Job ID = 6454465 SRX = SRX215500 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:10:54 prefetch.2.10.7: 1) Downloading 'SRR646466'... 2020-06-21T09:10:54 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:13:49 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:13:50 prefetch.2.10.7: 'SRR646466' is valid 2020-06-21T09:13:50 prefetch.2.10.7: 1) 'SRR646466' was downloaded successfully Read 25651696 spots for SRR646466/SRR646466.sra Written 25651696 spots for SRR646466/SRR646466.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: 00:04:43 25651696 reads; of these: 25651696 (100.00%) were unpaired; of these: 5965310 (23.26%) aligned 0 times 15169938 (59.14%) aligned exactly 1 time 4516448 (17.61%) aligned >1 times 76.74% overall alignment rate Time searching: 00:04:43 Overall time: 00:04:43 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] 9146149 / 19686386 = 0.4646 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 18:23:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX215500/SRX215500.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX215500/SRX215500.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX215500/SRX215500.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX215500/SRX215500.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 18:23:15: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:23:15: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:23:20: 1000000 INFO @ Sun, 21 Jun 2020 18:23:25: 2000000 INFO @ Sun, 21 Jun 2020 18:23:31: 3000000 INFO @ Sun, 21 Jun 2020 18:23:36: 4000000 INFO @ Sun, 21 Jun 2020 18:23:42: 5000000 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 18:23:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX215500/SRX215500.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX215500/SRX215500.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX215500/SRX215500.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX215500/SRX215500.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 18:23:45: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:23:45: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:23:47: 6000000 INFO @ Sun, 21 Jun 2020 18:23:50: 1000000 INFO @ Sun, 21 Jun 2020 18:23:53: 7000000 INFO @ Sun, 21 Jun 2020 18:23:55: 2000000 INFO @ Sun, 21 Jun 2020 18:23:59: 8000000 INFO @ Sun, 21 Jun 2020 18:24:00: 3000000 INFO @ Sun, 21 Jun 2020 18:24:05: 9000000 INFO @ Sun, 21 Jun 2020 18:24:05: 4000000 INFO @ Sun, 21 Jun 2020 18:24:10: 5000000 INFO @ Sun, 21 Jun 2020 18:24:10: 10000000 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 18:24:13: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:24:13: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:24:13: #1 total tags in treatment: 10540237 INFO @ Sun, 21 Jun 2020 18:24:13: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:24:13: #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 18:24:14: #1 tags after filtering in treatment: 10540200 INFO @ Sun, 21 Jun 2020 18:24:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:24:14: #1 finished! INFO @ Sun, 21 Jun 2020 18:24:14: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:24:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:24:15: #2 number of paired peaks: 1470 INFO @ Sun, 21 Jun 2020 18:24:15: start model_add_line... INFO @ Sun, 21 Jun 2020 18:24:15: start X-correlation... INFO @ Sun, 21 Jun 2020 18:24:15: end of X-cor INFO @ Sun, 21 Jun 2020 18:24:15: #2 finished! INFO @ Sun, 21 Jun 2020 18:24:15: #2 predicted fragment length is 241 bps INFO @ Sun, 21 Jun 2020 18:24:15: #2 alternative fragment length(s) may be 4,241 bps INFO @ Sun, 21 Jun 2020 18:24:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX215500/SRX215500.05_model.r INFO @ Sun, 21 Jun 2020 18:24:15: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:24:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:24:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX215500/SRX215500.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX215500/SRX215500.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX215500/SRX215500.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX215500/SRX215500.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 18:24:15: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:24:15: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:24:15: 6000000 INFO @ Sun, 21 Jun 2020 18:24:20: 7000000 INFO @ Sun, 21 Jun 2020 18:24:20: 1000000 INFO @ Sun, 21 Jun 2020 18:24:25: 2000000 INFO @ Sun, 21 Jun 2020 18:24:25: 8000000 INFO @ Sun, 21 Jun 2020 18:24:29: 3000000 INFO @ Sun, 21 Jun 2020 18:24:30: 9000000 INFO @ Sun, 21 Jun 2020 18:24:34: 4000000 INFO @ Sun, 21 Jun 2020 18:24:35: 10000000 INFO @ Sun, 21 Jun 2020 18:24:37: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:24:37: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:24:37: #1 total tags in treatment: 10540237 INFO @ Sun, 21 Jun 2020 18:24:37: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:24:37: #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 18:24:38: #1 tags after filtering in treatment: 10540200 INFO @ Sun, 21 Jun 2020 18:24:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:24:38: #1 finished! INFO @ Sun, 21 Jun 2020 18:24:38: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:24:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:24:39: #2 number of paired peaks: 1470 INFO @ Sun, 21 Jun 2020 18:24:39: start model_add_line... INFO @ Sun, 21 Jun 2020 18:24:39: start X-correlation... INFO @ Sun, 21 Jun 2020 18:24:39: end of X-cor INFO @ Sun, 21 Jun 2020 18:24:39: #2 finished! INFO @ Sun, 21 Jun 2020 18:24:39: #2 predicted fragment length is 241 bps INFO @ Sun, 21 Jun 2020 18:24:39: #2 alternative fragment length(s) may be 4,241 bps INFO @ Sun, 21 Jun 2020 18:24:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX215500/SRX215500.10_model.r INFO @ Sun, 21 Jun 2020 18:24:39: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:24:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:24:39: 5000000 INFO @ Sun, 21 Jun 2020 18:24:41: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:24:44: 6000000 INFO @ Sun, 21 Jun 2020 18:24:48: 7000000 INFO @ Sun, 21 Jun 2020 18:24:53: 8000000 INFO @ Sun, 21 Jun 2020 18:24:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX215500/SRX215500.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:24:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX215500/SRX215500.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:24:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX215500/SRX215500.05_summits.bed INFO @ Sun, 21 Jun 2020 18:24:54: Done! pass1 - making usageList (805 chroms): 3 millis pass2 - checking and writing primary data (17931 records, 4 fields): 35 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:24:58: 9000000 INFO @ Sun, 21 Jun 2020 18:25:03: 10000000 INFO @ Sun, 21 Jun 2020 18:25:05: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:25:05: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:25:05: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:25:05: #1 total tags in treatment: 10540237 INFO @ Sun, 21 Jun 2020 18:25:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:25:05: #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 18:25:06: #1 tags after filtering in treatment: 10540200 INFO @ Sun, 21 Jun 2020 18:25:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:25:06: #1 finished! INFO @ Sun, 21 Jun 2020 18:25:06: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:25:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:25:07: #2 number of paired peaks: 1470 INFO @ Sun, 21 Jun 2020 18:25:07: start model_add_line... INFO @ Sun, 21 Jun 2020 18:25:07: start X-correlation... INFO @ Sun, 21 Jun 2020 18:25:07: end of X-cor INFO @ Sun, 21 Jun 2020 18:25:07: #2 finished! INFO @ Sun, 21 Jun 2020 18:25:07: #2 predicted fragment length is 241 bps INFO @ Sun, 21 Jun 2020 18:25:07: #2 alternative fragment length(s) may be 4,241 bps INFO @ Sun, 21 Jun 2020 18:25:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX215500/SRX215500.20_model.r INFO @ Sun, 21 Jun 2020 18:25:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:25:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:25:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX215500/SRX215500.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:25:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX215500/SRX215500.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:25:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX215500/SRX215500.10_summits.bed INFO @ Sun, 21 Jun 2020 18:25:18: Done! pass1 - making usageList (648 chroms): 3 millis pass2 - checking and writing primary data (9694 records, 4 fields): 24 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:25:32: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:25:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX215500/SRX215500.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:25:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX215500/SRX215500.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:25:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX215500/SRX215500.20_summits.bed INFO @ Sun, 21 Jun 2020 18:25:44: Done! pass1 - making usageList (378 chroms): 1 millis pass2 - checking and writing primary data (2924 records, 4 fields): 13 millis CompletedMACS2peakCalling