Job ID = 6456902 SRX = SRX4053329 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:07:39 prefetch.2.10.7: 1) Downloading 'SRR7132384'... 2020-06-21T11:07:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:08:27 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:08:27 prefetch.2.10.7: 'SRR7132384' is valid 2020-06-21T11:08:27 prefetch.2.10.7: 1) 'SRR7132384' was downloaded successfully 2020-06-21T11:08:27 prefetch.2.10.7: 'SRR7132384' has 0 unresolved dependencies Read 4782793 spots for SRR7132384/SRR7132384.sra Written 4782793 spots for SRR7132384/SRR7132384.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: 00:01:11 4782793 reads; of these: 4782793 (100.00%) were unpaired; of these: 662801 (13.86%) aligned 0 times 3353935 (70.13%) aligned exactly 1 time 766057 (16.02%) aligned >1 times 86.14% overall alignment rate Time searching: 00:01:11 Overall time: 00:01:11 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] 694551 / 4119992 = 0.1686 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 20:11:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4053329/SRX4053329.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4053329/SRX4053329.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4053329/SRX4053329.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4053329/SRX4053329.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 20:11:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:11:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:11:16: 1000000 INFO @ Sun, 21 Jun 2020 20:11:23: 2000000 INFO @ Sun, 21 Jun 2020 20:11:29: 3000000 INFO @ Sun, 21 Jun 2020 20:11:32: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:11:32: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:11:32: #1 total tags in treatment: 3425441 INFO @ Sun, 21 Jun 2020 20:11:32: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:11:32: #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 20:11:33: #1 tags after filtering in treatment: 3425284 INFO @ Sun, 21 Jun 2020 20:11:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:11:33: #1 finished! INFO @ Sun, 21 Jun 2020 20:11:33: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:11:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:11:33: #2 number of paired peaks: 6452 INFO @ Sun, 21 Jun 2020 20:11:33: start model_add_line... INFO @ Sun, 21 Jun 2020 20:11:33: start X-correlation... INFO @ Sun, 21 Jun 2020 20:11:33: end of X-cor INFO @ Sun, 21 Jun 2020 20:11:33: #2 finished! INFO @ Sun, 21 Jun 2020 20:11:33: #2 predicted fragment length is 266 bps INFO @ Sun, 21 Jun 2020 20:11:33: #2 alternative fragment length(s) may be 3,266 bps INFO @ Sun, 21 Jun 2020 20:11:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4053329/SRX4053329.05_model.r INFO @ Sun, 21 Jun 2020 20:11:33: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:11:33: #3 Pre-compute pvalue-qvalue table... 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 20:11:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4053329/SRX4053329.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4053329/SRX4053329.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4053329/SRX4053329.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4053329/SRX4053329.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 20:11:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:11:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:11:44: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:11:45: 1000000 INFO @ Sun, 21 Jun 2020 20:11:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4053329/SRX4053329.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:11:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4053329/SRX4053329.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:11:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4053329/SRX4053329.05_summits.bed INFO @ Sun, 21 Jun 2020 20:11:48: Done! pass1 - making usageList (170 chroms): 1 millis pass2 - checking and writing primary data (777 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:11:51: 2000000 INFO @ Sun, 21 Jun 2020 20:11:56: 3000000 INFO @ Sun, 21 Jun 2020 20:11:58: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:11:58: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:11:58: #1 total tags in treatment: 3425441 INFO @ Sun, 21 Jun 2020 20:11:58: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:11:58: #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 20:11:59: #1 tags after filtering in treatment: 3425284 INFO @ Sun, 21 Jun 2020 20:11:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:11:59: #1 finished! INFO @ Sun, 21 Jun 2020 20:11:59: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:11:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:11:59: #2 number of paired peaks: 6452 INFO @ Sun, 21 Jun 2020 20:11:59: start model_add_line... INFO @ Sun, 21 Jun 2020 20:11:59: start X-correlation... INFO @ Sun, 21 Jun 2020 20:11:59: end of X-cor INFO @ Sun, 21 Jun 2020 20:11:59: #2 finished! INFO @ Sun, 21 Jun 2020 20:11:59: #2 predicted fragment length is 266 bps INFO @ Sun, 21 Jun 2020 20:11:59: #2 alternative fragment length(s) may be 3,266 bps INFO @ Sun, 21 Jun 2020 20:11:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4053329/SRX4053329.10_model.r INFO @ Sun, 21 Jun 2020 20:11:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:11:59: #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 20:12:09: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:12:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4053329/SRX4053329.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4053329/SRX4053329.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4053329/SRX4053329.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4053329/SRX4053329.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 20:12:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:12:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:12:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4053329/SRX4053329.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:12:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4053329/SRX4053329.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:12:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4053329/SRX4053329.10_summits.bed INFO @ Sun, 21 Jun 2020 20:12:14: Done! pass1 - making usageList (93 chroms): 0 millis pass2 - checking and writing primary data (300 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:12:16: 1000000 INFO @ Sun, 21 Jun 2020 20:12:21: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:12:26: 3000000 INFO @ Sun, 21 Jun 2020 20:12:29: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:12:29: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:12:29: #1 total tags in treatment: 3425441 INFO @ Sun, 21 Jun 2020 20:12:29: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:12:29: #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 20:12:29: #1 tags after filtering in treatment: 3425284 INFO @ Sun, 21 Jun 2020 20:12:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:12:29: #1 finished! INFO @ Sun, 21 Jun 2020 20:12:29: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:12:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:12:30: #2 number of paired peaks: 6452 INFO @ Sun, 21 Jun 2020 20:12:30: start model_add_line... INFO @ Sun, 21 Jun 2020 20:12:30: start X-correlation... INFO @ Sun, 21 Jun 2020 20:12:30: end of X-cor INFO @ Sun, 21 Jun 2020 20:12:30: #2 finished! INFO @ Sun, 21 Jun 2020 20:12:30: #2 predicted fragment length is 266 bps INFO @ Sun, 21 Jun 2020 20:12:30: #2 alternative fragment length(s) may be 3,266 bps INFO @ Sun, 21 Jun 2020 20:12:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4053329/SRX4053329.20_model.r INFO @ Sun, 21 Jun 2020 20:12:30: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:12:30: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:12:41: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:12:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4053329/SRX4053329.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:12:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4053329/SRX4053329.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:12:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4053329/SRX4053329.20_summits.bed INFO @ Sun, 21 Jun 2020 20:12:45: Done! pass1 - making usageList (61 chroms): 1 millis pass2 - checking and writing primary data (126 records, 4 fields): 3 millis CompletedMACS2peakCalling