Job ID = 6458393 SRX = SRX511133 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:29:34 prefetch.2.10.7: 1) Downloading 'SRR1217238'... 2020-06-21T12:29:34 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:31:55 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:31:56 prefetch.2.10.7: 'SRR1217238' is valid 2020-06-21T12:31:56 prefetch.2.10.7: 1) 'SRR1217238' was downloaded successfully Read 10244227 spots for SRR1217238/SRR1217238.sra Written 10244227 spots for SRR1217238/SRR1217238.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: 00:03:09 10244227 reads; of these: 10244227 (100.00%) were unpaired; of these: 328711 (3.21%) aligned 0 times 6799880 (66.38%) aligned exactly 1 time 3115636 (30.41%) aligned >1 times 96.79% overall alignment rate Time searching: 00:03:09 Overall time: 00:03:09 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] 1702360 / 9915516 = 0.1717 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 21:38:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX511133/SRX511133.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX511133/SRX511133.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX511133/SRX511133.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX511133/SRX511133.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 21:38:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:38:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:38:45: 1000000 INFO @ Sun, 21 Jun 2020 21:38:50: 2000000 INFO @ Sun, 21 Jun 2020 21:38:54: 3000000 INFO @ Sun, 21 Jun 2020 21:38:59: 4000000 INFO @ Sun, 21 Jun 2020 21:39:04: 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 21:39:09: 6000000 INFO @ Sun, 21 Jun 2020 21:39:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX511133/SRX511133.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX511133/SRX511133.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX511133/SRX511133.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX511133/SRX511133.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 21:39:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:39:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:39:15: 7000000 INFO @ Sun, 21 Jun 2020 21:39:16: 1000000 INFO @ Sun, 21 Jun 2020 21:39:20: 8000000 INFO @ Sun, 21 Jun 2020 21:39:21: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:39:21: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:39:21: #1 total tags in treatment: 8213156 INFO @ Sun, 21 Jun 2020 21:39:21: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:39:21: #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 21:39:21: 2000000 INFO @ Sun, 21 Jun 2020 21:39:22: #1 tags after filtering in treatment: 8213057 INFO @ Sun, 21 Jun 2020 21:39:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:39:22: #1 finished! INFO @ Sun, 21 Jun 2020 21:39:22: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:39:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:39:23: #2 number of paired peaks: 4534 INFO @ Sun, 21 Jun 2020 21:39:23: start model_add_line... INFO @ Sun, 21 Jun 2020 21:39:23: start X-correlation... INFO @ Sun, 21 Jun 2020 21:39:23: end of X-cor INFO @ Sun, 21 Jun 2020 21:39:23: #2 finished! INFO @ Sun, 21 Jun 2020 21:39:23: #2 predicted fragment length is 208 bps INFO @ Sun, 21 Jun 2020 21:39:23: #2 alternative fragment length(s) may be 208 bps INFO @ Sun, 21 Jun 2020 21:39:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX511133/SRX511133.05_model.r INFO @ Sun, 21 Jun 2020 21:39:23: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:39:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:39:27: 3000000 INFO @ Sun, 21 Jun 2020 21:39:33: 4000000 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 21:39:38: 5000000 INFO @ Sun, 21 Jun 2020 21:39:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX511133/SRX511133.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX511133/SRX511133.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX511133/SRX511133.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX511133/SRX511133.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 21:39:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:39:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:39:44: 6000000 INFO @ Sun, 21 Jun 2020 21:39:45: 1000000 INFO @ Sun, 21 Jun 2020 21:39:46: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:39:50: 7000000 INFO @ Sun, 21 Jun 2020 21:39:51: 2000000 INFO @ Sun, 21 Jun 2020 21:39:56: 8000000 INFO @ Sun, 21 Jun 2020 21:39:57: 3000000 INFO @ Sun, 21 Jun 2020 21:39:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX511133/SRX511133.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:39:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX511133/SRX511133.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:39:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX511133/SRX511133.05_summits.bed INFO @ Sun, 21 Jun 2020 21:39:57: Done! pass1 - making usageList (603 chroms): 2 millis pass2 - checking and writing primary data (6229 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:39:57: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:39:57: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:39:57: #1 total tags in treatment: 8213156 INFO @ Sun, 21 Jun 2020 21:39:57: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:39:57: #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 21:39:58: #1 tags after filtering in treatment: 8213057 INFO @ Sun, 21 Jun 2020 21:39:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:39:58: #1 finished! INFO @ Sun, 21 Jun 2020 21:39:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:39:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:39:59: #2 number of paired peaks: 4534 INFO @ Sun, 21 Jun 2020 21:39:59: start model_add_line... INFO @ Sun, 21 Jun 2020 21:39:59: start X-correlation... INFO @ Sun, 21 Jun 2020 21:39:59: end of X-cor INFO @ Sun, 21 Jun 2020 21:39:59: #2 finished! INFO @ Sun, 21 Jun 2020 21:39:59: #2 predicted fragment length is 208 bps INFO @ Sun, 21 Jun 2020 21:39:59: #2 alternative fragment length(s) may be 208 bps INFO @ Sun, 21 Jun 2020 21:39:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX511133/SRX511133.10_model.r INFO @ Sun, 21 Jun 2020 21:39:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:39:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:40:02: 4000000 INFO @ Sun, 21 Jun 2020 21:40:08: 5000000 INFO @ Sun, 21 Jun 2020 21:40:13: 6000000 INFO @ Sun, 21 Jun 2020 21:40:19: 7000000 INFO @ Sun, 21 Jun 2020 21:40:22: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:40:25: 8000000 INFO @ Sun, 21 Jun 2020 21:40:26: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:40:26: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:40:26: #1 total tags in treatment: 8213156 INFO @ Sun, 21 Jun 2020 21:40:26: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:40:26: #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 21:40:26: #1 tags after filtering in treatment: 8213057 INFO @ Sun, 21 Jun 2020 21:40:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:40:26: #1 finished! INFO @ Sun, 21 Jun 2020 21:40:26: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:40:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:40:27: #2 number of paired peaks: 4534 INFO @ Sun, 21 Jun 2020 21:40:27: start model_add_line... INFO @ Sun, 21 Jun 2020 21:40:27: start X-correlation... INFO @ Sun, 21 Jun 2020 21:40:27: end of X-cor INFO @ Sun, 21 Jun 2020 21:40:27: #2 finished! INFO @ Sun, 21 Jun 2020 21:40:27: #2 predicted fragment length is 208 bps INFO @ Sun, 21 Jun 2020 21:40:27: #2 alternative fragment length(s) may be 208 bps INFO @ Sun, 21 Jun 2020 21:40:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX511133/SRX511133.20_model.r INFO @ Sun, 21 Jun 2020 21:40:27: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:40:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:40:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX511133/SRX511133.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:40:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX511133/SRX511133.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:40:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX511133/SRX511133.10_summits.bed INFO @ Sun, 21 Jun 2020 21:40:33: Done! pass1 - making usageList (442 chroms): 2 millis pass2 - checking and writing primary data (4877 records, 4 fields): 18 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:40:50: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:41:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX511133/SRX511133.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:41:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX511133/SRX511133.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:41:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX511133/SRX511133.20_summits.bed INFO @ Sun, 21 Jun 2020 21:41:01: Done! pass1 - making usageList (184 chroms): 1 millis pass2 - checking and writing primary data (3603 records, 4 fields): 13 millis CompletedMACS2peakCalling