Job ID = 6453237 SRX = SRX110759 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:16:19 prefetch.2.10.7: 1) Downloading 'SRR388341'... 2020-06-21T08:16:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:17:31 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:17:32 prefetch.2.10.7: 'SRR388341' is valid 2020-06-21T08:17:32 prefetch.2.10.7: 1) 'SRR388341' was downloaded successfully Read 16794645 spots for SRR388341/SRR388341.sra Written 16794645 spots for SRR388341/SRR388341.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: 00:04:36 16794645 reads; of these: 16794645 (100.00%) were unpaired; of these: 5298521 (31.55%) aligned 0 times 6216689 (37.02%) aligned exactly 1 time 5279435 (31.44%) aligned >1 times 68.45% overall alignment rate Time searching: 00:04:36 Overall time: 00:04:36 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] 4306042 / 11496124 = 0.3746 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 17:25:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX110759/SRX110759.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX110759/SRX110759.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX110759/SRX110759.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX110759/SRX110759.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 17:25:04: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:25:04: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:25:08: 1000000 INFO @ Sun, 21 Jun 2020 17:25:12: 2000000 INFO @ Sun, 21 Jun 2020 17:25:17: 3000000 INFO @ Sun, 21 Jun 2020 17:25:21: 4000000 INFO @ Sun, 21 Jun 2020 17:25:25: 5000000 INFO @ Sun, 21 Jun 2020 17:25:30: 6000000 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 17:25:34: 7000000 INFO @ Sun, 21 Jun 2020 17:25:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX110759/SRX110759.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX110759/SRX110759.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX110759/SRX110759.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX110759/SRX110759.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 17:25:34: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:25:34: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:25:35: #1 tag size is determined as 18 bps INFO @ Sun, 21 Jun 2020 17:25:35: #1 tag size = 18 INFO @ Sun, 21 Jun 2020 17:25:35: #1 total tags in treatment: 7190082 INFO @ Sun, 21 Jun 2020 17:25:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:25:35: #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 17:25:35: #1 tags after filtering in treatment: 7190072 INFO @ Sun, 21 Jun 2020 17:25:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:25:35: #1 finished! INFO @ Sun, 21 Jun 2020 17:25:35: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:25:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:25:36: #2 number of paired peaks: 3678 INFO @ Sun, 21 Jun 2020 17:25:36: start model_add_line... INFO @ Sun, 21 Jun 2020 17:25:36: start X-correlation... INFO @ Sun, 21 Jun 2020 17:25:36: end of X-cor INFO @ Sun, 21 Jun 2020 17:25:36: #2 finished! INFO @ Sun, 21 Jun 2020 17:25:36: #2 predicted fragment length is 82 bps INFO @ Sun, 21 Jun 2020 17:25:36: #2 alternative fragment length(s) may be 82 bps INFO @ Sun, 21 Jun 2020 17:25:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX110759/SRX110759.05_model.r INFO @ Sun, 21 Jun 2020 17:25:36: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:25:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:25:38: 1000000 INFO @ Sun, 21 Jun 2020 17:25:42: 2000000 INFO @ Sun, 21 Jun 2020 17:25:46: 3000000 INFO @ Sun, 21 Jun 2020 17:25:51: 4000000 INFO @ Sun, 21 Jun 2020 17:25:54: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:25:55: 5000000 INFO @ Sun, 21 Jun 2020 17:25:59: 6000000 INFO @ Sun, 21 Jun 2020 17:26:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX110759/SRX110759.05_peaks.xls BedGraph に変換中... INFO @ Sun, 21 Jun 2020 17:26:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX110759/SRX110759.05_peaks.narrowPeak 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 17:26:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX110759/SRX110759.05_summits.bed INFO @ Sun, 21 Jun 2020 17:26:02: Done! pass1 - making usageList (143 chroms): 2 millis pass2 - checking and writing primary data (7394 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:26:04: 7000000 INFO @ Sun, 21 Jun 2020 17:26:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX110759/SRX110759.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX110759/SRX110759.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX110759/SRX110759.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX110759/SRX110759.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 17:26:04: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:26:04: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:26:05: #1 tag size is determined as 18 bps INFO @ Sun, 21 Jun 2020 17:26:05: #1 tag size = 18 INFO @ Sun, 21 Jun 2020 17:26:05: #1 total tags in treatment: 7190082 INFO @ Sun, 21 Jun 2020 17:26:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:26:05: #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 17:26:05: #1 tags after filtering in treatment: 7190072 INFO @ Sun, 21 Jun 2020 17:26:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:26:05: #1 finished! INFO @ Sun, 21 Jun 2020 17:26:05: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:26:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:26:06: #2 number of paired peaks: 3678 INFO @ Sun, 21 Jun 2020 17:26:06: start model_add_line... INFO @ Sun, 21 Jun 2020 17:26:06: start X-correlation... INFO @ Sun, 21 Jun 2020 17:26:06: end of X-cor INFO @ Sun, 21 Jun 2020 17:26:06: #2 finished! INFO @ Sun, 21 Jun 2020 17:26:06: #2 predicted fragment length is 82 bps INFO @ Sun, 21 Jun 2020 17:26:06: #2 alternative fragment length(s) may be 82 bps INFO @ Sun, 21 Jun 2020 17:26:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX110759/SRX110759.10_model.r INFO @ Sun, 21 Jun 2020 17:26:06: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:26:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:26:08: 1000000 INFO @ Sun, 21 Jun 2020 17:26:12: 2000000 INFO @ Sun, 21 Jun 2020 17:26:17: 3000000 INFO @ Sun, 21 Jun 2020 17:26:21: 4000000 INFO @ Sun, 21 Jun 2020 17:26:23: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:26:25: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:26:29: 6000000 INFO @ Sun, 21 Jun 2020 17:26:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX110759/SRX110759.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:26:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX110759/SRX110759.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:26:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX110759/SRX110759.10_summits.bed INFO @ Sun, 21 Jun 2020 17:26:32: Done! pass1 - making usageList (102 chroms): 2 millis pass2 - checking and writing primary data (4907 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:26:34: 7000000 INFO @ Sun, 21 Jun 2020 17:26:35: #1 tag size is determined as 18 bps INFO @ Sun, 21 Jun 2020 17:26:35: #1 tag size = 18 INFO @ Sun, 21 Jun 2020 17:26:35: #1 total tags in treatment: 7190082 INFO @ Sun, 21 Jun 2020 17:26:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:26:35: #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 17:26:35: #1 tags after filtering in treatment: 7190072 INFO @ Sun, 21 Jun 2020 17:26:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:26:35: #1 finished! INFO @ Sun, 21 Jun 2020 17:26:35: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:26:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:26:36: #2 number of paired peaks: 3678 INFO @ Sun, 21 Jun 2020 17:26:36: start model_add_line... INFO @ Sun, 21 Jun 2020 17:26:36: start X-correlation... INFO @ Sun, 21 Jun 2020 17:26:36: end of X-cor INFO @ Sun, 21 Jun 2020 17:26:36: #2 finished! INFO @ Sun, 21 Jun 2020 17:26:36: #2 predicted fragment length is 82 bps INFO @ Sun, 21 Jun 2020 17:26:36: #2 alternative fragment length(s) may be 82 bps INFO @ Sun, 21 Jun 2020 17:26:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX110759/SRX110759.20_model.r INFO @ Sun, 21 Jun 2020 17:26:36: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:26:36: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:26:53: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:27:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX110759/SRX110759.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:27:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX110759/SRX110759.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:27:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX110759/SRX110759.20_summits.bed INFO @ Sun, 21 Jun 2020 17:27:01: Done! pass1 - making usageList (56 chroms): 1 millis pass2 - checking and writing primary data (3068 records, 4 fields): 6 millis CompletedMACS2peakCalling