Job ID = 6454819 SRX = SRX2592418 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:27:29 prefetch.2.10.7: 1) Downloading 'SRR5289695'... 2020-06-21T09:27:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:33:56 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:33:56 prefetch.2.10.7: 1) 'SRR5289695' was downloaded successfully Read 30352586 spots for SRR5289695/SRR5289695.sra Written 30352586 spots for SRR5289695/SRR5289695.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: 00:09:24 30352586 reads; of these: 30352586 (100.00%) were unpaired; of these: 2555131 (8.42%) aligned 0 times 22716384 (74.84%) aligned exactly 1 time 5081071 (16.74%) aligned >1 times 91.58% overall alignment rate Time searching: 00:09:24 Overall time: 00:09:24 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 12 files... [bam_rmdupse_core] 9445470 / 27797455 = 0.3398 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 18:52:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592418/SRX2592418.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592418/SRX2592418.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592418/SRX2592418.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592418/SRX2592418.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 18:52:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:52:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:52:45: 1000000 INFO @ Sun, 21 Jun 2020 18:52:52: 2000000 INFO @ Sun, 21 Jun 2020 18:52:58: 3000000 INFO @ Sun, 21 Jun 2020 18:53:05: 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 18:53:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592418/SRX2592418.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592418/SRX2592418.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592418/SRX2592418.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592418/SRX2592418.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 18:53:08: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:53:08: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:53:12: 5000000 INFO @ Sun, 21 Jun 2020 18:53:16: 1000000 INFO @ Sun, 21 Jun 2020 18:53:20: 6000000 INFO @ Sun, 21 Jun 2020 18:53:25: 2000000 INFO @ Sun, 21 Jun 2020 18:53:27: 7000000 INFO @ Sun, 21 Jun 2020 18:53:33: 3000000 INFO @ Sun, 21 Jun 2020 18:53:35: 8000000 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 18:53:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592418/SRX2592418.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592418/SRX2592418.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592418/SRX2592418.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592418/SRX2592418.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 18:53:39: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:53:39: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:53:41: 4000000 INFO @ Sun, 21 Jun 2020 18:53:43: 9000000 INFO @ Sun, 21 Jun 2020 18:53:46: 1000000 INFO @ Sun, 21 Jun 2020 18:53:49: 5000000 INFO @ Sun, 21 Jun 2020 18:53:51: 10000000 INFO @ Sun, 21 Jun 2020 18:53:54: 2000000 INFO @ Sun, 21 Jun 2020 18:53:57: 6000000 INFO @ Sun, 21 Jun 2020 18:53:59: 11000000 INFO @ Sun, 21 Jun 2020 18:54:02: 3000000 INFO @ Sun, 21 Jun 2020 18:54:05: 7000000 INFO @ Sun, 21 Jun 2020 18:54:07: 12000000 INFO @ Sun, 21 Jun 2020 18:54:10: 4000000 INFO @ Sun, 21 Jun 2020 18:54:13: 8000000 INFO @ Sun, 21 Jun 2020 18:54:14: 13000000 INFO @ Sun, 21 Jun 2020 18:54:18: 5000000 INFO @ Sun, 21 Jun 2020 18:54:21: 9000000 INFO @ Sun, 21 Jun 2020 18:54:22: 14000000 INFO @ Sun, 21 Jun 2020 18:54:26: 6000000 INFO @ Sun, 21 Jun 2020 18:54:29: 10000000 INFO @ Sun, 21 Jun 2020 18:54:30: 15000000 INFO @ Sun, 21 Jun 2020 18:54:34: 7000000 INFO @ Sun, 21 Jun 2020 18:54:37: 11000000 INFO @ Sun, 21 Jun 2020 18:54:38: 16000000 INFO @ Sun, 21 Jun 2020 18:54:41: 8000000 INFO @ Sun, 21 Jun 2020 18:54:45: 12000000 INFO @ Sun, 21 Jun 2020 18:54:46: 17000000 INFO @ Sun, 21 Jun 2020 18:54:49: 9000000 INFO @ Sun, 21 Jun 2020 18:54:54: 13000000 INFO @ Sun, 21 Jun 2020 18:54:54: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:54:57: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:54:57: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:54:57: #1 total tags in treatment: 18351985 INFO @ Sun, 21 Jun 2020 18:54:57: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:54:57: #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 18:54:57: 10000000 INFO @ Sun, 21 Jun 2020 18:54:57: #1 tags after filtering in treatment: 18351885 INFO @ Sun, 21 Jun 2020 18:54:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:54:57: #1 finished! INFO @ Sun, 21 Jun 2020 18:54:57: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:54:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:54:59: #2 number of paired peaks: 3107 INFO @ Sun, 21 Jun 2020 18:54:59: start model_add_line... INFO @ Sun, 21 Jun 2020 18:54:59: start X-correlation... INFO @ Sun, 21 Jun 2020 18:54:59: end of X-cor INFO @ Sun, 21 Jun 2020 18:54:59: #2 finished! INFO @ Sun, 21 Jun 2020 18:54:59: #2 predicted fragment length is 187 bps INFO @ Sun, 21 Jun 2020 18:54:59: #2 alternative fragment length(s) may be 3,187 bps INFO @ Sun, 21 Jun 2020 18:54:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592418/SRX2592418.05_model.r INFO @ Sun, 21 Jun 2020 18:54:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:54:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:55:02: 14000000 INFO @ Sun, 21 Jun 2020 18:55:05: 11000000 INFO @ Sun, 21 Jun 2020 18:55:10: 15000000 INFO @ Sun, 21 Jun 2020 18:55:13: 12000000 INFO @ Sun, 21 Jun 2020 18:55:19: 16000000 INFO @ Sun, 21 Jun 2020 18:55:20: 13000000 INFO @ Sun, 21 Jun 2020 18:55:27: 17000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:55:28: 14000000 INFO @ Sun, 21 Jun 2020 18:55:35: 18000000 INFO @ Sun, 21 Jun 2020 18:55:37: 15000000 INFO @ Sun, 21 Jun 2020 18:55:38: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:55:38: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:55:38: #1 total tags in treatment: 18351985 INFO @ Sun, 21 Jun 2020 18:55:38: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:55:38: #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 18:55:39: #1 tags after filtering in treatment: 18351885 INFO @ Sun, 21 Jun 2020 18:55:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:55:39: #1 finished! INFO @ Sun, 21 Jun 2020 18:55:39: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:55:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:55:41: #2 number of paired peaks: 3107 INFO @ Sun, 21 Jun 2020 18:55:41: start model_add_line... INFO @ Sun, 21 Jun 2020 18:55:41: start X-correlation... INFO @ Sun, 21 Jun 2020 18:55:41: end of X-cor INFO @ Sun, 21 Jun 2020 18:55:41: #2 finished! INFO @ Sun, 21 Jun 2020 18:55:41: #2 predicted fragment length is 187 bps INFO @ Sun, 21 Jun 2020 18:55:41: #2 alternative fragment length(s) may be 3,187 bps INFO @ Sun, 21 Jun 2020 18:55:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592418/SRX2592418.10_model.r INFO @ Sun, 21 Jun 2020 18:55:41: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:55:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:55:43: 16000000 INFO @ Sun, 21 Jun 2020 18:55:50: 17000000 INFO @ Sun, 21 Jun 2020 18:55:51: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:55:56: 18000000 INFO @ Sun, 21 Jun 2020 18:55:58: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:55:58: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:55:58: #1 total tags in treatment: 18351985 INFO @ Sun, 21 Jun 2020 18:55:58: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:55:58: #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 18:55:59: #1 tags after filtering in treatment: 18351885 INFO @ Sun, 21 Jun 2020 18:55:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:55:59: #1 finished! INFO @ Sun, 21 Jun 2020 18:55:59: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:55:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:56:01: #2 number of paired peaks: 3107 INFO @ Sun, 21 Jun 2020 18:56:01: start model_add_line... INFO @ Sun, 21 Jun 2020 18:56:01: start X-correlation... INFO @ Sun, 21 Jun 2020 18:56:01: end of X-cor INFO @ Sun, 21 Jun 2020 18:56:01: #2 finished! INFO @ Sun, 21 Jun 2020 18:56:01: #2 predicted fragment length is 187 bps INFO @ Sun, 21 Jun 2020 18:56:01: #2 alternative fragment length(s) may be 3,187 bps INFO @ Sun, 21 Jun 2020 18:56:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592418/SRX2592418.20_model.r INFO @ Sun, 21 Jun 2020 18:56:01: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:56:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:56:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592418/SRX2592418.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:56:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592418/SRX2592418.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:56:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592418/SRX2592418.05_summits.bed INFO @ Sun, 21 Jun 2020 18:56:17: Done! pass1 - making usageList (202 chroms): 3 millis pass2 - checking and writing primary data (16301 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:56:31: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:56:51: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:56:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592418/SRX2592418.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:56:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592418/SRX2592418.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:56:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592418/SRX2592418.10_summits.bed INFO @ Sun, 21 Jun 2020 18:56:53: Done! pass1 - making usageList (171 chroms): 2 millis pass2 - checking and writing primary data (11760 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:57:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592418/SRX2592418.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:57:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592418/SRX2592418.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:57:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592418/SRX2592418.20_summits.bed INFO @ Sun, 21 Jun 2020 18:57:13: Done! pass1 - making usageList (121 chroms): 1 millis pass2 - checking and writing primary data (5991 records, 4 fields): 11 millis CompletedMACS2peakCalling