Job ID = 6452445 SRX = SRX013065 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:36:12 prefetch.2.10.7: 1) Downloading 'SRR030331'... 2020-06-21T07:36:12 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:37:24 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:37:24 prefetch.2.10.7: 'SRR030331' is valid 2020-06-21T07:37:24 prefetch.2.10.7: 1) 'SRR030331' was downloaded successfully Read 7018791 spots for SRR030331/SRR030331.sra Written 7018791 spots for SRR030331/SRR030331.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: 00:01:05 7018791 reads; of these: 7018791 (100.00%) were unpaired; of these: 165635 (2.36%) aligned 0 times 6060548 (86.35%) aligned exactly 1 time 792608 (11.29%) aligned >1 times 97.64% overall alignment rate Time searching: 00:01:05 Overall time: 00:01:05 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] 511434 / 6853156 = 0.0746 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 16:40:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013065/SRX013065.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013065/SRX013065.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013065/SRX013065.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013065/SRX013065.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 16:40:46: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:40:46: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:40:51: 1000000 INFO @ Sun, 21 Jun 2020 16:40:56: 2000000 INFO @ Sun, 21 Jun 2020 16:41:01: 3000000 INFO @ Sun, 21 Jun 2020 16:41:06: 4000000 INFO @ Sun, 21 Jun 2020 16:41:11: 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 16:41:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013065/SRX013065.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013065/SRX013065.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013065/SRX013065.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013065/SRX013065.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 16:41:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:41:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:41:17: 6000000 INFO @ Sun, 21 Jun 2020 16:41:19: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:41:19: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:41:19: #1 total tags in treatment: 6341722 INFO @ Sun, 21 Jun 2020 16:41:19: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:41:19: #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 16:41:19: #1 tags after filtering in treatment: 6341562 INFO @ Sun, 21 Jun 2020 16:41:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:41:19: #1 finished! INFO @ Sun, 21 Jun 2020 16:41:19: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:41:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:41:20: #2 number of paired peaks: 2356 INFO @ Sun, 21 Jun 2020 16:41:20: start model_add_line... INFO @ Sun, 21 Jun 2020 16:41:20: start X-correlation... INFO @ Sun, 21 Jun 2020 16:41:20: end of X-cor INFO @ Sun, 21 Jun 2020 16:41:20: #2 finished! INFO @ Sun, 21 Jun 2020 16:41:20: #2 predicted fragment length is 143 bps INFO @ Sun, 21 Jun 2020 16:41:20: #2 alternative fragment length(s) may be 143 bps INFO @ Sun, 21 Jun 2020 16:41:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013065/SRX013065.05_model.r INFO @ Sun, 21 Jun 2020 16:41:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:41:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:41:21: 1000000 INFO @ Sun, 21 Jun 2020 16:41:26: 2000000 INFO @ Sun, 21 Jun 2020 16:41:32: 3000000 INFO @ Sun, 21 Jun 2020 16:41:33: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:41:37: 4000000 INFO @ Sun, 21 Jun 2020 16:41:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013065/SRX013065.05_peaks.xls INFO @ Sun, 21 Jun 2020 16:41:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013065/SRX013065.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:41:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013065/SRX013065.05_summits.bed INFO @ Sun, 21 Jun 2020 16:41:40: Done! pass1 - making usageList (115 chroms): 2 millis pass2 - checking and writing primary data (7262 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:41:42: 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 16:41:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013065/SRX013065.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013065/SRX013065.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013065/SRX013065.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013065/SRX013065.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 16:41:46: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:41:46: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:41:48: 6000000 INFO @ Sun, 21 Jun 2020 16:41:50: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:41:50: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:41:50: #1 total tags in treatment: 6341722 INFO @ Sun, 21 Jun 2020 16:41:50: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:41:50: #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 16:41:50: #1 tags after filtering in treatment: 6341562 INFO @ Sun, 21 Jun 2020 16:41:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:41:50: #1 finished! INFO @ Sun, 21 Jun 2020 16:41:50: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:41:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:41:51: #2 number of paired peaks: 2356 INFO @ Sun, 21 Jun 2020 16:41:51: start model_add_line... INFO @ Sun, 21 Jun 2020 16:41:51: start X-correlation... INFO @ Sun, 21 Jun 2020 16:41:51: end of X-cor INFO @ Sun, 21 Jun 2020 16:41:51: #2 finished! INFO @ Sun, 21 Jun 2020 16:41:51: #2 predicted fragment length is 143 bps INFO @ Sun, 21 Jun 2020 16:41:51: #2 alternative fragment length(s) may be 143 bps INFO @ Sun, 21 Jun 2020 16:41:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013065/SRX013065.10_model.r INFO @ Sun, 21 Jun 2020 16:41:51: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:41:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:41:51: 1000000 INFO @ Sun, 21 Jun 2020 16:41:57: 2000000 INFO @ Sun, 21 Jun 2020 16:42:02: 3000000 INFO @ Sun, 21 Jun 2020 16:42:04: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:42:07: 4000000 INFO @ Sun, 21 Jun 2020 16:42:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013065/SRX013065.10_peaks.xls INFO @ Sun, 21 Jun 2020 16:42:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013065/SRX013065.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:42:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013065/SRX013065.10_summits.bed INFO @ Sun, 21 Jun 2020 16:42:11: Done! BedGraph に変換しました。 BigWig に変換中... pass1 - making usageList (72 chroms): 2 millis pass2 - checking and writing primary data (4033 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:42:13: 5000000 INFO @ Sun, 21 Jun 2020 16:42:18: 6000000 INFO @ Sun, 21 Jun 2020 16:42:20: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:42:20: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:42:20: #1 total tags in treatment: 6341722 INFO @ Sun, 21 Jun 2020 16:42:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:42:20: #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 16:42:20: #1 tags after filtering in treatment: 6341562 INFO @ Sun, 21 Jun 2020 16:42:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:42:20: #1 finished! INFO @ Sun, 21 Jun 2020 16:42:20: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:42:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:42:21: #2 number of paired peaks: 2356 INFO @ Sun, 21 Jun 2020 16:42:21: start model_add_line... INFO @ Sun, 21 Jun 2020 16:42:21: start X-correlation... INFO @ Sun, 21 Jun 2020 16:42:21: end of X-cor INFO @ Sun, 21 Jun 2020 16:42:21: #2 finished! INFO @ Sun, 21 Jun 2020 16:42:21: #2 predicted fragment length is 143 bps INFO @ Sun, 21 Jun 2020 16:42:21: #2 alternative fragment length(s) may be 143 bps INFO @ Sun, 21 Jun 2020 16:42:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013065/SRX013065.20_model.r INFO @ Sun, 21 Jun 2020 16:42:21: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:42:21: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 16:42:35: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:42:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013065/SRX013065.20_peaks.xls INFO @ Sun, 21 Jun 2020 16:42:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013065/SRX013065.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:42:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013065/SRX013065.20_summits.bed INFO @ Sun, 21 Jun 2020 16:42:42: Done! pass1 - making usageList (51 chroms): 1 millis pass2 - checking and writing primary data (1527 records, 4 fields): 5 millis CompletedMACS2peakCalling