Job ID = 6455717 SRX = SRX288014 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:15:21 prefetch.2.10.7: 1) Downloading 'SRR870203'... 2020-06-21T10:15:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:19:35 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:19:36 prefetch.2.10.7: 'SRR870203' is valid 2020-06-21T10:19:36 prefetch.2.10.7: 1) 'SRR870203' was downloaded successfully Read 13374099 spots for SRR870203/SRR870203.sra Written 13374099 spots for SRR870203/SRR870203.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: 00:04:19 13374099 reads; of these: 13374099 (100.00%) were unpaired; of these: 1135278 (8.49%) aligned 0 times 6006104 (44.91%) aligned exactly 1 time 6232717 (46.60%) aligned >1 times 91.51% overall alignment rate Time searching: 00:04:19 Overall time: 00:04:19 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] 2137153 / 12238821 = 0.1746 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 19:27:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX288014/SRX288014.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX288014/SRX288014.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX288014/SRX288014.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX288014/SRX288014.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 19:27:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:27:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:28:03: 1000000 INFO @ Sun, 21 Jun 2020 19:28:09: 2000000 INFO @ Sun, 21 Jun 2020 19:28:15: 3000000 INFO @ Sun, 21 Jun 2020 19:28:21: 4000000 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 19:28:26: 5000000 INFO @ Sun, 21 Jun 2020 19:28:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX288014/SRX288014.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX288014/SRX288014.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX288014/SRX288014.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX288014/SRX288014.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 19:28:27: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:28:27: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:28:33: 6000000 INFO @ Sun, 21 Jun 2020 19:28:34: 1000000 INFO @ Sun, 21 Jun 2020 19:28:40: 7000000 INFO @ Sun, 21 Jun 2020 19:28:41: 2000000 INFO @ Sun, 21 Jun 2020 19:28:47: 8000000 INFO @ Sun, 21 Jun 2020 19:28:48: 3000000 INFO @ Sun, 21 Jun 2020 19:28:54: 9000000 INFO @ Sun, 21 Jun 2020 19:28:55: 4000000 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 19:28:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX288014/SRX288014.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX288014/SRX288014.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX288014/SRX288014.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX288014/SRX288014.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 19:28:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:28:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:29:01: 10000000 INFO @ Sun, 21 Jun 2020 19:29:02: 5000000 INFO @ Sun, 21 Jun 2020 19:29:02: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:29:02: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:29:02: #1 total tags in treatment: 10101668 INFO @ Sun, 21 Jun 2020 19:29:02: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:29:02: #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 19:29:03: #1 tags after filtering in treatment: 10101667 INFO @ Sun, 21 Jun 2020 19:29:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:29:03: #1 finished! INFO @ Sun, 21 Jun 2020 19:29:03: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:29:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:29:03: #2 number of paired peaks: 2115 INFO @ Sun, 21 Jun 2020 19:29:03: start model_add_line... INFO @ Sun, 21 Jun 2020 19:29:03: start X-correlation... INFO @ Sun, 21 Jun 2020 19:29:03: end of X-cor INFO @ Sun, 21 Jun 2020 19:29:03: #2 finished! INFO @ Sun, 21 Jun 2020 19:29:03: #2 predicted fragment length is 107 bps INFO @ Sun, 21 Jun 2020 19:29:03: #2 alternative fragment length(s) may be 4,107 bps INFO @ Sun, 21 Jun 2020 19:29:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX288014/SRX288014.05_model.r INFO @ Sun, 21 Jun 2020 19:29:03: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:29:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:29:05: 1000000 INFO @ Sun, 21 Jun 2020 19:29:09: 6000000 INFO @ Sun, 21 Jun 2020 19:29:12: 2000000 INFO @ Sun, 21 Jun 2020 19:29:16: 7000000 INFO @ Sun, 21 Jun 2020 19:29:19: 3000000 INFO @ Sun, 21 Jun 2020 19:29:24: 8000000 INFO @ Sun, 21 Jun 2020 19:29:24: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:29:26: 4000000 INFO @ Sun, 21 Jun 2020 19:29:31: 9000000 INFO @ Sun, 21 Jun 2020 19:29:33: 5000000 INFO @ Sun, 21 Jun 2020 19:29:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX288014/SRX288014.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:29:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX288014/SRX288014.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:29:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX288014/SRX288014.05_summits.bed INFO @ Sun, 21 Jun 2020 19:29:35: Done! pass1 - making usageList (1102 chroms): 2 millis pass2 - checking and writing primary data (4180 records, 4 fields): 30 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:29:38: 10000000 INFO @ Sun, 21 Jun 2020 19:29:39: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:29:39: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:29:39: #1 total tags in treatment: 10101668 INFO @ Sun, 21 Jun 2020 19:29:39: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:29:39: #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 19:29:39: #1 tags after filtering in treatment: 10101667 INFO @ Sun, 21 Jun 2020 19:29:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:29:39: #1 finished! INFO @ Sun, 21 Jun 2020 19:29:39: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:29:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:29:40: 6000000 INFO @ Sun, 21 Jun 2020 19:29:40: #2 number of paired peaks: 2115 INFO @ Sun, 21 Jun 2020 19:29:40: start model_add_line... INFO @ Sun, 21 Jun 2020 19:29:40: start X-correlation... INFO @ Sun, 21 Jun 2020 19:29:40: end of X-cor INFO @ Sun, 21 Jun 2020 19:29:40: #2 finished! INFO @ Sun, 21 Jun 2020 19:29:40: #2 predicted fragment length is 107 bps INFO @ Sun, 21 Jun 2020 19:29:40: #2 alternative fragment length(s) may be 4,107 bps INFO @ Sun, 21 Jun 2020 19:29:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX288014/SRX288014.10_model.r INFO @ Sun, 21 Jun 2020 19:29:40: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:29:40: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:29:46: 7000000 INFO @ Sun, 21 Jun 2020 19:29:53: 8000000 INFO @ Sun, 21 Jun 2020 19:29:59: 9000000 INFO @ Sun, 21 Jun 2020 19:30:02: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:30:06: 10000000 INFO @ Sun, 21 Jun 2020 19:30:06: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:30:06: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:30:06: #1 total tags in treatment: 10101668 INFO @ Sun, 21 Jun 2020 19:30:06: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:30:06: #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 19:30:07: #1 tags after filtering in treatment: 10101667 INFO @ Sun, 21 Jun 2020 19:30:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:30:07: #1 finished! INFO @ Sun, 21 Jun 2020 19:30:07: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:30:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:30:07: #2 number of paired peaks: 2115 INFO @ Sun, 21 Jun 2020 19:30:07: start model_add_line... INFO @ Sun, 21 Jun 2020 19:30:08: start X-correlation... INFO @ Sun, 21 Jun 2020 19:30:08: end of X-cor INFO @ Sun, 21 Jun 2020 19:30:08: #2 finished! INFO @ Sun, 21 Jun 2020 19:30:08: #2 predicted fragment length is 107 bps INFO @ Sun, 21 Jun 2020 19:30:08: #2 alternative fragment length(s) may be 4,107 bps INFO @ Sun, 21 Jun 2020 19:30:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX288014/SRX288014.20_model.r INFO @ Sun, 21 Jun 2020 19:30:08: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:30:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:30:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX288014/SRX288014.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:30:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX288014/SRX288014.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:30:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX288014/SRX288014.10_summits.bed INFO @ Sun, 21 Jun 2020 19:30:12: Done! pass1 - making usageList (788 chroms): 1 millis pass2 - checking and writing primary data (2171 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:30:30: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:30:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX288014/SRX288014.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:30:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX288014/SRX288014.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:30:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX288014/SRX288014.20_summits.bed INFO @ Sun, 21 Jun 2020 19:30:41: Done! pass1 - making usageList (429 chroms): 1 millis pass2 - checking and writing primary data (911 records, 4 fields): 13 millis CompletedMACS2peakCalling