Job ID = 6456643 SRX = SRX3873733 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:01:01 prefetch.2.10.7: 1) Downloading 'SRR6927798'... 2020-06-21T11:01:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:02:37 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:02:37 prefetch.2.10.7: 'SRR6927798' is valid 2020-06-21T11:02:37 prefetch.2.10.7: 1) 'SRR6927798' was downloaded successfully 2020-06-21T11:02:37 prefetch.2.10.7: 'SRR6927798' has 0 unresolved dependencies Read 9594732 spots for SRR6927798/SRR6927798.sra Written 9594732 spots for SRR6927798/SRR6927798.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: 00:02:30 9594732 reads; of these: 9594732 (100.00%) were unpaired; of these: 611409 (6.37%) aligned 0 times 7466124 (77.81%) aligned exactly 1 time 1517199 (15.81%) aligned >1 times 93.63% overall alignment rate Time searching: 00:02:30 Overall time: 00:02:30 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] 1691431 / 8983323 = 0.1883 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 20:08:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3873733/SRX3873733.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3873733/SRX3873733.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3873733/SRX3873733.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3873733/SRX3873733.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 20:08:28: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:08:28: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:08:35: 1000000 INFO @ Sun, 21 Jun 2020 20:08:42: 2000000 INFO @ Sun, 21 Jun 2020 20:08:48: 3000000 INFO @ Sun, 21 Jun 2020 20:08:55: 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 20:08:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3873733/SRX3873733.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3873733/SRX3873733.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3873733/SRX3873733.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3873733/SRX3873733.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 20:08:58: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:08:58: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:09:02: 5000000 INFO @ Sun, 21 Jun 2020 20:09:05: 1000000 INFO @ Sun, 21 Jun 2020 20:09:09: 6000000 INFO @ Sun, 21 Jun 2020 20:09:11: 2000000 INFO @ Sun, 21 Jun 2020 20:09:16: 7000000 INFO @ Sun, 21 Jun 2020 20:09:18: 3000000 INFO @ Sun, 21 Jun 2020 20:09:18: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 20:09:18: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 20:09:18: #1 total tags in treatment: 7291892 INFO @ Sun, 21 Jun 2020 20:09:18: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:09:18: #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 20:09:19: #1 tags after filtering in treatment: 7291689 INFO @ Sun, 21 Jun 2020 20:09:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:09:19: #1 finished! INFO @ Sun, 21 Jun 2020 20:09:19: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:09:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:09:20: #2 number of paired peaks: 4855 INFO @ Sun, 21 Jun 2020 20:09:20: start model_add_line... INFO @ Sun, 21 Jun 2020 20:09:20: start X-correlation... INFO @ Sun, 21 Jun 2020 20:09:20: end of X-cor INFO @ Sun, 21 Jun 2020 20:09:20: #2 finished! INFO @ Sun, 21 Jun 2020 20:09:20: #2 predicted fragment length is 186 bps INFO @ Sun, 21 Jun 2020 20:09:20: #2 alternative fragment length(s) may be 186 bps INFO @ Sun, 21 Jun 2020 20:09:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3873733/SRX3873733.05_model.r INFO @ Sun, 21 Jun 2020 20:09:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:09:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:09:25: 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 20:09:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3873733/SRX3873733.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3873733/SRX3873733.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3873733/SRX3873733.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3873733/SRX3873733.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 20:09:28: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:09:28: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:09:32: 5000000 INFO @ Sun, 21 Jun 2020 20:09:35: 1000000 INFO @ Sun, 21 Jun 2020 20:09:39: 6000000 INFO @ Sun, 21 Jun 2020 20:09:42: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:09:43: 2000000 INFO @ Sun, 21 Jun 2020 20:09:47: 7000000 INFO @ Sun, 21 Jun 2020 20:09:49: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 20:09:49: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 20:09:49: #1 total tags in treatment: 7291892 INFO @ Sun, 21 Jun 2020 20:09:49: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:09:49: #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 20:09:49: #1 tags after filtering in treatment: 7291689 INFO @ Sun, 21 Jun 2020 20:09:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:09:49: #1 finished! INFO @ Sun, 21 Jun 2020 20:09:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:09:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:09:50: #2 number of paired peaks: 4855 INFO @ Sun, 21 Jun 2020 20:09:50: start model_add_line... INFO @ Sun, 21 Jun 2020 20:09:50: start X-correlation... INFO @ Sun, 21 Jun 2020 20:09:50: end of X-cor INFO @ Sun, 21 Jun 2020 20:09:50: #2 finished! INFO @ Sun, 21 Jun 2020 20:09:50: #2 predicted fragment length is 186 bps INFO @ Sun, 21 Jun 2020 20:09:50: #2 alternative fragment length(s) may be 186 bps INFO @ Sun, 21 Jun 2020 20:09:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3873733/SRX3873733.10_model.r INFO @ Sun, 21 Jun 2020 20:09:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:09:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:09:51: 3000000 INFO @ Sun, 21 Jun 2020 20:09:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3873733/SRX3873733.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:09:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3873733/SRX3873733.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:09:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3873733/SRX3873733.05_summits.bed INFO @ Sun, 21 Jun 2020 20:09:53: Done! pass1 - making usageList (158 chroms): 2 millis pass2 - checking and writing primary data (7376 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:09:58: 4000000 INFO @ Sun, 21 Jun 2020 20:10:05: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:10:11: 6000000 INFO @ Sun, 21 Jun 2020 20:10:12: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:10:19: 7000000 INFO @ Sun, 21 Jun 2020 20:10:21: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 20:10:21: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 20:10:21: #1 total tags in treatment: 7291892 INFO @ Sun, 21 Jun 2020 20:10:21: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:10:21: #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 20:10:21: #1 tags after filtering in treatment: 7291689 INFO @ Sun, 21 Jun 2020 20:10:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:10:21: #1 finished! INFO @ Sun, 21 Jun 2020 20:10:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:10:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:10:22: #2 number of paired peaks: 4855 INFO @ Sun, 21 Jun 2020 20:10:22: start model_add_line... INFO @ Sun, 21 Jun 2020 20:10:22: start X-correlation... INFO @ Sun, 21 Jun 2020 20:10:22: end of X-cor INFO @ Sun, 21 Jun 2020 20:10:22: #2 finished! INFO @ Sun, 21 Jun 2020 20:10:22: #2 predicted fragment length is 186 bps INFO @ Sun, 21 Jun 2020 20:10:22: #2 alternative fragment length(s) may be 186 bps INFO @ Sun, 21 Jun 2020 20:10:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3873733/SRX3873733.20_model.r INFO @ Sun, 21 Jun 2020 20:10:22: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:10:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:10:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3873733/SRX3873733.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:10:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3873733/SRX3873733.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:10:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3873733/SRX3873733.10_summits.bed INFO @ Sun, 21 Jun 2020 20:10:23: Done! pass1 - making usageList (131 chroms): 2 millis pass2 - checking and writing primary data (5580 records, 4 fields): 11 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:10:44: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:10:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3873733/SRX3873733.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:10:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3873733/SRX3873733.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:10:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3873733/SRX3873733.20_summits.bed INFO @ Sun, 21 Jun 2020 20:10:55: Done! pass1 - making usageList (99 chroms): 2 millis pass2 - checking and writing primary data (3638 records, 4 fields): 7 millis CompletedMACS2peakCalling