Job ID = 6455732 SRX = SRX288029 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:29:51 prefetch.2.10.7: 1) Downloading 'SRR870218'... 2020-06-21T10:29:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:32:10 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:32:11 prefetch.2.10.7: 'SRR870218' is valid 2020-06-21T10:32:11 prefetch.2.10.7: 1) 'SRR870218' was downloaded successfully Read 14103697 spots for SRR870218/SRR870218.sra Written 14103697 spots for SRR870218/SRR870218.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: 00:04:19 14103697 reads; of these: 14103697 (100.00%) were unpaired; of these: 1204321 (8.54%) aligned 0 times 9012943 (63.90%) aligned exactly 1 time 3886433 (27.56%) aligned >1 times 91.46% overall alignment rate Time searching: 00:04:19 Overall time: 00:04:19 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] 3868320 / 12899376 = 0.2999 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 19:40:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX288029/SRX288029.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX288029/SRX288029.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX288029/SRX288029.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX288029/SRX288029.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 19:40:36: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:40:36: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:40:43: 1000000 INFO @ Sun, 21 Jun 2020 19:40:49: 2000000 INFO @ Sun, 21 Jun 2020 19:40:56: 3000000 INFO @ Sun, 21 Jun 2020 19:41:02: 4000000 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 19:41:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX288029/SRX288029.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX288029/SRX288029.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX288029/SRX288029.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX288029/SRX288029.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 19:41:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:41:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:41:09: 5000000 INFO @ Sun, 21 Jun 2020 19:41:13: 1000000 INFO @ Sun, 21 Jun 2020 19:41:15: 6000000 INFO @ Sun, 21 Jun 2020 19:41:19: 2000000 INFO @ Sun, 21 Jun 2020 19:41:22: 7000000 INFO @ Sun, 21 Jun 2020 19:41:25: 3000000 INFO @ Sun, 21 Jun 2020 19:41:29: 8000000 INFO @ Sun, 21 Jun 2020 19:41:31: 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 19:41:35: 9000000 INFO @ Sun, 21 Jun 2020 19:41:35: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:41:35: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:41:35: #1 total tags in treatment: 9031056 INFO @ Sun, 21 Jun 2020 19:41:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:41:35: #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 19:41:36: #1 tags after filtering in treatment: 9031024 INFO @ Sun, 21 Jun 2020 19:41:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:41:36: #1 finished! INFO @ Sun, 21 Jun 2020 19:41:36: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:41:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:41:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX288029/SRX288029.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX288029/SRX288029.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX288029/SRX288029.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX288029/SRX288029.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 19:41:36: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:41:36: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:41:36: #2 number of paired peaks: 1880 INFO @ Sun, 21 Jun 2020 19:41:36: start model_add_line... INFO @ Sun, 21 Jun 2020 19:41:37: start X-correlation... INFO @ Sun, 21 Jun 2020 19:41:37: end of X-cor INFO @ Sun, 21 Jun 2020 19:41:37: #2 finished! INFO @ Sun, 21 Jun 2020 19:41:37: #2 predicted fragment length is 143 bps INFO @ Sun, 21 Jun 2020 19:41:37: #2 alternative fragment length(s) may be 143 bps INFO @ Sun, 21 Jun 2020 19:41:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX288029/SRX288029.05_model.r INFO @ Sun, 21 Jun 2020 19:41:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:41:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:41:37: 5000000 INFO @ Sun, 21 Jun 2020 19:41:43: 6000000 INFO @ Sun, 21 Jun 2020 19:41:43: 1000000 INFO @ Sun, 21 Jun 2020 19:41:49: 7000000 INFO @ Sun, 21 Jun 2020 19:41:49: 2000000 INFO @ Sun, 21 Jun 2020 19:41:55: 3000000 INFO @ Sun, 21 Jun 2020 19:41:55: 8000000 INFO @ Sun, 21 Jun 2020 19:41:56: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:42:01: 4000000 INFO @ Sun, 21 Jun 2020 19:42:01: 9000000 INFO @ Sun, 21 Jun 2020 19:42:01: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:42:01: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:42:01: #1 total tags in treatment: 9031056 INFO @ Sun, 21 Jun 2020 19:42:01: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:42:01: #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 19:42:02: #1 tags after filtering in treatment: 9031024 INFO @ Sun, 21 Jun 2020 19:42:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:42:02: #1 finished! INFO @ Sun, 21 Jun 2020 19:42:02: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:42:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:42:02: #2 number of paired peaks: 1880 INFO @ Sun, 21 Jun 2020 19:42:02: start model_add_line... INFO @ Sun, 21 Jun 2020 19:42:02: start X-correlation... INFO @ Sun, 21 Jun 2020 19:42:02: end of X-cor INFO @ Sun, 21 Jun 2020 19:42:02: #2 finished! INFO @ Sun, 21 Jun 2020 19:42:02: #2 predicted fragment length is 143 bps INFO @ Sun, 21 Jun 2020 19:42:02: #2 alternative fragment length(s) may be 143 bps INFO @ Sun, 21 Jun 2020 19:42:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX288029/SRX288029.10_model.r INFO @ Sun, 21 Jun 2020 19:42:02: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:42:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:42:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX288029/SRX288029.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:42:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX288029/SRX288029.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:42:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX288029/SRX288029.05_summits.bed INFO @ Sun, 21 Jun 2020 19:42:06: Done! pass1 - making usageList (640 chroms): 2 millis INFO @ Sun, 21 Jun 2020 19:42:06: 5000000 pass2 - checking and writing primary data (6351 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:42:11: 6000000 INFO @ Sun, 21 Jun 2020 19:42:17: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:42:22: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:42:23: 8000000 INFO @ Sun, 21 Jun 2020 19:42:28: 9000000 INFO @ Sun, 21 Jun 2020 19:42:28: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:42:28: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:42:28: #1 total tags in treatment: 9031056 INFO @ Sun, 21 Jun 2020 19:42:28: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:42:28: #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 19:42:29: #1 tags after filtering in treatment: 9031024 INFO @ Sun, 21 Jun 2020 19:42:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:42:29: #1 finished! INFO @ Sun, 21 Jun 2020 19:42:29: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:42:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:42:29: #2 number of paired peaks: 1880 INFO @ Sun, 21 Jun 2020 19:42:29: start model_add_line... INFO @ Sun, 21 Jun 2020 19:42:30: start X-correlation... INFO @ Sun, 21 Jun 2020 19:42:30: end of X-cor INFO @ Sun, 21 Jun 2020 19:42:30: #2 finished! INFO @ Sun, 21 Jun 2020 19:42:30: #2 predicted fragment length is 143 bps INFO @ Sun, 21 Jun 2020 19:42:30: #2 alternative fragment length(s) may be 143 bps INFO @ Sun, 21 Jun 2020 19:42:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX288029/SRX288029.20_model.r INFO @ Sun, 21 Jun 2020 19:42:30: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:42:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:42:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX288029/SRX288029.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:42:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX288029/SRX288029.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:42:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX288029/SRX288029.10_summits.bed INFO @ Sun, 21 Jun 2020 19:42:33: Done! pass1 - making usageList (544 chroms): 1 millis pass2 - checking and writing primary data (4252 records, 4 fields): 18 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:42:49: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:42:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX288029/SRX288029.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:42:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX288029/SRX288029.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:42:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX288029/SRX288029.20_summits.bed INFO @ Sun, 21 Jun 2020 19:42:58: Done! pass1 - making usageList (491 chroms): 2 millis pass2 - checking and writing primary data (2628 records, 4 fields): 15 millis CompletedMACS2peakCalling