Job ID = 6458988 SRX = SRX5849999 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:50:07 prefetch.2.10.7: 1) Downloading 'SRR9074476'... 2020-06-21T12:50:07 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:57:31 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:57:31 prefetch.2.10.7: 1) 'SRR9074476' was downloaded successfully 2020-06-21T12:57:31 prefetch.2.10.7: 'SRR9074476' has 0 unresolved dependencies Read 61710970 spots for SRR9074476/SRR9074476.sra Written 61710970 spots for SRR9074476/SRR9074476.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: 00:07:31 61710970 reads; of these: 61710970 (100.00%) were unpaired; of these: 52189256 (84.57%) aligned 0 times 7372757 (11.95%) aligned exactly 1 time 2148957 (3.48%) aligned >1 times 15.43% overall alignment rate Time searching: 00:07:31 Overall time: 00:07:31 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] 1627089 / 9521714 = 0.1709 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 22:11:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5849999/SRX5849999.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5849999/SRX5849999.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5849999/SRX5849999.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5849999/SRX5849999.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 22:11:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:11:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:11:08: 1000000 INFO @ Sun, 21 Jun 2020 22:11:13: 2000000 INFO @ Sun, 21 Jun 2020 22:11:18: 3000000 INFO @ Sun, 21 Jun 2020 22:11:23: 4000000 INFO @ Sun, 21 Jun 2020 22:11:28: 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 22:11:33: 6000000 INFO @ Sun, 21 Jun 2020 22:11:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5849999/SRX5849999.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5849999/SRX5849999.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5849999/SRX5849999.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5849999/SRX5849999.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 22:11:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:11:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:11:38: 7000000 INFO @ Sun, 21 Jun 2020 22:11:39: 1000000 INFO @ Sun, 21 Jun 2020 22:11:43: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:11:43: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:11:43: #1 total tags in treatment: 7894625 INFO @ Sun, 21 Jun 2020 22:11:43: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:11:43: #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 22:11:43: #1 tags after filtering in treatment: 7894468 INFO @ Sun, 21 Jun 2020 22:11:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:11:43: #1 finished! INFO @ Sun, 21 Jun 2020 22:11:43: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:11:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:11:44: #2 number of paired peaks: 2855 INFO @ Sun, 21 Jun 2020 22:11:44: start model_add_line... INFO @ Sun, 21 Jun 2020 22:11:44: start X-correlation... INFO @ Sun, 21 Jun 2020 22:11:44: end of X-cor INFO @ Sun, 21 Jun 2020 22:11:44: #2 finished! INFO @ Sun, 21 Jun 2020 22:11:44: #2 predicted fragment length is 133 bps INFO @ Sun, 21 Jun 2020 22:11:44: #2 alternative fragment length(s) may be 3,133,165 bps INFO @ Sun, 21 Jun 2020 22:11:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5849999/SRX5849999.05_model.r INFO @ Sun, 21 Jun 2020 22:11:44: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:11:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:11:45: 2000000 INFO @ Sun, 21 Jun 2020 22:11:51: 3000000 INFO @ Sun, 21 Jun 2020 22:11:56: 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 22:12:02: 5000000 INFO @ Sun, 21 Jun 2020 22:12:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5849999/SRX5849999.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5849999/SRX5849999.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5849999/SRX5849999.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5849999/SRX5849999.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 22:12:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:12:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:12:04: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:12:08: 6000000 INFO @ Sun, 21 Jun 2020 22:12:09: 1000000 INFO @ Sun, 21 Jun 2020 22:12:14: 2000000 INFO @ Sun, 21 Jun 2020 22:12:14: 7000000 INFO @ Sun, 21 Jun 2020 22:12:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5849999/SRX5849999.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:12:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5849999/SRX5849999.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:12:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5849999/SRX5849999.05_summits.bed INFO @ Sun, 21 Jun 2020 22:12:14: Done! pass1 - making usageList (352 chroms): 2 millis pass2 - checking and writing primary data (3835 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:12:19: 3000000 INFO @ Sun, 21 Jun 2020 22:12:19: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:12:19: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:12:19: #1 total tags in treatment: 7894625 INFO @ Sun, 21 Jun 2020 22:12:19: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:12:19: #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 22:12:20: #1 tags after filtering in treatment: 7894468 INFO @ Sun, 21 Jun 2020 22:12:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:12:20: #1 finished! INFO @ Sun, 21 Jun 2020 22:12:20: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:12:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:12:20: #2 number of paired peaks: 2855 INFO @ Sun, 21 Jun 2020 22:12:20: start model_add_line... INFO @ Sun, 21 Jun 2020 22:12:21: start X-correlation... INFO @ Sun, 21 Jun 2020 22:12:21: end of X-cor INFO @ Sun, 21 Jun 2020 22:12:21: #2 finished! INFO @ Sun, 21 Jun 2020 22:12:21: #2 predicted fragment length is 133 bps INFO @ Sun, 21 Jun 2020 22:12:21: #2 alternative fragment length(s) may be 3,133,165 bps INFO @ Sun, 21 Jun 2020 22:12:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5849999/SRX5849999.10_model.r INFO @ Sun, 21 Jun 2020 22:12:21: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:12:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:12:24: 4000000 INFO @ Sun, 21 Jun 2020 22:12:29: 5000000 INFO @ Sun, 21 Jun 2020 22:12:34: 6000000 INFO @ Sun, 21 Jun 2020 22:12:40: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:12:40: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:12:45: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:12:45: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:12:45: #1 total tags in treatment: 7894625 INFO @ Sun, 21 Jun 2020 22:12:45: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:12:45: #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 22:12:45: #1 tags after filtering in treatment: 7894468 INFO @ Sun, 21 Jun 2020 22:12:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:12:45: #1 finished! INFO @ Sun, 21 Jun 2020 22:12:45: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:12:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:12:46: #2 number of paired peaks: 2855 INFO @ Sun, 21 Jun 2020 22:12:46: start model_add_line... INFO @ Sun, 21 Jun 2020 22:12:46: start X-correlation... INFO @ Sun, 21 Jun 2020 22:12:46: end of X-cor INFO @ Sun, 21 Jun 2020 22:12:46: #2 finished! INFO @ Sun, 21 Jun 2020 22:12:46: #2 predicted fragment length is 133 bps INFO @ Sun, 21 Jun 2020 22:12:46: #2 alternative fragment length(s) may be 3,133,165 bps INFO @ Sun, 21 Jun 2020 22:12:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5849999/SRX5849999.20_model.r INFO @ Sun, 21 Jun 2020 22:12:46: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:12:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:12:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5849999/SRX5849999.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:12:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5849999/SRX5849999.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:12:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5849999/SRX5849999.10_summits.bed INFO @ Sun, 21 Jun 2020 22:12:49: Done! pass1 - making usageList (185 chroms): 1 millis pass2 - checking and writing primary data (1111 records, 4 fields): 8 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:13:07: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:13:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5849999/SRX5849999.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:13:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5849999/SRX5849999.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:13:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5849999/SRX5849999.20_summits.bed INFO @ Sun, 21 Jun 2020 22:13:19: Done! pass1 - making usageList (129 chroms): 1 millis pass2 - checking and writing primary data (328 records, 4 fields): 6 millis CompletedMACS2peakCalling