Job ID = 6455815 SRX = SRX3009522 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:37:44 prefetch.2.10.7: 1) Downloading 'SRR5832223'... 2020-06-21T10:37:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:40:05 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:40:05 prefetch.2.10.7: 'SRR5832223' is valid 2020-06-21T10:40:05 prefetch.2.10.7: 1) 'SRR5832223' was downloaded successfully Read 10647897 spots for SRR5832223/SRR5832223.sra Written 10647897 spots for SRR5832223/SRR5832223.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: 00:02:39 10647897 reads; of these: 10647897 (100.00%) were unpaired; of these: 5115413 (48.04%) aligned 0 times 3704642 (34.79%) aligned exactly 1 time 1827842 (17.17%) aligned >1 times 51.96% overall alignment rate Time searching: 00:02:39 Overall time: 00:02:39 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] 2831152 / 5532484 = 0.5117 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 19:44:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3009522/SRX3009522.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3009522/SRX3009522.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3009522/SRX3009522.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3009522/SRX3009522.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 19:44:56: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:44:56: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:45:02: 1000000 INFO @ Sun, 21 Jun 2020 19:45:07: 2000000 INFO @ Sun, 21 Jun 2020 19:45:11: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:45:11: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:45:11: #1 total tags in treatment: 2701332 INFO @ Sun, 21 Jun 2020 19:45:11: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:45:11: #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 19:45:11: #1 tags after filtering in treatment: 2701030 INFO @ Sun, 21 Jun 2020 19:45:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:45:11: #1 finished! INFO @ Sun, 21 Jun 2020 19:45:11: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:45:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:45:11: #2 number of paired peaks: 1420 INFO @ Sun, 21 Jun 2020 19:45:11: start model_add_line... INFO @ Sun, 21 Jun 2020 19:45:11: start X-correlation... INFO @ Sun, 21 Jun 2020 19:45:11: end of X-cor INFO @ Sun, 21 Jun 2020 19:45:11: #2 finished! INFO @ Sun, 21 Jun 2020 19:45:11: #2 predicted fragment length is 145 bps INFO @ Sun, 21 Jun 2020 19:45:11: #2 alternative fragment length(s) may be 145 bps INFO @ Sun, 21 Jun 2020 19:45:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3009522/SRX3009522.05_model.r INFO @ Sun, 21 Jun 2020 19:45:11: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:45:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:45:18: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:45:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3009522/SRX3009522.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:45:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3009522/SRX3009522.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:45:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3009522/SRX3009522.05_summits.bed INFO @ Sun, 21 Jun 2020 19:45:21: Done! pass1 - making usageList (441 chroms): 2 millis pass2 - checking and writing primary data (1684 records, 4 fields): 15 millis CompletedMACS2peakCalling 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 19:45:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3009522/SRX3009522.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3009522/SRX3009522.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3009522/SRX3009522.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3009522/SRX3009522.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 19:45:26: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:45:26: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:45:32: 1000000 INFO @ Sun, 21 Jun 2020 19:45:37: 2000000 INFO @ Sun, 21 Jun 2020 19:45:41: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:45:41: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:45:41: #1 total tags in treatment: 2701332 INFO @ Sun, 21 Jun 2020 19:45:41: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:45:41: #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 19:45:41: #1 tags after filtering in treatment: 2701030 INFO @ Sun, 21 Jun 2020 19:45:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:45:41: #1 finished! INFO @ Sun, 21 Jun 2020 19:45:41: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:45:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:45:41: #2 number of paired peaks: 1420 INFO @ Sun, 21 Jun 2020 19:45:41: start model_add_line... INFO @ Sun, 21 Jun 2020 19:45:41: start X-correlation... INFO @ Sun, 21 Jun 2020 19:45:41: end of X-cor INFO @ Sun, 21 Jun 2020 19:45:41: #2 finished! INFO @ Sun, 21 Jun 2020 19:45:41: #2 predicted fragment length is 145 bps INFO @ Sun, 21 Jun 2020 19:45:41: #2 alternative fragment length(s) may be 145 bps INFO @ Sun, 21 Jun 2020 19:45:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3009522/SRX3009522.10_model.r INFO @ Sun, 21 Jun 2020 19:45:41: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:45:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:45:48: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:45:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3009522/SRX3009522.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:45:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3009522/SRX3009522.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:45:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3009522/SRX3009522.10_summits.bed INFO @ Sun, 21 Jun 2020 19:45:51: Done! pass1 - making usageList (250 chroms): 1 millis pass2 - checking and writing primary data (533 records, 4 fields): 8 millis CompletedMACS2peakCalling 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 19:45:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3009522/SRX3009522.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3009522/SRX3009522.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3009522/SRX3009522.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3009522/SRX3009522.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 19:45:56: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:45:56: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:46:02: 1000000 INFO @ Sun, 21 Jun 2020 19:46:07: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:46:11: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:46:11: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:46:11: #1 total tags in treatment: 2701332 INFO @ Sun, 21 Jun 2020 19:46:11: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:46:11: #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 19:46:11: #1 tags after filtering in treatment: 2701030 INFO @ Sun, 21 Jun 2020 19:46:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:46:11: #1 finished! INFO @ Sun, 21 Jun 2020 19:46:11: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:46:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:46:12: #2 number of paired peaks: 1420 INFO @ Sun, 21 Jun 2020 19:46:12: start model_add_line... INFO @ Sun, 21 Jun 2020 19:46:12: start X-correlation... INFO @ Sun, 21 Jun 2020 19:46:12: end of X-cor INFO @ Sun, 21 Jun 2020 19:46:12: #2 finished! INFO @ Sun, 21 Jun 2020 19:46:12: #2 predicted fragment length is 145 bps INFO @ Sun, 21 Jun 2020 19:46:12: #2 alternative fragment length(s) may be 145 bps INFO @ Sun, 21 Jun 2020 19:46:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3009522/SRX3009522.20_model.r INFO @ Sun, 21 Jun 2020 19:46:12: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:46:12: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:46:18: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:46:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3009522/SRX3009522.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:46:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3009522/SRX3009522.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:46:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3009522/SRX3009522.20_summits.bed INFO @ Sun, 21 Jun 2020 19:46:21: Done! pass1 - making usageList (118 chroms): 1 millis pass2 - checking and writing primary data (170 records, 4 fields): 3 millis CompletedMACS2peakCalling