Job ID = 6453433 SRX = SRX1134708 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:25:41 prefetch.2.10.7: 1) Downloading 'SRR2147089'... 2020-06-21T08:25:41 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:29:27 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:29:27 prefetch.2.10.7: 1) 'SRR2147089' was downloaded successfully 2020-06-21T08:29:27 prefetch.2.10.7: 'SRR2147089' has 0 unresolved dependencies Read 21857555 spots for SRR2147089/SRR2147089.sra Written 21857555 spots for SRR2147089/SRR2147089.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: 00:04:31 21857555 reads; of these: 21857555 (100.00%) were unpaired; of these: 2656886 (12.16%) aligned 0 times 16894247 (77.29%) aligned exactly 1 time 2306422 (10.55%) aligned >1 times 87.84% overall alignment rate Time searching: 00:04:31 Overall time: 00:04:31 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_sort_core] merging from 8 files... [bam_rmdupse_core] 12574796 / 19200669 = 0.6549 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 17:39:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1134708/SRX1134708.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1134708/SRX1134708.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1134708/SRX1134708.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1134708/SRX1134708.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 17:39:07: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:39:07: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:39:12: 1000000 INFO @ Sun, 21 Jun 2020 17:39:18: 2000000 INFO @ Sun, 21 Jun 2020 17:39:23: 3000000 INFO @ Sun, 21 Jun 2020 17:39:28: 4000000 INFO @ Sun, 21 Jun 2020 17:39:33: 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 17:39:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1134708/SRX1134708.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1134708/SRX1134708.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1134708/SRX1134708.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1134708/SRX1134708.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 17:39:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:39:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:39:39: 6000000 INFO @ Sun, 21 Jun 2020 17:39:43: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:39:43: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:39:43: #1 total tags in treatment: 6625873 INFO @ Sun, 21 Jun 2020 17:39:43: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:39:43: #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 17:39:43: #1 tags after filtering in treatment: 6625702 INFO @ Sun, 21 Jun 2020 17:39:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:39:43: #1 finished! INFO @ Sun, 21 Jun 2020 17:39:43: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:39:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:39:44: #2 number of paired peaks: 3508 INFO @ Sun, 21 Jun 2020 17:39:44: start model_add_line... INFO @ Sun, 21 Jun 2020 17:39:44: start X-correlation... INFO @ Sun, 21 Jun 2020 17:39:44: end of X-cor INFO @ Sun, 21 Jun 2020 17:39:44: #2 finished! INFO @ Sun, 21 Jun 2020 17:39:44: #2 predicted fragment length is 205 bps INFO @ Sun, 21 Jun 2020 17:39:44: #2 alternative fragment length(s) may be 205 bps INFO @ Sun, 21 Jun 2020 17:39:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1134708/SRX1134708.05_model.r INFO @ Sun, 21 Jun 2020 17:39:44: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:39:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:39:44: 1000000 INFO @ Sun, 21 Jun 2020 17:39:50: 2000000 INFO @ Sun, 21 Jun 2020 17:39:57: 3000000 INFO @ Sun, 21 Jun 2020 17:40:03: 4000000 INFO @ Sun, 21 Jun 2020 17:40:04: #3 Call peaks for each chromosome... 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 17:40:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1134708/SRX1134708.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1134708/SRX1134708.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1134708/SRX1134708.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1134708/SRX1134708.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 17:40:07: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:40:07: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:40:09: 5000000 INFO @ Sun, 21 Jun 2020 17:40:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1134708/SRX1134708.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:40:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1134708/SRX1134708.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:40:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1134708/SRX1134708.05_summits.bed INFO @ Sun, 21 Jun 2020 17:40:13: Done! INFO @ Sun, 21 Jun 2020 17:40:13: 1000000 pass1 - making usageList (190 chroms): 2 millis pass2 - checking and writing primary data (5595 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:40:16: 6000000 INFO @ Sun, 21 Jun 2020 17:40:19: 2000000 INFO @ Sun, 21 Jun 2020 17:40:20: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:40:20: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:40:20: #1 total tags in treatment: 6625873 INFO @ Sun, 21 Jun 2020 17:40:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:40:20: #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 17:40:20: #1 tags after filtering in treatment: 6625702 INFO @ Sun, 21 Jun 2020 17:40:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:40:20: #1 finished! INFO @ Sun, 21 Jun 2020 17:40:20: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:40:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:40:21: #2 number of paired peaks: 3508 INFO @ Sun, 21 Jun 2020 17:40:21: start model_add_line... INFO @ Sun, 21 Jun 2020 17:40:21: start X-correlation... INFO @ Sun, 21 Jun 2020 17:40:21: end of X-cor INFO @ Sun, 21 Jun 2020 17:40:21: #2 finished! INFO @ Sun, 21 Jun 2020 17:40:21: #2 predicted fragment length is 205 bps INFO @ Sun, 21 Jun 2020 17:40:21: #2 alternative fragment length(s) may be 205 bps INFO @ Sun, 21 Jun 2020 17:40:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1134708/SRX1134708.10_model.r INFO @ Sun, 21 Jun 2020 17:40:21: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:40:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:40:24: 3000000 INFO @ Sun, 21 Jun 2020 17:40:29: 4000000 INFO @ Sun, 21 Jun 2020 17:40:34: 5000000 INFO @ Sun, 21 Jun 2020 17:40:40: 6000000 INFO @ Sun, 21 Jun 2020 17:40:40: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:40:43: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:40:43: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:40:43: #1 total tags in treatment: 6625873 INFO @ Sun, 21 Jun 2020 17:40:43: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:40:43: #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 17:40:44: #1 tags after filtering in treatment: 6625702 INFO @ Sun, 21 Jun 2020 17:40:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:40:44: #1 finished! INFO @ Sun, 21 Jun 2020 17:40:44: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:40:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:40:44: #2 number of paired peaks: 3508 INFO @ Sun, 21 Jun 2020 17:40:44: start model_add_line... INFO @ Sun, 21 Jun 2020 17:40:44: start X-correlation... INFO @ Sun, 21 Jun 2020 17:40:44: end of X-cor INFO @ Sun, 21 Jun 2020 17:40:44: #2 finished! INFO @ Sun, 21 Jun 2020 17:40:44: #2 predicted fragment length is 205 bps INFO @ Sun, 21 Jun 2020 17:40:44: #2 alternative fragment length(s) may be 205 bps INFO @ Sun, 21 Jun 2020 17:40:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1134708/SRX1134708.20_model.r INFO @ Sun, 21 Jun 2020 17:40:44: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:40:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:40:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1134708/SRX1134708.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:40:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1134708/SRX1134708.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:40:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1134708/SRX1134708.10_summits.bed INFO @ Sun, 21 Jun 2020 17:40:49: Done! pass1 - making usageList (117 chroms): 1 millis pass2 - checking and writing primary data (4055 records, 4 fields): 8 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:41:03: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:41:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1134708/SRX1134708.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:41:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1134708/SRX1134708.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:41:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1134708/SRX1134708.20_summits.bed INFO @ Sun, 21 Jun 2020 17:41:11: Done! pass1 - making usageList (80 chroms): 2 millis pass2 - checking and writing primary data (2768 records, 4 fields): 6 millis CompletedMACS2peakCalling