Job ID = 6457211 SRX = SRX4563533 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:37:40 prefetch.2.10.7: 1) Downloading 'SRR7706260'... 2020-06-21T11:37:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:39:32 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:39:33 prefetch.2.10.7: 'SRR7706260' is valid 2020-06-21T11:39:33 prefetch.2.10.7: 1) 'SRR7706260' was downloaded successfully Read 7110787 spots for SRR7706260/SRR7706260.sra Written 7110787 spots for SRR7706260/SRR7706260.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: 00:01:43 7110787 reads; of these: 7110787 (100.00%) were unpaired; of these: 1672810 (23.52%) aligned 0 times 4115506 (57.88%) aligned exactly 1 time 1322471 (18.60%) aligned >1 times 76.48% overall alignment rate Time searching: 00:01:43 Overall time: 00:01:43 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] 1590921 / 5437977 = 0.2926 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 20:43:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4563533/SRX4563533.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4563533/SRX4563533.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4563533/SRX4563533.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4563533/SRX4563533.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 20:43:26: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:43:26: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:43:31: 1000000 INFO @ Sun, 21 Jun 2020 20:43:36: 2000000 INFO @ Sun, 21 Jun 2020 20:43:42: 3000000 INFO @ Sun, 21 Jun 2020 20:43:46: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:43:46: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:43:46: #1 total tags in treatment: 3847056 INFO @ Sun, 21 Jun 2020 20:43:46: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:43:46: #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 20:43:46: #1 tags after filtering in treatment: 3846871 INFO @ Sun, 21 Jun 2020 20:43:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:43:46: #1 finished! INFO @ Sun, 21 Jun 2020 20:43:46: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:43:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:43:47: #2 number of paired peaks: 1435 INFO @ Sun, 21 Jun 2020 20:43:47: start model_add_line... INFO @ Sun, 21 Jun 2020 20:43:47: start X-correlation... INFO @ Sun, 21 Jun 2020 20:43:47: end of X-cor INFO @ Sun, 21 Jun 2020 20:43:47: #2 finished! INFO @ Sun, 21 Jun 2020 20:43:47: #2 predicted fragment length is 223 bps INFO @ Sun, 21 Jun 2020 20:43:47: #2 alternative fragment length(s) may be 223 bps INFO @ Sun, 21 Jun 2020 20:43:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4563533/SRX4563533.05_model.r INFO @ Sun, 21 Jun 2020 20:43:47: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:43:47: #3 Pre-compute pvalue-qvalue table... 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 20:43:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4563533/SRX4563533.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4563533/SRX4563533.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4563533/SRX4563533.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4563533/SRX4563533.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 20:43:56: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:43:56: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:43:56: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:44:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4563533/SRX4563533.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:44:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4563533/SRX4563533.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:44:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4563533/SRX4563533.05_summits.bed INFO @ Sun, 21 Jun 2020 20:44:01: Done! pass1 - making usageList (522 chroms): 1 millis pass2 - checking and writing primary data (2187 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:44:01: 1000000 INFO @ Sun, 21 Jun 2020 20:44:06: 2000000 INFO @ Sun, 21 Jun 2020 20:44:12: 3000000 INFO @ Sun, 21 Jun 2020 20:44:16: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:44:16: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:44:16: #1 total tags in treatment: 3847056 INFO @ Sun, 21 Jun 2020 20:44:16: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:44:16: #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 20:44:17: #1 tags after filtering in treatment: 3846871 INFO @ Sun, 21 Jun 2020 20:44:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:44:17: #1 finished! INFO @ Sun, 21 Jun 2020 20:44:17: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:44:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:44:17: #2 number of paired peaks: 1435 INFO @ Sun, 21 Jun 2020 20:44:17: start model_add_line... INFO @ Sun, 21 Jun 2020 20:44:17: start X-correlation... INFO @ Sun, 21 Jun 2020 20:44:17: end of X-cor INFO @ Sun, 21 Jun 2020 20:44:17: #2 finished! INFO @ Sun, 21 Jun 2020 20:44:17: #2 predicted fragment length is 223 bps INFO @ Sun, 21 Jun 2020 20:44:17: #2 alternative fragment length(s) may be 223 bps INFO @ Sun, 21 Jun 2020 20:44:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4563533/SRX4563533.10_model.r INFO @ Sun, 21 Jun 2020 20:44:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:44:17: #3 Pre-compute pvalue-qvalue table... 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 20:44:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4563533/SRX4563533.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4563533/SRX4563533.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4563533/SRX4563533.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4563533/SRX4563533.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 20:44:26: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:44:26: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:44:26: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:44:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4563533/SRX4563533.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:44:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4563533/SRX4563533.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:44:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4563533/SRX4563533.10_summits.bed INFO @ Sun, 21 Jun 2020 20:44:31: Done! pass1 - making usageList (322 chroms): 1 millis pass2 - checking and writing primary data (1241 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:44:31: 1000000 INFO @ Sun, 21 Jun 2020 20:44:36: 2000000 INFO @ Sun, 21 Jun 2020 20:44:42: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:44:46: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:44:46: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:44:46: #1 total tags in treatment: 3847056 INFO @ Sun, 21 Jun 2020 20:44:46: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:44:46: #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 20:44:47: #1 tags after filtering in treatment: 3846871 INFO @ Sun, 21 Jun 2020 20:44:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:44:47: #1 finished! INFO @ Sun, 21 Jun 2020 20:44:47: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:44:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:44:47: #2 number of paired peaks: 1435 INFO @ Sun, 21 Jun 2020 20:44:47: start model_add_line... INFO @ Sun, 21 Jun 2020 20:44:47: start X-correlation... INFO @ Sun, 21 Jun 2020 20:44:47: end of X-cor INFO @ Sun, 21 Jun 2020 20:44:47: #2 finished! INFO @ Sun, 21 Jun 2020 20:44:47: #2 predicted fragment length is 223 bps INFO @ Sun, 21 Jun 2020 20:44:47: #2 alternative fragment length(s) may be 223 bps INFO @ Sun, 21 Jun 2020 20:44:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4563533/SRX4563533.20_model.r INFO @ Sun, 21 Jun 2020 20:44:47: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:44:47: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:44:56: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:45:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4563533/SRX4563533.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:45:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4563533/SRX4563533.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:45:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4563533/SRX4563533.20_summits.bed INFO @ Sun, 21 Jun 2020 20:45:01: Done! pass1 - making usageList (134 chroms): 1 millis pass2 - checking and writing primary data (580 records, 4 fields): 6 millis CompletedMACS2peakCalling