Job ID = 6454919 SRX = SRX2592501 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:20:59 prefetch.2.10.7: 1) Downloading 'SRR5289778'... 2020-06-21T09:20:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:22:37 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:22:38 prefetch.2.10.7: 'SRR5289778' is valid 2020-06-21T09:22:38 prefetch.2.10.7: 1) 'SRR5289778' was downloaded successfully Read 14909251 spots for SRR5289778/SRR5289778.sra Written 14909251 spots for SRR5289778/SRR5289778.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: 00:03:14 14909251 reads; of these: 14909251 (100.00%) were unpaired; of these: 3259518 (21.86%) aligned 0 times 10394565 (69.72%) aligned exactly 1 time 1255168 (8.42%) aligned >1 times 78.14% overall alignment rate Time searching: 00:03:14 Overall time: 00:03:14 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_sort_core] merging from 8 files... [bam_rmdupse_core] 3141996 / 11649733 = 0.2697 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 18:30:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592501/SRX2592501.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592501/SRX2592501.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592501/SRX2592501.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592501/SRX2592501.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 18:30:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:30:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:30:59: 1000000 INFO @ Sun, 21 Jun 2020 18:31:04: 2000000 INFO @ Sun, 21 Jun 2020 18:31:11: 3000000 INFO @ Sun, 21 Jun 2020 18:31:16: 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 18:31:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592501/SRX2592501.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592501/SRX2592501.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592501/SRX2592501.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592501/SRX2592501.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 18:31:22: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:31:22: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:31:22: 5000000 INFO @ Sun, 21 Jun 2020 18:31:28: 6000000 INFO @ Sun, 21 Jun 2020 18:31:29: 1000000 INFO @ Sun, 21 Jun 2020 18:31:34: 7000000 INFO @ Sun, 21 Jun 2020 18:31:36: 2000000 INFO @ Sun, 21 Jun 2020 18:31:40: 8000000 INFO @ Sun, 21 Jun 2020 18:31:43: 3000000 INFO @ Sun, 21 Jun 2020 18:31:44: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:31:44: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:31:44: #1 total tags in treatment: 8507737 INFO @ Sun, 21 Jun 2020 18:31:44: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:31:44: #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 18:31:44: #1 tags after filtering in treatment: 8507508 INFO @ Sun, 21 Jun 2020 18:31:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:31:44: #1 finished! INFO @ Sun, 21 Jun 2020 18:31:44: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:31:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:31:45: #2 number of paired peaks: 9548 INFO @ Sun, 21 Jun 2020 18:31:45: start model_add_line... INFO @ Sun, 21 Jun 2020 18:31:46: start X-correlation... INFO @ Sun, 21 Jun 2020 18:31:46: end of X-cor INFO @ Sun, 21 Jun 2020 18:31:46: #2 finished! INFO @ Sun, 21 Jun 2020 18:31:46: #2 predicted fragment length is 206 bps INFO @ Sun, 21 Jun 2020 18:31:46: #2 alternative fragment length(s) may be 206 bps INFO @ Sun, 21 Jun 2020 18:31:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592501/SRX2592501.05_model.r INFO @ Sun, 21 Jun 2020 18:31:46: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:31:46: #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 18:31:50: 4000000 INFO @ Sun, 21 Jun 2020 18:31:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592501/SRX2592501.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592501/SRX2592501.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592501/SRX2592501.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592501/SRX2592501.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 18:31:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:31:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:31:57: 5000000 INFO @ Sun, 21 Jun 2020 18:31:58: 1000000 INFO @ Sun, 21 Jun 2020 18:32:04: 6000000 INFO @ Sun, 21 Jun 2020 18:32:04: 2000000 INFO @ Sun, 21 Jun 2020 18:32:10: 3000000 INFO @ Sun, 21 Jun 2020 18:32:11: 7000000 INFO @ Sun, 21 Jun 2020 18:32:16: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:32:17: 4000000 INFO @ Sun, 21 Jun 2020 18:32:18: 8000000 INFO @ Sun, 21 Jun 2020 18:32:21: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:32:21: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:32:21: #1 total tags in treatment: 8507737 INFO @ Sun, 21 Jun 2020 18:32:21: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:32:21: #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 18:32:22: #1 tags after filtering in treatment: 8507508 INFO @ Sun, 21 Jun 2020 18:32:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:32:22: #1 finished! INFO @ Sun, 21 Jun 2020 18:32:22: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:32:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:32:23: #2 number of paired peaks: 9548 INFO @ Sun, 21 Jun 2020 18:32:23: start model_add_line... INFO @ Sun, 21 Jun 2020 18:32:23: start X-correlation... INFO @ Sun, 21 Jun 2020 18:32:23: 5000000 INFO @ Sun, 21 Jun 2020 18:32:23: end of X-cor INFO @ Sun, 21 Jun 2020 18:32:23: #2 finished! INFO @ Sun, 21 Jun 2020 18:32:23: #2 predicted fragment length is 206 bps INFO @ Sun, 21 Jun 2020 18:32:23: #2 alternative fragment length(s) may be 206 bps INFO @ Sun, 21 Jun 2020 18:32:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592501/SRX2592501.10_model.r INFO @ Sun, 21 Jun 2020 18:32:23: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:32:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:32:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592501/SRX2592501.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:32:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592501/SRX2592501.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:32:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592501/SRX2592501.05_summits.bed INFO @ Sun, 21 Jun 2020 18:32:28: Done! pass1 - making usageList (98 chroms): 3 millis pass2 - checking and writing primary data (10701 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:32:30: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:32:37: 7000000 INFO @ Sun, 21 Jun 2020 18:32:44: 8000000 INFO @ Sun, 21 Jun 2020 18:32:48: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:32:48: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:32:48: #1 total tags in treatment: 8507737 INFO @ Sun, 21 Jun 2020 18:32:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:32:48: #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 18:32:48: #1 tags after filtering in treatment: 8507508 INFO @ Sun, 21 Jun 2020 18:32:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:32:48: #1 finished! INFO @ Sun, 21 Jun 2020 18:32:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:32:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:32:50: #2 number of paired peaks: 9548 INFO @ Sun, 21 Jun 2020 18:32:50: start model_add_line... INFO @ Sun, 21 Jun 2020 18:32:50: start X-correlation... INFO @ Sun, 21 Jun 2020 18:32:50: end of X-cor INFO @ Sun, 21 Jun 2020 18:32:50: #2 finished! INFO @ Sun, 21 Jun 2020 18:32:50: #2 predicted fragment length is 206 bps INFO @ Sun, 21 Jun 2020 18:32:50: #2 alternative fragment length(s) may be 206 bps INFO @ Sun, 21 Jun 2020 18:32:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592501/SRX2592501.20_model.r INFO @ Sun, 21 Jun 2020 18:32:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:32:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:32:54: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:33:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592501/SRX2592501.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:33:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592501/SRX2592501.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:33:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592501/SRX2592501.10_summits.bed INFO @ Sun, 21 Jun 2020 18:33:06: Done! pass1 - making usageList (66 chroms): 2 millis pass2 - checking and writing primary data (8450 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:33:20: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:33:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592501/SRX2592501.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:33:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592501/SRX2592501.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:33:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592501/SRX2592501.20_summits.bed INFO @ Sun, 21 Jun 2020 18:33:32: Done! pass1 - making usageList (46 chroms): 2 millis pass2 - checking and writing primary data (6278 records, 4 fields): 12 millis CompletedMACS2peakCalling