Job ID = 6453896 SRX = SRX1561065 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:56:04 prefetch.2.10.7: 1) Downloading 'SRR3145067'... 2020-06-21T08:56:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:57:18 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:57:19 prefetch.2.10.7: 'SRR3145067' is valid 2020-06-21T08:57:19 prefetch.2.10.7: 1) 'SRR3145067' was downloaded successfully Read 11186422 spots for SRR3145067/SRR3145067.sra Written 11186422 spots for SRR3145067/SRR3145067.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: 00:01:38 11186422 reads; of these: 11186422 (100.00%) were unpaired; of these: 5989950 (53.55%) aligned 0 times 4494192 (40.18%) aligned exactly 1 time 702280 (6.28%) aligned >1 times 46.45% overall alignment rate Time searching: 00:01:38 Overall time: 00:01:38 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] 1052642 / 5196472 = 0.2026 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 18:01:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1561065/SRX1561065.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1561065/SRX1561065.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1561065/SRX1561065.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1561065/SRX1561065.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 18:01:24: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:01:24: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:01:32: 1000000 INFO @ Sun, 21 Jun 2020 18:01:39: 2000000 INFO @ Sun, 21 Jun 2020 18:01:46: 3000000 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 18:01:53: 4000000 INFO @ Sun, 21 Jun 2020 18:01:54: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:01:54: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:01:54: #1 total tags in treatment: 4143830 INFO @ Sun, 21 Jun 2020 18:01:54: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:01:54: #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 18:01:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1561065/SRX1561065.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1561065/SRX1561065.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1561065/SRX1561065.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1561065/SRX1561065.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 18:01:54: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:01:54: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:01:55: #1 tags after filtering in treatment: 4143716 INFO @ Sun, 21 Jun 2020 18:01:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:01:55: #1 finished! INFO @ Sun, 21 Jun 2020 18:01:55: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:01:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:01:55: #2 number of paired peaks: 2029 INFO @ Sun, 21 Jun 2020 18:01:55: start model_add_line... INFO @ Sun, 21 Jun 2020 18:01:55: start X-correlation... INFO @ Sun, 21 Jun 2020 18:01:55: end of X-cor INFO @ Sun, 21 Jun 2020 18:01:55: #2 finished! INFO @ Sun, 21 Jun 2020 18:01:55: #2 predicted fragment length is 180 bps INFO @ Sun, 21 Jun 2020 18:01:55: #2 alternative fragment length(s) may be 4,180,201 bps INFO @ Sun, 21 Jun 2020 18:01:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1561065/SRX1561065.05_model.r INFO @ Sun, 21 Jun 2020 18:01:55: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:01:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:02:01: 1000000 INFO @ Sun, 21 Jun 2020 18:02:04: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:02:07: 2000000 INFO @ Sun, 21 Jun 2020 18:02:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1561065/SRX1561065.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:02:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1561065/SRX1561065.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:02:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1561065/SRX1561065.05_summits.bed INFO @ Sun, 21 Jun 2020 18:02:09: Done! pass1 - making usageList (363 chroms): 1 millis pass2 - checking and writing primary data (705 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:02:13: 3000000 INFO @ Sun, 21 Jun 2020 18:02:19: 4000000 INFO @ Sun, 21 Jun 2020 18:02:20: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:02:20: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:02:20: #1 total tags in treatment: 4143830 INFO @ Sun, 21 Jun 2020 18:02:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:02:20: #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 18:02:20: #1 tags after filtering in treatment: 4143716 INFO @ Sun, 21 Jun 2020 18:02:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:02:20: #1 finished! INFO @ Sun, 21 Jun 2020 18:02:20: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:02:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:02:21: #2 number of paired peaks: 2029 INFO @ Sun, 21 Jun 2020 18:02:21: start model_add_line... INFO @ Sun, 21 Jun 2020 18:02:21: start X-correlation... INFO @ Sun, 21 Jun 2020 18:02:21: end of X-cor INFO @ Sun, 21 Jun 2020 18:02:21: #2 finished! INFO @ Sun, 21 Jun 2020 18:02:21: #2 predicted fragment length is 180 bps INFO @ Sun, 21 Jun 2020 18:02:21: #2 alternative fragment length(s) may be 4,180,201 bps INFO @ Sun, 21 Jun 2020 18:02:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1561065/SRX1561065.10_model.r INFO @ Sun, 21 Jun 2020 18:02:21: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:02:21: #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 18:02:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1561065/SRX1561065.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1561065/SRX1561065.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1561065/SRX1561065.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1561065/SRX1561065.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 18:02:24: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:02:24: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:02:30: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:02:32: 1000000 INFO @ Sun, 21 Jun 2020 18:02:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1561065/SRX1561065.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:02:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1561065/SRX1561065.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:02:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1561065/SRX1561065.10_summits.bed INFO @ Sun, 21 Jun 2020 18:02:34: Done! pass1 - making usageList (186 chroms): 1 millis pass2 - checking and writing primary data (274 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:02:39: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:02:46: 3000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:02:54: 4000000 INFO @ Sun, 21 Jun 2020 18:02:55: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:02:55: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:02:55: #1 total tags in treatment: 4143830 INFO @ Sun, 21 Jun 2020 18:02:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:02:55: #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 18:02:55: #1 tags after filtering in treatment: 4143716 INFO @ Sun, 21 Jun 2020 18:02:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:02:55: #1 finished! INFO @ Sun, 21 Jun 2020 18:02:55: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:02:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:02:56: #2 number of paired peaks: 2029 INFO @ Sun, 21 Jun 2020 18:02:56: start model_add_line... INFO @ Sun, 21 Jun 2020 18:02:56: start X-correlation... INFO @ Sun, 21 Jun 2020 18:02:56: end of X-cor INFO @ Sun, 21 Jun 2020 18:02:56: #2 finished! INFO @ Sun, 21 Jun 2020 18:02:56: #2 predicted fragment length is 180 bps INFO @ Sun, 21 Jun 2020 18:02:56: #2 alternative fragment length(s) may be 4,180,201 bps INFO @ Sun, 21 Jun 2020 18:02:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1561065/SRX1561065.20_model.r INFO @ Sun, 21 Jun 2020 18:02:56: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:02:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:03:05: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:03:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1561065/SRX1561065.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:03:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1561065/SRX1561065.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:03:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1561065/SRX1561065.20_summits.bed INFO @ Sun, 21 Jun 2020 18:03:10: Done! pass1 - making usageList (62 chroms): 1 millis pass2 - checking and writing primary data (84 records, 4 fields): 3 millis CompletedMACS2peakCalling