Sun, 21 Jun 2020 18:40:00: start model_add_line... INFO @ Sun, 21 Jun 2020 18:40:00: start X-correlation... INFO @ Sun, 21 Jun 2020 18:40:00: end of X-cor INFO @ Sun, 21 Jun 2020 18:40:00: #2 finished! INFO @ Sun, 21 Jun 2020 18:40:00: #2 predicted fragment length is 153 bps INFO @ Sun, 21 Jun 2020 18:40:00: #2 alternative fragment length(s) may be 153 bps INFO @ Sun, 21 Jun 2020 18:40:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2033489/SRX2033489.10_model.r INFO @ Sun, 21 Jun 2020 18:40:00: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:40:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:40:04: 1000000 INFO @ Sun, 21 Jun 2020 18:40:08: 2000000 INFO @ Sun, 21 Jun 2020 18:40:13: 3000000 INFO @ Sun, 21 Jun 2020 18:40:15: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:40:19: 4000000 INFO @ Sun, 21 Jun 2020 18:40:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2033489/SRX2033489.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:40:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2033489/SRX2033489.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:40:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2033489/SRX2033489.10_summits.bed INFO @ Sun, 21 Jun 2020 18:40:22: Done! pass1 - making usageList (204 chroms): 2 millis pass2 - checking and writing primary data (7564 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:40:24: 5000000 INFO @ Sun, 21 Jun 2020 18:40:29: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:40:29: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:40:29: #1 total tags in treatment: 5863857 INFO @ Sun, 21 Jun 2020 18:40:29: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:40:29: #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 18:40:29: #1 tags after filtering in treatment: 5863687 INFO @ Sun, 21 Jun 2020 18:40:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:40:29: #1 finished! INFO @ Sun, 21 Jun 2020 18:40:29: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:40:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:40:30: #2 number of paired peaks: 5071 INFO @ Sun, 21 Jun 2020 18:40:30: start model_add_line... INFO @ Sun, 21 Jun 2020 18:40:30: start X-correlation... INFO @ Sun, 21 Jun 2020 18:40:30: end of X-cor INFO @ Sun, 21 Jun 2020 18:40:30: #2 finished! INFO @ Sun, 21 Jun 2020 18:40:30: #2 predicted fragment length is 153 bps INFO @ Sun, 21 Jun 2020 18:40:30: #2 alternative fragment length(s) may be 153 bps INFO @ Sun, 21 Jun 2020 18:40:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2033489/SRX2033489.20_model.r INFO @ Sun, 21 Jun 2020 18:40:30: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:40:30: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:40:45: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:40:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2033489/SRX2033489.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:40:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2033489/SRX2033489.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:40:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2033489/SRX2033489.20_summits.bed INFO @ Sun, 21 Jun 2020 18:40:52: Done! pass1 - making usageList (150 chroms): 1 millis pass2 - checking and writing primary data (4792 records, 4 fields): 13 millis CompletedMACS2peakCalling