Job ID = 6453144 SRX = SRX104967 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:02:23 prefetch.2.10.7: 1) Downloading 'SRR363411'... 2020-06-21T08:02:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:07:15 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:07:16 prefetch.2.10.7: 'SRR363411' is valid 2020-06-21T08:07:16 prefetch.2.10.7: 1) 'SRR363411' was downloaded successfully Read 23143797 spots for SRR363411/SRR363411.sra Written 23143797 spots for SRR363411/SRR363411.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: 00:04:49 23143797 reads; of these: 23143797 (100.00%) were unpaired; of these: 934425 (4.04%) aligned 0 times 17351426 (74.97%) aligned exactly 1 time 4857946 (20.99%) aligned >1 times 95.96% overall alignment rate Time searching: 00:04:49 Overall time: 00:04:49 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] 3591484 / 22209372 = 0.1617 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 17:17:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX104967/SRX104967.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX104967/SRX104967.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX104967/SRX104967.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX104967/SRX104967.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 17:17:35: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:17:35: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:17:42: 1000000 INFO @ Sun, 21 Jun 2020 17:17:48: 2000000 INFO @ Sun, 21 Jun 2020 17:17:55: 3000000 INFO @ Sun, 21 Jun 2020 17:18:02: 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 17:18:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX104967/SRX104967.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX104967/SRX104967.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX104967/SRX104967.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX104967/SRX104967.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 17:18:05: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:18:05: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:18:09: 5000000 INFO @ Sun, 21 Jun 2020 17:18:12: 1000000 INFO @ Sun, 21 Jun 2020 17:18:16: 6000000 INFO @ Sun, 21 Jun 2020 17:18:20: 2000000 INFO @ Sun, 21 Jun 2020 17:18:24: 7000000 INFO @ Sun, 21 Jun 2020 17:18:27: 3000000 INFO @ Sun, 21 Jun 2020 17:18:31: 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 17:18:34: 4000000 INFO @ Sun, 21 Jun 2020 17:18:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX104967/SRX104967.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX104967/SRX104967.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX104967/SRX104967.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX104967/SRX104967.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 17:18:35: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:18:35: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:18:39: 9000000 INFO @ Sun, 21 Jun 2020 17:18:41: 5000000 INFO @ Sun, 21 Jun 2020 17:18:43: 1000000 INFO @ Sun, 21 Jun 2020 17:18:46: 10000000 INFO @ Sun, 21 Jun 2020 17:18:48: 6000000 INFO @ Sun, 21 Jun 2020 17:18:51: 2000000 INFO @ Sun, 21 Jun 2020 17:18:54: 11000000 INFO @ Sun, 21 Jun 2020 17:18:55: 7000000 INFO @ Sun, 21 Jun 2020 17:18:59: 3000000 INFO @ Sun, 21 Jun 2020 17:19:02: 12000000 INFO @ Sun, 21 Jun 2020 17:19:03: 8000000 INFO @ Sun, 21 Jun 2020 17:19:07: 4000000 INFO @ Sun, 21 Jun 2020 17:19:10: 13000000 INFO @ Sun, 21 Jun 2020 17:19:10: 9000000 INFO @ Sun, 21 Jun 2020 17:19:14: 5000000 INFO @ Sun, 21 Jun 2020 17:19:18: 14000000 INFO @ Sun, 21 Jun 2020 17:19:18: 10000000 INFO @ Sun, 21 Jun 2020 17:19:22: 6000000 INFO @ Sun, 21 Jun 2020 17:19:25: 11000000 INFO @ Sun, 21 Jun 2020 17:19:26: 15000000 INFO @ Sun, 21 Jun 2020 17:19:30: 7000000 INFO @ Sun, 21 Jun 2020 17:19:33: 12000000 INFO @ Sun, 21 Jun 2020 17:19:34: 16000000 INFO @ Sun, 21 Jun 2020 17:19:38: 8000000 INFO @ Sun, 21 Jun 2020 17:19:40: 13000000 INFO @ Sun, 21 Jun 2020 17:19:42: 17000000 INFO @ Sun, 21 Jun 2020 17:19:45: 9000000 INFO @ Sun, 21 Jun 2020 17:19:48: 14000000 INFO @ Sun, 21 Jun 2020 17:19:49: 18000000 INFO @ Sun, 21 Jun 2020 17:19:53: 10000000 INFO @ Sun, 21 Jun 2020 17:19:54: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:19:54: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:19:54: #1 total tags in treatment: 18617888 INFO @ Sun, 21 Jun 2020 17:19:54: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:19:54: #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 17:19:55: #1 tags after filtering in treatment: 18617884 INFO @ Sun, 21 Jun 2020 17:19:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:19:55: #1 finished! INFO @ Sun, 21 Jun 2020 17:19:55: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:19:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:19:55: 15000000 INFO @ Sun, 21 Jun 2020 17:19:56: #2 number of paired peaks: 1096 INFO @ Sun, 21 Jun 2020 17:19:56: start model_add_line... INFO @ Sun, 21 Jun 2020 17:19:57: start X-correlation... INFO @ Sun, 21 Jun 2020 17:19:57: end of X-cor INFO @ Sun, 21 Jun 2020 17:19:57: #2 finished! INFO @ Sun, 21 Jun 2020 17:19:57: #2 predicted fragment length is 139 bps INFO @ Sun, 21 Jun 2020 17:19:57: #2 alternative fragment length(s) may be 4,139,156 bps INFO @ Sun, 21 Jun 2020 17:19:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX104967/SRX104967.05_model.r INFO @ Sun, 21 Jun 2020 17:19:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:19:57: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:20:01: 11000000 INFO @ Sun, 21 Jun 2020 17:20:03: 16000000 INFO @ Sun, 21 Jun 2020 17:20:08: 12000000 INFO @ Sun, 21 Jun 2020 17:20:11: 17000000 INFO @ Sun, 21 Jun 2020 17:20:16: 13000000 INFO @ Sun, 21 Jun 2020 17:20:18: 18000000 INFO @ Sun, 21 Jun 2020 17:20:22: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:20:22: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:20:22: #1 total tags in treatment: 18617888 INFO @ Sun, 21 Jun 2020 17:20:22: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:20:22: #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 17:20:23: 14000000 INFO @ Sun, 21 Jun 2020 17:20:23: #1 tags after filtering in treatment: 18617884 INFO @ Sun, 21 Jun 2020 17:20:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:20:23: #1 finished! INFO @ Sun, 21 Jun 2020 17:20:23: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:20:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:20:25: #2 number of paired peaks: 1096 INFO @ Sun, 21 Jun 2020 17:20:25: start model_add_line... INFO @ Sun, 21 Jun 2020 17:20:25: start X-correlation... INFO @ Sun, 21 Jun 2020 17:20:25: end of X-cor INFO @ Sun, 21 Jun 2020 17:20:25: #2 finished! INFO @ Sun, 21 Jun 2020 17:20:25: #2 predicted fragment length is 139 bps INFO @ Sun, 21 Jun 2020 17:20:25: #2 alternative fragment length(s) may be 4,139,156 bps INFO @ Sun, 21 Jun 2020 17:20:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX104967/SRX104967.10_model.r INFO @ Sun, 21 Jun 2020 17:20:25: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:20:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:20:30: 15000000 INFO @ Sun, 21 Jun 2020 17:20:37: 16000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:20:40: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:20:44: 17000000 INFO @ Sun, 21 Jun 2020 17:20:50: 18000000 INFO @ Sun, 21 Jun 2020 17:20:55: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:20:55: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:20:55: #1 total tags in treatment: 18617888 INFO @ Sun, 21 Jun 2020 17:20:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:20:55: #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 17:20:55: #1 tags after filtering in treatment: 18617884 INFO @ Sun, 21 Jun 2020 17:20:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:20:55: #1 finished! INFO @ Sun, 21 Jun 2020 17:20:55: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:20:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:20:57: #2 number of paired peaks: 1096 INFO @ Sun, 21 Jun 2020 17:20:57: start model_add_line... INFO @ Sun, 21 Jun 2020 17:20:57: start X-correlation... INFO @ Sun, 21 Jun 2020 17:20:57: end of X-cor INFO @ Sun, 21 Jun 2020 17:20:57: #2 finished! INFO @ Sun, 21 Jun 2020 17:20:57: #2 predicted fragment length is 139 bps INFO @ Sun, 21 Jun 2020 17:20:57: #2 alternative fragment length(s) may be 4,139,156 bps INFO @ Sun, 21 Jun 2020 17:20:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX104967/SRX104967.20_model.r INFO @ Sun, 21 Jun 2020 17:20:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:20:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:21:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX104967/SRX104967.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:21:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX104967/SRX104967.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:21:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX104967/SRX104967.05_summits.bed INFO @ Sun, 21 Jun 2020 17:21:00: Done! pass1 - making usageList (301 chroms): 2 millis pass2 - checking and writing primary data (2923 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:21:09: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:21:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX104967/SRX104967.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:21:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX104967/SRX104967.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:21:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX104967/SRX104967.10_summits.bed INFO @ Sun, 21 Jun 2020 17:21:31: Done! pass1 - making usageList (218 chroms): 1 millis pass2 - checking and writing primary data (812 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:21:39: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:21:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX104967/SRX104967.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:21:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX104967/SRX104967.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:21:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX104967/SRX104967.20_summits.bed INFO @ Sun, 21 Jun 2020 17:21:59: Done! pass1 - making usageList (127 chroms): 1 millis pass2 - checking and writing primary data (250 records, 4 fields): 5 millis CompletedMACS2peakCalling