Job ID = 6453081 SRX = SRX1032391 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:58:29 prefetch.2.10.7: 1) Downloading 'SRR2031889'... 2020-06-21T07:58:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:01:16 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:01:16 prefetch.2.10.7: 1) 'SRR2031889' was downloaded successfully Read 24558754 spots for SRR2031889/SRR2031889.sra Written 24558754 spots for SRR2031889/SRR2031889.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: 00:06:42 24558754 reads; of these: 24558754 (100.00%) were unpaired; of these: 745823 (3.04%) aligned 0 times 18922794 (77.05%) aligned exactly 1 time 4890137 (19.91%) aligned >1 times 96.96% overall alignment rate Time searching: 00:06:42 Overall time: 00:06:42 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] 4620479 / 23812931 = 0.1940 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 17:15:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1032391/SRX1032391.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1032391/SRX1032391.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1032391/SRX1032391.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1032391/SRX1032391.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 17:15:19: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:15:19: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:15:24: 1000000 INFO @ Sun, 21 Jun 2020 17:15:29: 2000000 INFO @ Sun, 21 Jun 2020 17:15:34: 3000000 INFO @ Sun, 21 Jun 2020 17:15:38: 4000000 INFO @ Sun, 21 Jun 2020 17:15:43: 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 17:15:48: 6000000 INFO @ Sun, 21 Jun 2020 17:15:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1032391/SRX1032391.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1032391/SRX1032391.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1032391/SRX1032391.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1032391/SRX1032391.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 17:15:49: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:15:49: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:15:53: 7000000 INFO @ Sun, 21 Jun 2020 17:15:54: 1000000 INFO @ Sun, 21 Jun 2020 17:15:57: 8000000 INFO @ Sun, 21 Jun 2020 17:15:59: 2000000 INFO @ Sun, 21 Jun 2020 17:16:02: 9000000 INFO @ Sun, 21 Jun 2020 17:16:04: 3000000 INFO @ Sun, 21 Jun 2020 17:16:07: 10000000 INFO @ Sun, 21 Jun 2020 17:16:09: 4000000 INFO @ Sun, 21 Jun 2020 17:16:12: 11000000 INFO @ Sun, 21 Jun 2020 17:16:14: 5000000 INFO @ Sun, 21 Jun 2020 17:16:16: 12000000 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 17:16:19: 6000000 INFO @ Sun, 21 Jun 2020 17:16:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1032391/SRX1032391.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1032391/SRX1032391.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1032391/SRX1032391.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1032391/SRX1032391.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 17:16:20: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:16:20: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:16:21: 13000000 INFO @ Sun, 21 Jun 2020 17:16:24: 7000000 INFO @ Sun, 21 Jun 2020 17:16:25: 1000000 INFO @ Sun, 21 Jun 2020 17:16:26: 14000000 INFO @ Sun, 21 Jun 2020 17:16:28: 8000000 INFO @ Sun, 21 Jun 2020 17:16:31: 2000000 INFO @ Sun, 21 Jun 2020 17:16:31: 15000000 INFO @ Sun, 21 Jun 2020 17:16:33: 9000000 INFO @ Sun, 21 Jun 2020 17:16:36: 3000000 INFO @ Sun, 21 Jun 2020 17:16:36: 16000000 INFO @ Sun, 21 Jun 2020 17:16:38: 10000000 INFO @ Sun, 21 Jun 2020 17:16:41: 17000000 INFO @ Sun, 21 Jun 2020 17:16:41: 4000000 INFO @ Sun, 21 Jun 2020 17:16:43: 11000000 INFO @ Sun, 21 Jun 2020 17:16:46: 18000000 INFO @ Sun, 21 Jun 2020 17:16:47: 5000000 INFO @ Sun, 21 Jun 2020 17:16:47: 12000000 INFO @ Sun, 21 Jun 2020 17:16:50: 19000000 INFO @ Sun, 21 Jun 2020 17:16:52: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:16:52: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:16:52: #1 total tags in treatment: 19192452 INFO @ Sun, 21 Jun 2020 17:16:52: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:16:52: #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 17:16:52: 6000000 INFO @ Sun, 21 Jun 2020 17:16:52: 13000000 INFO @ Sun, 21 Jun 2020 17:16:52: #1 tags after filtering in treatment: 19192451 INFO @ Sun, 21 Jun 2020 17:16:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:16:52: #1 finished! INFO @ Sun, 21 Jun 2020 17:16:52: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:16:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:16:54: #2 number of paired peaks: 1053 INFO @ Sun, 21 Jun 2020 17:16:54: start model_add_line... INFO @ Sun, 21 Jun 2020 17:16:54: start X-correlation... INFO @ Sun, 21 Jun 2020 17:16:54: end of X-cor INFO @ Sun, 21 Jun 2020 17:16:54: #2 finished! INFO @ Sun, 21 Jun 2020 17:16:54: #2 predicted fragment length is 126 bps INFO @ Sun, 21 Jun 2020 17:16:54: #2 alternative fragment length(s) may be 126 bps INFO @ Sun, 21 Jun 2020 17:16:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1032391/SRX1032391.05_model.r INFO @ Sun, 21 Jun 2020 17:16:54: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:16:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:16:57: 14000000 INFO @ Sun, 21 Jun 2020 17:16:57: 7000000 INFO @ Sun, 21 Jun 2020 17:17:01: 15000000 INFO @ Sun, 21 Jun 2020 17:17:02: 8000000 INFO @ Sun, 21 Jun 2020 17:17:06: 16000000 INFO @ Sun, 21 Jun 2020 17:17:07: 9000000 INFO @ Sun, 21 Jun 2020 17:17:11: 17000000 INFO @ Sun, 21 Jun 2020 17:17:12: 10000000 INFO @ Sun, 21 Jun 2020 17:17:16: 18000000 INFO @ Sun, 21 Jun 2020 17:17:17: 11000000 INFO @ Sun, 21 Jun 2020 17:17:21: 19000000 INFO @ Sun, 21 Jun 2020 17:17:22: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:17:22: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:17:22: #1 total tags in treatment: 19192452 INFO @ Sun, 21 Jun 2020 17:17:22: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:17:22: #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 17:17:22: 12000000 INFO @ Sun, 21 Jun 2020 17:17:23: #1 tags after filtering in treatment: 19192451 INFO @ Sun, 21 Jun 2020 17:17:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:17:23: #1 finished! INFO @ Sun, 21 Jun 2020 17:17:23: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:17:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:17:24: #2 number of paired peaks: 1053 INFO @ Sun, 21 Jun 2020 17:17:24: start model_add_line... INFO @ Sun, 21 Jun 2020 17:17:24: start X-correlation... INFO @ Sun, 21 Jun 2020 17:17:24: end of X-cor INFO @ Sun, 21 Jun 2020 17:17:24: #2 finished! INFO @ Sun, 21 Jun 2020 17:17:24: #2 predicted fragment length is 126 bps INFO @ Sun, 21 Jun 2020 17:17:24: #2 alternative fragment length(s) may be 126 bps INFO @ Sun, 21 Jun 2020 17:17:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1032391/SRX1032391.10_model.r INFO @ Sun, 21 Jun 2020 17:17:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:17:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:17:27: 13000000 INFO @ Sun, 21 Jun 2020 17:17:33: 14000000 INFO @ Sun, 21 Jun 2020 17:17:38: 15000000 INFO @ Sun, 21 Jun 2020 17:17:38: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:17:43: 16000000 INFO @ Sun, 21 Jun 2020 17:17:48: 17000000 INFO @ Sun, 21 Jun 2020 17:17:53: 18000000 INFO @ Sun, 21 Jun 2020 17:17:59: 19000000 INFO @ Sun, 21 Jun 2020 17:17:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1032391/SRX1032391.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:17:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1032391/SRX1032391.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:17:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1032391/SRX1032391.05_summits.bed INFO @ Sun, 21 Jun 2020 17:17:59: Done! INFO @ Sun, 21 Jun 2020 17:18:00: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:18:00: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:18:00: #1 total tags in treatment: 19192452 INFO @ Sun, 21 Jun 2020 17:18:00: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:18:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) pass1 - making usageList (622 chroms): 3 millis pass2 - checking and writing primary data (9705 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:18:00: #1 tags after filtering in treatment: 19192451 INFO @ Sun, 21 Jun 2020 17:18:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:18:00: #1 finished! INFO @ Sun, 21 Jun 2020 17:18:00: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:18:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:18:02: #2 number of paired peaks: 1053 INFO @ Sun, 21 Jun 2020 17:18:02: start model_add_line... INFO @ Sun, 21 Jun 2020 17:18:02: start X-correlation... INFO @ Sun, 21 Jun 2020 17:18:02: end of X-cor INFO @ Sun, 21 Jun 2020 17:18:02: #2 finished! INFO @ Sun, 21 Jun 2020 17:18:02: #2 predicted fragment length is 126 bps INFO @ Sun, 21 Jun 2020 17:18:02: #2 alternative fragment length(s) may be 126 bps INFO @ Sun, 21 Jun 2020 17:18:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1032391/SRX1032391.20_model.r INFO @ Sun, 21 Jun 2020 17:18:02: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:18:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:18:09: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:18:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1032391/SRX1032391.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:18:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1032391/SRX1032391.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:18:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1032391/SRX1032391.10_summits.bed INFO @ Sun, 21 Jun 2020 17:18:31: Done! pass1 - making usageList (485 chroms): 1 millis pass2 - checking and writing primary data (6452 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:18:45: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:19:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1032391/SRX1032391.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:19:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1032391/SRX1032391.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:19:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1032391/SRX1032391.20_summits.bed INFO @ Sun, 21 Jun 2020 17:19:06: Done! pass1 - making usageList (286 chroms): 1 millis pass2 - checking and writing primary data (3049 records, 4 fields): 11 millis CompletedMACS2peakCalling