Job ID = 6452744 SRX = SRX030148 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:00:38 prefetch.2.10.7: 1) Downloading 'SRR071262'... 2020-06-21T08:00:38 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:02:29 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:02:30 prefetch.2.10.7: 'SRR071262' is valid 2020-06-21T08:02:30 prefetch.2.10.7: 1) 'SRR071262' was downloaded successfully Read 23027607 spots for SRR071262/SRR071262.sra Written 23027607 spots for SRR071262/SRR071262.sra 2020-06-21T08:03:40 prefetch.2.10.7: 1) Downloading 'SRR071263'... 2020-06-21T08:03:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:06:27 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:06:28 prefetch.2.10.7: 'SRR071263' is valid 2020-06-21T08:06:28 prefetch.2.10.7: 1) 'SRR071263' was downloaded successfully Read 27468934 spots for SRR071263/SRR071263.sra Written 27468934 spots for SRR071263/SRR071263.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:10:38 50496541 reads; of these: 50496541 (100.00%) were unpaired; of these: 12239873 (24.24%) aligned 0 times 27696237 (54.85%) aligned exactly 1 time 10560431 (20.91%) aligned >1 times 75.76% overall alignment rate Time searching: 00:10:39 Overall time: 00:10:39 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] 32614916 / 38256668 = 0.8525 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 17:23:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX030148/SRX030148.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX030148/SRX030148.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX030148/SRX030148.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX030148/SRX030148.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 17:23:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:23:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:23:39: 1000000 INFO @ Sun, 21 Jun 2020 17:23:44: 2000000 INFO @ Sun, 21 Jun 2020 17:23:49: 3000000 INFO @ Sun, 21 Jun 2020 17:23:54: 4000000 INFO @ Sun, 21 Jun 2020 17:23:59: 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 17:24:02: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:24:02: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:24:02: #1 total tags in treatment: 5641752 INFO @ Sun, 21 Jun 2020 17:24:02: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:24:02: #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 17:24:03: #1 tags after filtering in treatment: 5641740 INFO @ Sun, 21 Jun 2020 17:24:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:24:03: #1 finished! INFO @ Sun, 21 Jun 2020 17:24:03: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:24:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:24:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX030148/SRX030148.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX030148/SRX030148.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX030148/SRX030148.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX030148/SRX030148.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 17:24:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:24:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:24:03: #2 number of paired peaks: 4884 INFO @ Sun, 21 Jun 2020 17:24:03: start model_add_line... INFO @ Sun, 21 Jun 2020 17:24:04: start X-correlation... INFO @ Sun, 21 Jun 2020 17:24:04: end of X-cor INFO @ Sun, 21 Jun 2020 17:24:04: #2 finished! INFO @ Sun, 21 Jun 2020 17:24:04: #2 predicted fragment length is 181 bps INFO @ Sun, 21 Jun 2020 17:24:04: #2 alternative fragment length(s) may be 181 bps INFO @ Sun, 21 Jun 2020 17:24:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX030148/SRX030148.05_model.r INFO @ Sun, 21 Jun 2020 17:24:04: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:24:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:24:09: 1000000 INFO @ Sun, 21 Jun 2020 17:24:14: 2000000 INFO @ Sun, 21 Jun 2020 17:24:18: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:24:20: 3000000 INFO @ Sun, 21 Jun 2020 17:24:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX030148/SRX030148.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:24:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX030148/SRX030148.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:24:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX030148/SRX030148.05_summits.bed INFO @ Sun, 21 Jun 2020 17:24:24: Done! pass1 - making usageList (1006 chroms): 2 millis pass2 - checking and writing primary data (6518 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:24:25: 4000000 INFO @ Sun, 21 Jun 2020 17:24:31: 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 @ Sun, 21 Jun 2020 17:24:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX030148/SRX030148.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX030148/SRX030148.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX030148/SRX030148.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX030148/SRX030148.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 17:24:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:24:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:24:34: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:24:34: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:24:34: #1 total tags in treatment: 5641752 INFO @ Sun, 21 Jun 2020 17:24:34: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:24:34: #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 17:24:34: #1 tags after filtering in treatment: 5641740 INFO @ Sun, 21 Jun 2020 17:24:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:24:34: #1 finished! INFO @ Sun, 21 Jun 2020 17:24:34: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:24:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:24:35: #2 number of paired peaks: 4884 INFO @ Sun, 21 Jun 2020 17:24:35: start model_add_line... INFO @ Sun, 21 Jun 2020 17:24:35: start X-correlation... INFO @ Sun, 21 Jun 2020 17:24:35: end of X-cor INFO @ Sun, 21 Jun 2020 17:24:35: #2 finished! INFO @ Sun, 21 Jun 2020 17:24:35: #2 predicted fragment length is 181 bps INFO @ Sun, 21 Jun 2020 17:24:35: #2 alternative fragment length(s) may be 181 bps INFO @ Sun, 21 Jun 2020 17:24:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX030148/SRX030148.10_model.r INFO @ Sun, 21 Jun 2020 17:24:35: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:24:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:24:39: 1000000 INFO @ Sun, 21 Jun 2020 17:24:44: 2000000 INFO @ Sun, 21 Jun 2020 17:24:49: 3000000 INFO @ Sun, 21 Jun 2020 17:24:50: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:24:55: 4000000 INFO @ Sun, 21 Jun 2020 17:24:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX030148/SRX030148.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:24:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX030148/SRX030148.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:24:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX030148/SRX030148.10_summits.bed INFO @ Sun, 21 Jun 2020 17:24:56: Done! pass1 - making usageList (875 chroms): 2 millis pass2 - checking and writing primary data (5160 records, 4 fields): 25 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:25:00: 5000000 INFO @ Sun, 21 Jun 2020 17:25:03: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:25:03: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:25:03: #1 total tags in treatment: 5641752 INFO @ Sun, 21 Jun 2020 17:25:03: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:25:03: #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 17:25:04: #1 tags after filtering in treatment: 5641740 INFO @ Sun, 21 Jun 2020 17:25:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:25:04: #1 finished! INFO @ Sun, 21 Jun 2020 17:25:04: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:25:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:25:04: #2 number of paired peaks: 4884 INFO @ Sun, 21 Jun 2020 17:25:04: start model_add_line... INFO @ Sun, 21 Jun 2020 17:25:05: start X-correlation... INFO @ Sun, 21 Jun 2020 17:25:05: end of X-cor INFO @ Sun, 21 Jun 2020 17:25:05: #2 finished! INFO @ Sun, 21 Jun 2020 17:25:05: #2 predicted fragment length is 181 bps INFO @ Sun, 21 Jun 2020 17:25:05: #2 alternative fragment length(s) may be 181 bps INFO @ Sun, 21 Jun 2020 17:25:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX030148/SRX030148.20_model.r INFO @ Sun, 21 Jun 2020 17:25:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:25:05: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:25:20: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:25:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX030148/SRX030148.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:25:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX030148/SRX030148.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:25:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX030148/SRX030148.20_summits.bed INFO @ Sun, 21 Jun 2020 17:25:26: Done! pass1 - making usageList (755 chroms): 2 millis pass2 - checking and writing primary data (3978 records, 4 fields): 21 millis CompletedMACS2peakCalling