Job ID = 6453876 SRX = SRX1550610 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:40:02 prefetch.2.10.7: 1) Downloading 'SRR3130854'... 2020-06-21T08:40:02 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:40:48 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:40:48 prefetch.2.10.7: 'SRR3130854' is valid 2020-06-21T08:40:48 prefetch.2.10.7: 1) 'SRR3130854' was downloaded successfully Read 4000000 spots for SRR3130854/SRR3130854.sra Written 4000000 spots for SRR3130854/SRR3130854.sra 2020-06-21T08:41:10 prefetch.2.10.7: 1) Downloading 'SRR3130855'... 2020-06-21T08:41:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:42:14 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:42:14 prefetch.2.10.7: 'SRR3130855' is valid 2020-06-21T08:42:14 prefetch.2.10.7: 1) 'SRR3130855' was downloaded successfully Read 4000000 spots for SRR3130855/SRR3130855.sra Written 4000000 spots for SRR3130855/SRR3130855.sra 2020-06-21T08:42:37 prefetch.2.10.7: 1) Downloading 'SRR3130856'... 2020-06-21T08:42:37 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:43:13 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:43:13 prefetch.2.10.7: 'SRR3130856' is valid 2020-06-21T08:43:13 prefetch.2.10.7: 1) 'SRR3130856' was downloaded successfully Read 4000000 spots for SRR3130856/SRR3130856.sra Written 4000000 spots for SRR3130856/SRR3130856.sra 2020-06-21T08:43:35 prefetch.2.10.7: 1) Downloading 'SRR3130857'... 2020-06-21T08:43:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:44:06 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:44:06 prefetch.2.10.7: 'SRR3130857' is valid 2020-06-21T08:44:06 prefetch.2.10.7: 1) 'SRR3130857' was downloaded successfully Read 1748530 spots for SRR3130857/SRR3130857.sra Written 1748530 spots for SRR3130857/SRR3130857.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: 00:01:32 13748530 reads; of these: 13748530 (100.00%) were unpaired; of these: 10551340 (76.75%) aligned 0 times 2626576 (19.10%) aligned exactly 1 time 570614 (4.15%) aligned >1 times 23.25% overall alignment rate Time searching: 00:01:32 Overall time: 00:01:32 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_rmdupse_core] 1034966 / 3197190 = 0.3237 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 17:47:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1550610/SRX1550610.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1550610/SRX1550610.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1550610/SRX1550610.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1550610/SRX1550610.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 17:47:13: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:47:13: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:47:19: 1000000 INFO @ Sun, 21 Jun 2020 17:47:26: 2000000 INFO @ Sun, 21 Jun 2020 17:47:27: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:47:27: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:47:27: #1 total tags in treatment: 2162224 INFO @ Sun, 21 Jun 2020 17:47:27: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:47:27: #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 17:47:28: #1 tags after filtering in treatment: 2162082 INFO @ Sun, 21 Jun 2020 17:47:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:47:28: #1 finished! INFO @ Sun, 21 Jun 2020 17:47:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:47:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:47:28: #2 number of paired peaks: 2461 INFO @ Sun, 21 Jun 2020 17:47:28: start model_add_line... INFO @ Sun, 21 Jun 2020 17:47:28: start X-correlation... INFO @ Sun, 21 Jun 2020 17:47:28: end of X-cor INFO @ Sun, 21 Jun 2020 17:47:28: #2 finished! INFO @ Sun, 21 Jun 2020 17:47:28: #2 predicted fragment length is 159 bps INFO @ Sun, 21 Jun 2020 17:47:28: #2 alternative fragment length(s) may be 159 bps INFO @ Sun, 21 Jun 2020 17:47:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1550610/SRX1550610.05_model.r INFO @ Sun, 21 Jun 2020 17:47:28: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:47:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:47:33: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:47:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1550610/SRX1550610.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:47:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1550610/SRX1550610.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:47:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1550610/SRX1550610.05_summits.bed INFO @ Sun, 21 Jun 2020 17:47:36: Done! pass1 - making usageList (380 chroms): 1 millis pass2 - checking and writing primary data (3362 records, 4 fields): 13 millis CompletedMACS2peakCalling 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 17:47:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1550610/SRX1550610.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1550610/SRX1550610.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1550610/SRX1550610.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1550610/SRX1550610.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 17:47:43: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:47:43: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:47:50: 1000000 INFO @ Sun, 21 Jun 2020 17:47:57: 2000000 INFO @ Sun, 21 Jun 2020 17:47:58: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:47:58: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:47:58: #1 total tags in treatment: 2162224 INFO @ Sun, 21 Jun 2020 17:47:58: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:47:58: #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 17:47:59: #1 tags after filtering in treatment: 2162082 INFO @ Sun, 21 Jun 2020 17:47:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:47:59: #1 finished! INFO @ Sun, 21 Jun 2020 17:47:59: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:47:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:47:59: #2 number of paired peaks: 2461 INFO @ Sun, 21 Jun 2020 17:47:59: start model_add_line... INFO @ Sun, 21 Jun 2020 17:47:59: start X-correlation... INFO @ Sun, 21 Jun 2020 17:47:59: end of X-cor INFO @ Sun, 21 Jun 2020 17:47:59: #2 finished! INFO @ Sun, 21 Jun 2020 17:47:59: #2 predicted fragment length is 159 bps INFO @ Sun, 21 Jun 2020 17:47:59: #2 alternative fragment length(s) may be 159 bps INFO @ Sun, 21 Jun 2020 17:47:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1550610/SRX1550610.10_model.r INFO @ Sun, 21 Jun 2020 17:47:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:47:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:48:05: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:48:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1550610/SRX1550610.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:48:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1550610/SRX1550610.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:48:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1550610/SRX1550610.10_summits.bed INFO @ Sun, 21 Jun 2020 17:48:07: Done! pass1 - making usageList (184 chroms): 1 millis pass2 - checking and writing primary data (1790 records, 4 fields): 7 millis CompletedMACS2peakCalling 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 17:48:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1550610/SRX1550610.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1550610/SRX1550610.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1550610/SRX1550610.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1550610/SRX1550610.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 17:48:13: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:48:13: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:48:19: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:48:25: 2000000 INFO @ Sun, 21 Jun 2020 17:48:26: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:48:26: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:48:26: #1 total tags in treatment: 2162224 INFO @ Sun, 21 Jun 2020 17:48:26: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:48:26: #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 17:48:26: #1 tags after filtering in treatment: 2162082 INFO @ Sun, 21 Jun 2020 17:48:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:48:26: #1 finished! INFO @ Sun, 21 Jun 2020 17:48:26: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:48:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:48:27: #2 number of paired peaks: 2461 INFO @ Sun, 21 Jun 2020 17:48:27: start model_add_line... INFO @ Sun, 21 Jun 2020 17:48:27: start X-correlation... INFO @ Sun, 21 Jun 2020 17:48:27: end of X-cor INFO @ Sun, 21 Jun 2020 17:48:27: #2 finished! INFO @ Sun, 21 Jun 2020 17:48:27: #2 predicted fragment length is 159 bps INFO @ Sun, 21 Jun 2020 17:48:27: #2 alternative fragment length(s) may be 159 bps INFO @ Sun, 21 Jun 2020 17:48:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1550610/SRX1550610.20_model.r INFO @ Sun, 21 Jun 2020 17:48:27: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:48:27: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:48:32: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:48:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1550610/SRX1550610.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:48:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1550610/SRX1550610.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:48:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1550610/SRX1550610.20_summits.bed INFO @ Sun, 21 Jun 2020 17:48:35: Done! pass1 - making usageList (103 chroms): 1 millis pass2 - checking and writing primary data (1095 records, 4 fields): 6 millis CompletedMACS2peakCalling