Job ID = 6528394 SRX = SRX5717031 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T15:07:06 prefetch.2.10.7: 1) Downloading 'SRR8936391'... 2020-06-29T15:07:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T15:09:15 prefetch.2.10.7: HTTPS download succeed 2020-06-29T15:09:15 prefetch.2.10.7: 1) 'SRR8936391' was downloaded successfully Read 28891286 spots for SRR8936391/SRR8936391.sra Written 28891286 spots for SRR8936391/SRR8936391.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: 00:07:19 28891286 reads; of these: 28891286 (100.00%) were unpaired; of these: 2319929 (8.03%) aligned 0 times 20551487 (71.13%) aligned exactly 1 time 6019870 (20.84%) aligned >1 times 91.97% overall alignment rate Time searching: 00:07:19 Overall time: 00:07:19 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 10638323 / 26571357 = 0.4004 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 @ Tue, 30 Jun 2020 00:29:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5717031/SRX5717031.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5717031/SRX5717031.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5717031/SRX5717031.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5717031/SRX5717031.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 @ Tue, 30 Jun 2020 00:29:00: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:29:00: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:29:05: 1000000 INFO @ Tue, 30 Jun 2020 00:29:10: 2000000 INFO @ Tue, 30 Jun 2020 00:29:15: 3000000 INFO @ Tue, 30 Jun 2020 00:29:20: 4000000 INFO @ Tue, 30 Jun 2020 00:29:25: 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 @ Tue, 30 Jun 2020 00:29:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5717031/SRX5717031.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5717031/SRX5717031.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5717031/SRX5717031.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5717031/SRX5717031.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 @ Tue, 30 Jun 2020 00:29:30: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:29:30: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:29:30: 6000000 INFO @ Tue, 30 Jun 2020 00:29:36: 1000000 INFO @ Tue, 30 Jun 2020 00:29:36: 7000000 INFO @ Tue, 30 Jun 2020 00:29:41: 2000000 INFO @ Tue, 30 Jun 2020 00:29:41: 8000000 INFO @ Tue, 30 Jun 2020 00:29:47: 3000000 INFO @ Tue, 30 Jun 2020 00:29:47: 9000000 INFO @ Tue, 30 Jun 2020 00:29:52: 10000000 INFO @ Tue, 30 Jun 2020 00:29:52: 4000000 INFO @ Tue, 30 Jun 2020 00:29:57: 11000000 INFO @ Tue, 30 Jun 2020 00:29:58: 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 @ Tue, 30 Jun 2020 00:30:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5717031/SRX5717031.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5717031/SRX5717031.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5717031/SRX5717031.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5717031/SRX5717031.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 @ Tue, 30 Jun 2020 00:30:00: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:30:00: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:30:03: 12000000 INFO @ Tue, 30 Jun 2020 00:30:03: 6000000 INFO @ Tue, 30 Jun 2020 00:30:06: 1000000 INFO @ Tue, 30 Jun 2020 00:30:08: 13000000 INFO @ Tue, 30 Jun 2020 00:30:09: 7000000 INFO @ Tue, 30 Jun 2020 00:30:11: 2000000 INFO @ Tue, 30 Jun 2020 00:30:14: 14000000 INFO @ Tue, 30 Jun 2020 00:30:14: 8000000 INFO @ Tue, 30 Jun 2020 00:30:17: 3000000 INFO @ Tue, 30 Jun 2020 00:30:19: 15000000 INFO @ Tue, 30 Jun 2020 00:30:20: 9000000 INFO @ Tue, 30 Jun 2020 00:30:23: 4000000 INFO @ Tue, 30 Jun 2020 00:30:24: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:30:24: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:30:24: #1 total tags in treatment: 15933034 INFO @ Tue, 30 Jun 2020 00:30:24: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:30:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 00:30:25: #1 tags after filtering in treatment: 15933034 INFO @ Tue, 30 Jun 2020 00:30:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 00:30:25: #1 finished! INFO @ Tue, 30 Jun 2020 00:30:25: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:30:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:30:25: 10000000 INFO @ Tue, 30 Jun 2020 00:30:26: #2 number of paired peaks: 1691 INFO @ Tue, 30 Jun 2020 00:30:26: start model_add_line... INFO @ Tue, 30 Jun 2020 00:30:26: start X-correlation... INFO @ Tue, 30 Jun 2020 00:30:26: end of X-cor INFO @ Tue, 30 Jun 2020 00:30:26: #2 finished! INFO @ Tue, 30 Jun 2020 00:30:26: #2 predicted fragment length is 115 bps INFO @ Tue, 30 Jun 2020 00:30:26: #2 alternative fragment length(s) may be 21,40,61,115,131,155,241,265,490,561,595 bps INFO @ Tue, 30 Jun 2020 00:30:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5717031/SRX5717031.05_model.r INFO @ Tue, 30 Jun 2020 00:30:26: #3 Call peaks... INFO @ Tue, 30 Jun 2020 00:30:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 00:30:29: 5000000 INFO @ Tue, 30 Jun 2020 00:30:31: 11000000 INFO @ Tue, 30 Jun 2020 00:30:34: 6000000 INFO @ Tue, 30 Jun 2020 00:30:36: 12000000 INFO @ Tue, 30 Jun 2020 00:30:40: 7000000 INFO @ Tue, 30 Jun 2020 00:30:41: 13000000 INFO @ Tue, 30 Jun 2020 00:30:45: 8000000 INFO @ Tue, 30 Jun 2020 00:30:47: 14000000 INFO @ Tue, 30 Jun 2020 00:30:51: 9000000 INFO @ Tue, 30 Jun 2020 00:30:52: 15000000 INFO @ Tue, 30 Jun 2020 00:30:56: 10000000 INFO @ Tue, 30 Jun 2020 00:30:58: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:30:58: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:30:58: #1 total tags in treatment: 15933034 INFO @ Tue, 30 Jun 2020 00:30:58: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:30:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 00:30:58: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 00:30:58: #1 tags after filtering in treatment: 15933034 INFO @ Tue, 30 Jun 2020 00:30:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 00:30:58: #1 finished! INFO @ Tue, 30 Jun 2020 00:30:58: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:30:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:30:59: #2 number of paired peaks: 1691 INFO @ Tue, 30 Jun 2020 00:30:59: start model_add_line... INFO @ Tue, 30 Jun 2020 00:30:59: start X-correlation... INFO @ Tue, 30 Jun 2020 00:30:59: end of X-cor INFO @ Tue, 30 Jun 2020 00:30:59: #2 finished! INFO @ Tue, 30 Jun 2020 00:30:59: #2 predicted fragment length is 115 bps INFO @ Tue, 30 Jun 2020 00:30:59: #2 alternative fragment length(s) may be 21,40,61,115,131,155,241,265,490,561,595 bps INFO @ Tue, 30 Jun 2020 00:30:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5717031/SRX5717031.10_model.r INFO @ Tue, 30 Jun 2020 00:30:59: #3 Call peaks... INFO @ Tue, 30 Jun 2020 00:30:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 00:31:02: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 00:31:07: 12000000 INFO @ Tue, 30 Jun 2020 00:31:12: 13000000 INFO @ Tue, 30 Jun 2020 00:31:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5717031/SRX5717031.05_peaks.xls INFO @ Tue, 30 Jun 2020 00:31:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5717031/SRX5717031.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:31:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5717031/SRX5717031.05_summits.bed INFO @ Tue, 30 Jun 2020 00:31:14: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2516 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 00:31:18: 14000000 INFO @ Tue, 30 Jun 2020 00:31:23: 15000000 INFO @ Tue, 30 Jun 2020 00:31:28: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:31:28: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:31:28: #1 total tags in treatment: 15933034 INFO @ Tue, 30 Jun 2020 00:31:28: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:31:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 00:31:28: #1 tags after filtering in treatment: 15933034 INFO @ Tue, 30 Jun 2020 00:31:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 00:31:28: #1 finished! INFO @ Tue, 30 Jun 2020 00:31:28: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:31:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:31:29: #2 number of paired peaks: 1691 INFO @ Tue, 30 Jun 2020 00:31:29: start model_add_line... INFO @ Tue, 30 Jun 2020 00:31:30: start X-correlation... INFO @ Tue, 30 Jun 2020 00:31:30: end of X-cor INFO @ Tue, 30 Jun 2020 00:31:30: #2 finished! INFO @ Tue, 30 Jun 2020 00:31:30: #2 predicted fragment length is 115 bps INFO @ Tue, 30 Jun 2020 00:31:30: #2 alternative fragment length(s) may be 21,40,61,115,131,155,241,265,490,561,595 bps INFO @ Tue, 30 Jun 2020 00:31:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5717031/SRX5717031.20_model.r INFO @ Tue, 30 Jun 2020 00:31:30: #3 Call peaks... INFO @ Tue, 30 Jun 2020 00:31:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 00:31:33: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 00:31:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5717031/SRX5717031.10_peaks.xls INFO @ Tue, 30 Jun 2020 00:31:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5717031/SRX5717031.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:31:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5717031/SRX5717031.10_summits.bed INFO @ Tue, 30 Jun 2020 00:31:49: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1240 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 00:32:03: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 00:32:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5717031/SRX5717031.20_peaks.xls INFO @ Tue, 30 Jun 2020 00:32:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5717031/SRX5717031.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:32:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5717031/SRX5717031.20_summits.bed INFO @ Tue, 30 Jun 2020 00:32:19: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (545 records, 4 fields): 1 millis CompletedMACS2peakCalling