Job ID = 6454151 SRX = SRX1840070 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:48:49 prefetch.2.10.7: 1) Downloading 'SRR3661296'... 2020-06-21T08:48:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:52:22 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:52:22 prefetch.2.10.7: 1) 'SRR3661296' was downloaded successfully Read 17277567 spots for SRR3661296/SRR3661296.sra Written 17277567 spots for SRR3661296/SRR3661296.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: 00:09:23 17277567 reads; of these: 17277567 (100.00%) were unpaired; of these: 941704 (5.45%) aligned 0 times 12186105 (70.53%) aligned exactly 1 time 4149758 (24.02%) aligned >1 times 94.55% overall alignment rate Time searching: 00:09:23 Overall time: 00:09:23 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] 7108939 / 16335863 = 0.4352 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 18:09:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1840070/SRX1840070.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1840070/SRX1840070.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1840070/SRX1840070.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1840070/SRX1840070.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 18:09:14: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:09:14: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:09:21: 1000000 INFO @ Sun, 21 Jun 2020 18:09:28: 2000000 INFO @ Sun, 21 Jun 2020 18:09:36: 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 18:09:43: 4000000 INFO @ Sun, 21 Jun 2020 18:09:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1840070/SRX1840070.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1840070/SRX1840070.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1840070/SRX1840070.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1840070/SRX1840070.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 18:09:44: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:09:44: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:09:51: 5000000 INFO @ Sun, 21 Jun 2020 18:09:52: 1000000 INFO @ Sun, 21 Jun 2020 18:09:59: 6000000 INFO @ Sun, 21 Jun 2020 18:10:00: 2000000 INFO @ Sun, 21 Jun 2020 18:10:07: 7000000 INFO @ Sun, 21 Jun 2020 18:10:08: 3000000 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 18:10:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1840070/SRX1840070.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1840070/SRX1840070.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1840070/SRX1840070.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1840070/SRX1840070.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 18:10:14: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:10:14: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:10:16: 8000000 INFO @ Sun, 21 Jun 2020 18:10:16: 4000000 INFO @ Sun, 21 Jun 2020 18:10:22: 1000000 INFO @ Sun, 21 Jun 2020 18:10:25: 5000000 INFO @ Sun, 21 Jun 2020 18:10:25: 9000000 INFO @ Sun, 21 Jun 2020 18:10:27: #1 tag size is determined as 101 bps INFO @ Sun, 21 Jun 2020 18:10:27: #1 tag size = 101 INFO @ Sun, 21 Jun 2020 18:10:27: #1 total tags in treatment: 9226924 INFO @ Sun, 21 Jun 2020 18:10:27: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:10:27: #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 18:10:27: #1 tags after filtering in treatment: 9226924 INFO @ Sun, 21 Jun 2020 18:10:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:10:27: #1 finished! INFO @ Sun, 21 Jun 2020 18:10:27: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:10:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:10:28: #2 number of paired peaks: 1218 INFO @ Sun, 21 Jun 2020 18:10:28: start model_add_line... INFO @ Sun, 21 Jun 2020 18:10:28: start X-correlation... INFO @ Sun, 21 Jun 2020 18:10:28: end of X-cor INFO @ Sun, 21 Jun 2020 18:10:28: #2 finished! INFO @ Sun, 21 Jun 2020 18:10:28: #2 predicted fragment length is 228 bps INFO @ Sun, 21 Jun 2020 18:10:28: #2 alternative fragment length(s) may be 228 bps INFO @ Sun, 21 Jun 2020 18:10:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1840070/SRX1840070.05_model.r INFO @ Sun, 21 Jun 2020 18:10:28: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:10:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:10:31: 2000000 INFO @ Sun, 21 Jun 2020 18:10:33: 6000000 INFO @ Sun, 21 Jun 2020 18:10:39: 3000000 INFO @ Sun, 21 Jun 2020 18:10:41: 7000000 INFO @ Sun, 21 Jun 2020 18:10:47: 4000000 INFO @ Sun, 21 Jun 2020 18:10:50: 8000000 INFO @ Sun, 21 Jun 2020 18:10:52: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:10:56: 5000000 INFO @ Sun, 21 Jun 2020 18:10:59: 9000000 INFO @ Sun, 21 Jun 2020 18:11:01: #1 tag size is determined as 101 bps INFO @ Sun, 21 Jun 2020 18:11:01: #1 tag size = 101 INFO @ Sun, 21 Jun 2020 18:11:01: #1 total tags in treatment: 9226924 INFO @ Sun, 21 Jun 2020 18:11:01: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:11:01: #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 18:11:01: #1 tags after filtering in treatment: 9226924 INFO @ Sun, 21 Jun 2020 18:11:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:11:01: #1 finished! INFO @ Sun, 21 Jun 2020 18:11:01: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:11:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:11:02: #2 number of paired peaks: 1218 INFO @ Sun, 21 Jun 2020 18:11:02: start model_add_line... INFO @ Sun, 21 Jun 2020 18:11:02: start X-correlation... INFO @ Sun, 21 Jun 2020 18:11:02: end of X-cor INFO @ Sun, 21 Jun 2020 18:11:02: #2 finished! INFO @ Sun, 21 Jun 2020 18:11:02: #2 predicted fragment length is 228 bps INFO @ Sun, 21 Jun 2020 18:11:02: #2 alternative fragment length(s) may be 228 bps INFO @ Sun, 21 Jun 2020 18:11:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1840070/SRX1840070.10_model.r INFO @ Sun, 21 Jun 2020 18:11:02: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:11:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:11:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1840070/SRX1840070.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:11:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1840070/SRX1840070.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:11:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1840070/SRX1840070.05_summits.bed INFO @ Sun, 21 Jun 2020 18:11:04: Done! INFO @ Sun, 21 Jun 2020 18:11:04: 6000000 pass1 - making usageList (733 chroms): 1 millis pass2 - checking and writing primary data (3451 records, 4 fields): 24 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:11:12: 7000000 INFO @ Sun, 21 Jun 2020 18:11:20: 8000000 INFO @ Sun, 21 Jun 2020 18:11:26: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:11:28: 9000000 INFO @ Sun, 21 Jun 2020 18:11:31: #1 tag size is determined as 101 bps INFO @ Sun, 21 Jun 2020 18:11:31: #1 tag size = 101 INFO @ Sun, 21 Jun 2020 18:11:31: #1 total tags in treatment: 9226924 INFO @ Sun, 21 Jun 2020 18:11:31: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:11:31: #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 18:11:31: #1 tags after filtering in treatment: 9226924 INFO @ Sun, 21 Jun 2020 18:11:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:11:31: #1 finished! INFO @ Sun, 21 Jun 2020 18:11:31: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:11:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:11:32: #2 number of paired peaks: 1218 INFO @ Sun, 21 Jun 2020 18:11:32: start model_add_line... INFO @ Sun, 21 Jun 2020 18:11:32: start X-correlation... INFO @ Sun, 21 Jun 2020 18:11:32: end of X-cor INFO @ Sun, 21 Jun 2020 18:11:32: #2 finished! INFO @ Sun, 21 Jun 2020 18:11:32: #2 predicted fragment length is 228 bps INFO @ Sun, 21 Jun 2020 18:11:32: #2 alternative fragment length(s) may be 228 bps INFO @ Sun, 21 Jun 2020 18:11:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1840070/SRX1840070.20_model.r INFO @ Sun, 21 Jun 2020 18:11:32: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:11:32: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:11:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1840070/SRX1840070.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:11:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1840070/SRX1840070.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:11:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1840070/SRX1840070.10_summits.bed INFO @ Sun, 21 Jun 2020 18:11:37: Done! pass1 - making usageList (642 chroms): 2 millis pass2 - checking and writing primary data (2287 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:11:56: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:12:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1840070/SRX1840070.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:12:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1840070/SRX1840070.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:12:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1840070/SRX1840070.20_summits.bed INFO @ Sun, 21 Jun 2020 18:12:07: Done! pass1 - making usageList (507 chroms): 1 millis pass2 - checking and writing primary data (1484 records, 4 fields): 18 millis CompletedMACS2peakCalling