Job ID = 6452701 SRX = SRX026742 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:44:21 prefetch.2.10.7: 1) Downloading 'SRR065628'... 2020-06-21T07:44:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:47:23 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:47:23 prefetch.2.10.7: 'SRR065628' is valid 2020-06-21T07:47:23 prefetch.2.10.7: 1) 'SRR065628' was downloaded successfully Read 7293970 spots for SRR065628/SRR065628.sra Written 7293970 spots for SRR065628/SRR065628.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: 00:01:12 7293970 reads; of these: 7293970 (100.00%) were unpaired; of these: 1326921 (18.19%) aligned 0 times 5220793 (71.58%) aligned exactly 1 time 746256 (10.23%) aligned >1 times 81.81% overall alignment rate Time searching: 00:01:12 Overall time: 00:01:12 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] 2065761 / 5967049 = 0.3462 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 16:51:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX026742/SRX026742.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX026742/SRX026742.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX026742/SRX026742.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX026742/SRX026742.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 16:51:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:51:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:51:11: 1000000 INFO @ Sun, 21 Jun 2020 16:51:17: 2000000 INFO @ Sun, 21 Jun 2020 16:51:22: 3000000 INFO @ Sun, 21 Jun 2020 16:51:27: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 16:51:27: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 16:51:27: #1 total tags in treatment: 3901288 INFO @ Sun, 21 Jun 2020 16:51:27: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:51:27: #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 16:51:27: #1 tags after filtering in treatment: 3901001 INFO @ Sun, 21 Jun 2020 16:51:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:51:27: #1 finished! INFO @ Sun, 21 Jun 2020 16:51:27: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:51:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:51:28: #2 number of paired peaks: 7332 INFO @ Sun, 21 Jun 2020 16:51:28: start model_add_line... INFO @ Sun, 21 Jun 2020 16:51:28: start X-correlation... INFO @ Sun, 21 Jun 2020 16:51:28: end of X-cor INFO @ Sun, 21 Jun 2020 16:51:28: #2 finished! INFO @ Sun, 21 Jun 2020 16:51:28: #2 predicted fragment length is 304 bps INFO @ Sun, 21 Jun 2020 16:51:28: #2 alternative fragment length(s) may be 304 bps INFO @ Sun, 21 Jun 2020 16:51:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX026742/SRX026742.05_model.r INFO @ Sun, 21 Jun 2020 16:51:28: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:51:28: #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 16:51:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX026742/SRX026742.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX026742/SRX026742.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX026742/SRX026742.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX026742/SRX026742.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 16:51:36: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:51:36: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:51:39: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:51:41: 1000000 INFO @ Sun, 21 Jun 2020 16:51:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX026742/SRX026742.05_peaks.xls INFO @ Sun, 21 Jun 2020 16:51:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX026742/SRX026742.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:51:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX026742/SRX026742.05_summits.bed INFO @ Sun, 21 Jun 2020 16:51:45: Done! pass1 - making usageList (317 chroms): 3 millis pass2 - checking and writing primary data (13544 records, 4 fields): 32 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:51:47: 2000000 INFO @ Sun, 21 Jun 2020 16:51:52: 3000000 INFO @ Sun, 21 Jun 2020 16:51:57: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 16:51:57: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 16:51:57: #1 total tags in treatment: 3901288 INFO @ Sun, 21 Jun 2020 16:51:57: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:51:57: #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 16:51:58: #1 tags after filtering in treatment: 3901001 INFO @ Sun, 21 Jun 2020 16:51:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:51:58: #1 finished! INFO @ Sun, 21 Jun 2020 16:51:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:51:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:51:58: #2 number of paired peaks: 7332 INFO @ Sun, 21 Jun 2020 16:51:58: start model_add_line... INFO @ Sun, 21 Jun 2020 16:51:58: start X-correlation... INFO @ Sun, 21 Jun 2020 16:51:58: end of X-cor INFO @ Sun, 21 Jun 2020 16:51:58: #2 finished! INFO @ Sun, 21 Jun 2020 16:51:58: #2 predicted fragment length is 304 bps INFO @ Sun, 21 Jun 2020 16:51:58: #2 alternative fragment length(s) may be 304 bps INFO @ Sun, 21 Jun 2020 16:51:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX026742/SRX026742.10_model.r INFO @ Sun, 21 Jun 2020 16:51:58: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:51:58: #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 16:52:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX026742/SRX026742.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX026742/SRX026742.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX026742/SRX026742.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX026742/SRX026742.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 16:52:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:52:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:52:09: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:52:11: 1000000 INFO @ Sun, 21 Jun 2020 16:52:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX026742/SRX026742.10_peaks.xls INFO @ Sun, 21 Jun 2020 16:52:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX026742/SRX026742.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:52:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX026742/SRX026742.10_summits.bed INFO @ Sun, 21 Jun 2020 16:52:15: Done! pass1 - making usageList (270 chroms): 5 millis pass2 - checking and writing primary data (6117 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:52:17: 2000000 INFO @ Sun, 21 Jun 2020 16:52:22: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 16:52:27: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 16:52:27: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 16:52:27: #1 total tags in treatment: 3901288 INFO @ Sun, 21 Jun 2020 16:52:27: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:52:27: #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 16:52:27: #1 tags after filtering in treatment: 3901001 INFO @ Sun, 21 Jun 2020 16:52:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:52:27: #1 finished! INFO @ Sun, 21 Jun 2020 16:52:27: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:52:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:52:28: #2 number of paired peaks: 7332 INFO @ Sun, 21 Jun 2020 16:52:28: start model_add_line... INFO @ Sun, 21 Jun 2020 16:52:28: start X-correlation... INFO @ Sun, 21 Jun 2020 16:52:28: end of X-cor INFO @ Sun, 21 Jun 2020 16:52:28: #2 finished! INFO @ Sun, 21 Jun 2020 16:52:28: #2 predicted fragment length is 304 bps INFO @ Sun, 21 Jun 2020 16:52:28: #2 alternative fragment length(s) may be 304 bps INFO @ Sun, 21 Jun 2020 16:52:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX026742/SRX026742.20_model.r INFO @ Sun, 21 Jun 2020 16:52:28: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:52:28: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 16:52:39: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:52:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX026742/SRX026742.20_peaks.xls INFO @ Sun, 21 Jun 2020 16:52:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX026742/SRX026742.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:52:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX026742/SRX026742.20_summits.bed INFO @ Sun, 21 Jun 2020 16:52:44: Done! pass1 - making usageList (218 chroms): 1 millis pass2 - checking and writing primary data (1811 records, 4 fields): 14 millis CompletedMACS2peakCalling