Job ID = 6459860 SRX = SRX914956 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T13:36:29 prefetch.2.10.7: 1) Downloading 'SRR1873266'... 2020-06-21T13:36:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:39:41 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:39:41 prefetch.2.10.7: 1) 'SRR1873266' was downloaded successfully Read 23148683 spots for SRR1873266/SRR1873266.sra Written 23148683 spots for SRR1873266/SRR1873266.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: 00:03:27 23148683 reads; of these: 23148683 (100.00%) were unpaired; of these: 2391286 (10.33%) aligned 0 times 18386732 (79.43%) aligned exactly 1 time 2370665 (10.24%) aligned >1 times 89.67% overall alignment rate Time searching: 00:03:27 Overall time: 00:03:27 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] 11945662 / 20757397 = 0.5755 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 22:48:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX914956/SRX914956.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX914956/SRX914956.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX914956/SRX914956.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX914956/SRX914956.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 22:48:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:48:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:48:10: 1000000 INFO @ Sun, 21 Jun 2020 22:48:15: 2000000 INFO @ Sun, 21 Jun 2020 22:48:20: 3000000 INFO @ Sun, 21 Jun 2020 22:48:24: 4000000 INFO @ Sun, 21 Jun 2020 22:48:29: 5000000 INFO @ Sun, 21 Jun 2020 22:48:34: 6000000 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 22:48:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX914956/SRX914956.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX914956/SRX914956.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX914956/SRX914956.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX914956/SRX914956.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 22:48:36: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:48:36: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:48:38: 7000000 INFO @ Sun, 21 Jun 2020 22:48:40: 1000000 INFO @ Sun, 21 Jun 2020 22:48:43: 8000000 INFO @ Sun, 21 Jun 2020 22:48:45: 2000000 INFO @ Sun, 21 Jun 2020 22:48:48: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 22:48:48: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 22:48:48: #1 total tags in treatment: 8811735 INFO @ Sun, 21 Jun 2020 22:48:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:48:48: #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 22:48:48: #1 tags after filtering in treatment: 8811589 INFO @ Sun, 21 Jun 2020 22:48:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:48:48: #1 finished! INFO @ Sun, 21 Jun 2020 22:48:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:48:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:48:49: #2 number of paired peaks: 1665 INFO @ Sun, 21 Jun 2020 22:48:49: start model_add_line... INFO @ Sun, 21 Jun 2020 22:48:49: start X-correlation... INFO @ Sun, 21 Jun 2020 22:48:49: end of X-cor INFO @ Sun, 21 Jun 2020 22:48:49: #2 finished! INFO @ Sun, 21 Jun 2020 22:48:49: #2 predicted fragment length is 189 bps INFO @ Sun, 21 Jun 2020 22:48:49: #2 alternative fragment length(s) may be 2,189 bps INFO @ Sun, 21 Jun 2020 22:48:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX914956/SRX914956.05_model.r INFO @ Sun, 21 Jun 2020 22:48:49: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:48:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:48:51: 3000000 INFO @ Sun, 21 Jun 2020 22:48:56: 4000000 INFO @ Sun, 21 Jun 2020 22:49:01: 5000000 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 22:49:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX914956/SRX914956.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX914956/SRX914956.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX914956/SRX914956.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX914956/SRX914956.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 22:49:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:49:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:49:06: 6000000 INFO @ Sun, 21 Jun 2020 22:49:11: 7000000 INFO @ Sun, 21 Jun 2020 22:49:12: 1000000 INFO @ Sun, 21 Jun 2020 22:49:17: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:49:17: 8000000 INFO @ Sun, 21 Jun 2020 22:49:18: 2000000 INFO @ Sun, 21 Jun 2020 22:49:21: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 22:49:21: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 22:49:21: #1 total tags in treatment: 8811735 INFO @ Sun, 21 Jun 2020 22:49:21: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:49:21: #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 22:49:22: #1 tags after filtering in treatment: 8811589 INFO @ Sun, 21 Jun 2020 22:49:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:49:22: #1 finished! INFO @ Sun, 21 Jun 2020 22:49:22: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:49:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:49:23: #2 number of paired peaks: 1665 INFO @ Sun, 21 Jun 2020 22:49:23: start model_add_line... INFO @ Sun, 21 Jun 2020 22:49:23: start X-correlation... INFO @ Sun, 21 Jun 2020 22:49:23: end of X-cor INFO @ Sun, 21 Jun 2020 22:49:23: #2 finished! INFO @ Sun, 21 Jun 2020 22:49:23: #2 predicted fragment length is 189 bps INFO @ Sun, 21 Jun 2020 22:49:23: #2 alternative fragment length(s) may be 2,189 bps INFO @ Sun, 21 Jun 2020 22:49:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX914956/SRX914956.10_model.r INFO @ Sun, 21 Jun 2020 22:49:23: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:49:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:49:24: 3000000 INFO @ Sun, 21 Jun 2020 22:49:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX914956/SRX914956.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:49:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX914956/SRX914956.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:49:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX914956/SRX914956.05_summits.bed INFO @ Sun, 21 Jun 2020 22:49:29: Done! pass1 - making usageList (153 chroms): 2 millis pass2 - checking and writing primary data (4045 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:49:30: 4000000 INFO @ Sun, 21 Jun 2020 22:49:36: 5000000 INFO @ Sun, 21 Jun 2020 22:49:41: 6000000 INFO @ Sun, 21 Jun 2020 22:49:47: 7000000 INFO @ Sun, 21 Jun 2020 22:49:50: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:49:53: 8000000 INFO @ Sun, 21 Jun 2020 22:49:57: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 22:49:57: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 22:49:57: #1 total tags in treatment: 8811735 INFO @ Sun, 21 Jun 2020 22:49:57: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:49:57: #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 22:49:58: #1 tags after filtering in treatment: 8811589 INFO @ Sun, 21 Jun 2020 22:49:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:49:58: #1 finished! INFO @ Sun, 21 Jun 2020 22:49:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:49:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:49:59: #2 number of paired peaks: 1665 INFO @ Sun, 21 Jun 2020 22:49:59: start model_add_line... INFO @ Sun, 21 Jun 2020 22:49:59: start X-correlation... INFO @ Sun, 21 Jun 2020 22:49:59: end of X-cor INFO @ Sun, 21 Jun 2020 22:49:59: #2 finished! INFO @ Sun, 21 Jun 2020 22:49:59: #2 predicted fragment length is 189 bps INFO @ Sun, 21 Jun 2020 22:49:59: #2 alternative fragment length(s) may be 2,189 bps INFO @ Sun, 21 Jun 2020 22:49:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX914956/SRX914956.20_model.r INFO @ Sun, 21 Jun 2020 22:49:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:49:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:50:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX914956/SRX914956.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:50:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX914956/SRX914956.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:50:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX914956/SRX914956.10_summits.bed INFO @ Sun, 21 Jun 2020 22:50:01: Done! pass1 - making usageList (114 chroms): 1 millis pass2 - checking and writing primary data (1425 records, 4 fields): 6 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:50:24: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:50:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX914956/SRX914956.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:50:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX914956/SRX914956.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:50:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX914956/SRX914956.20_summits.bed INFO @ Sun, 21 Jun 2020 22:50:34: Done! pass1 - making usageList (79 chroms): 1 millis pass2 - checking and writing primary data (316 records, 4 fields): 4 millis CompletedMACS2peakCalling