Job ID = 6508757 SRX = SRX467113 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T14:54:52 prefetch.2.10.7: 1) Downloading 'SRR1164537'... 2020-06-26T14:54:52 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T14:56:42 prefetch.2.10.7: HTTPS download succeed 2020-06-26T14:56:42 prefetch.2.10.7: 1) 'SRR1164537' was downloaded successfully Read 15921814 spots for SRR1164537/SRR1164537.sra Written 15921814 spots for SRR1164537/SRR1164537.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: 00:04:08 15921814 reads; of these: 15921814 (100.00%) were unpaired; of these: 1024217 (6.43%) aligned 0 times 11437526 (71.84%) aligned exactly 1 time 3460071 (21.73%) aligned >1 times 93.57% overall alignment rate Time searching: 00:04:09 Overall time: 00:04:09 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] 1504568 / 14897597 = 0.1010 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 @ Sat, 27 Jun 2020 00:06:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX467113/SRX467113.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX467113/SRX467113.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX467113/SRX467113.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX467113/SRX467113.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 @ Sat, 27 Jun 2020 00:06:09: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:06:09: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:06:16: 1000000 INFO @ Sat, 27 Jun 2020 00:06:22: 2000000 INFO @ Sat, 27 Jun 2020 00:06:28: 3000000 INFO @ Sat, 27 Jun 2020 00:06:36: 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 @ Sat, 27 Jun 2020 00:06:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX467113/SRX467113.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX467113/SRX467113.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX467113/SRX467113.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX467113/SRX467113.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 @ Sat, 27 Jun 2020 00:06:39: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:06:39: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:06:43: 5000000 INFO @ Sat, 27 Jun 2020 00:06:47: 1000000 INFO @ Sat, 27 Jun 2020 00:06:50: 6000000 INFO @ Sat, 27 Jun 2020 00:06:56: 2000000 INFO @ Sat, 27 Jun 2020 00:06:59: 7000000 INFO @ Sat, 27 Jun 2020 00:07:04: 3000000 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 @ Sat, 27 Jun 2020 00:07:07: 8000000 INFO @ Sat, 27 Jun 2020 00:07:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX467113/SRX467113.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX467113/SRX467113.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX467113/SRX467113.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX467113/SRX467113.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 @ Sat, 27 Jun 2020 00:07:09: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:07:09: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:07:13: 4000000 INFO @ Sat, 27 Jun 2020 00:07:16: 9000000 INFO @ Sat, 27 Jun 2020 00:07:17: 1000000 INFO @ Sat, 27 Jun 2020 00:07:22: 5000000 INFO @ Sat, 27 Jun 2020 00:07:24: 10000000 INFO @ Sat, 27 Jun 2020 00:07:25: 2000000 INFO @ Sat, 27 Jun 2020 00:07:30: 6000000 INFO @ Sat, 27 Jun 2020 00:07:32: 11000000 INFO @ Sat, 27 Jun 2020 00:07:33: 3000000 INFO @ Sat, 27 Jun 2020 00:07:39: 7000000 INFO @ Sat, 27 Jun 2020 00:07:40: 12000000 INFO @ Sat, 27 Jun 2020 00:07:41: 4000000 INFO @ Sat, 27 Jun 2020 00:07:48: 8000000 INFO @ Sat, 27 Jun 2020 00:07:48: 13000000 INFO @ Sat, 27 Jun 2020 00:07:49: 5000000 INFO @ Sat, 27 Jun 2020 00:07:52: #1 tag size is determined as 50 bps INFO @ Sat, 27 Jun 2020 00:07:52: #1 tag size = 50 INFO @ Sat, 27 Jun 2020 00:07:52: #1 total tags in treatment: 13393029 INFO @ Sat, 27 Jun 2020 00:07:52: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:07:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:07:52: #1 tags after filtering in treatment: 13392941 INFO @ Sat, 27 Jun 2020 00:07:52: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:07:52: #1 finished! INFO @ Sat, 27 Jun 2020 00:07:52: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:07:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:07:53: #2 number of paired peaks: 1807 INFO @ Sat, 27 Jun 2020 00:07:53: start model_add_line... INFO @ Sat, 27 Jun 2020 00:07:54: start X-correlation... INFO @ Sat, 27 Jun 2020 00:07:54: end of X-cor INFO @ Sat, 27 Jun 2020 00:07:54: #2 finished! INFO @ Sat, 27 Jun 2020 00:07:54: #2 predicted fragment length is 169 bps INFO @ Sat, 27 Jun 2020 00:07:54: #2 alternative fragment length(s) may be 4,169,178,181 bps INFO @ Sat, 27 Jun 2020 00:07:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX467113/SRX467113.05_model.r INFO @ Sat, 27 Jun 2020 00:07:54: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:07:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:07:57: 9000000 INFO @ Sat, 27 Jun 2020 00:07:57: 6000000 INFO @ Sat, 27 Jun 2020 00:08:05: 7000000 INFO @ Sat, 27 Jun 2020 00:08:06: 10000000 INFO @ Sat, 27 Jun 2020 00:08:13: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 27 Jun 2020 00:08:15: 11000000 INFO @ Sat, 27 Jun 2020 00:08:21: 9000000 INFO @ Sat, 27 Jun 2020 00:08:24: 12000000 INFO @ Sat, 27 Jun 2020 00:08:27: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:08:29: 10000000 INFO @ Sat, 27 Jun 2020 00:08:33: 13000000 INFO @ Sat, 27 Jun 2020 00:08:36: #1 tag size is determined as 50 bps INFO @ Sat, 27 Jun 2020 00:08:36: #1 tag size = 50 INFO @ Sat, 27 Jun 2020 00:08:36: #1 total tags in treatment: 13393029 INFO @ Sat, 27 Jun 2020 00:08:36: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:08:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:08:37: 11000000 INFO @ Sat, 27 Jun 2020 00:08:37: #1 tags after filtering in treatment: 13392941 INFO @ Sat, 27 Jun 2020 00:08:37: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:08:37: #1 finished! INFO @ Sat, 27 Jun 2020 00:08:37: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:08:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:08:38: #2 number of paired peaks: 1807 INFO @ Sat, 27 Jun 2020 00:08:38: start model_add_line... INFO @ Sat, 27 Jun 2020 00:08:38: start X-correlation... INFO @ Sat, 27 Jun 2020 00:08:38: end of X-cor INFO @ Sat, 27 Jun 2020 00:08:38: #2 finished! INFO @ Sat, 27 Jun 2020 00:08:38: #2 predicted fragment length is 169 bps INFO @ Sat, 27 Jun 2020 00:08:38: #2 alternative fragment length(s) may be 4,169,178,181 bps INFO @ Sat, 27 Jun 2020 00:08:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX467113/SRX467113.10_model.r INFO @ Sat, 27 Jun 2020 00:08:38: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:08:38: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 27 Jun 2020 00:08:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX467113/SRX467113.05_peaks.xls INFO @ Sat, 27 Jun 2020 00:08:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX467113/SRX467113.05_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:08:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX467113/SRX467113.05_summits.bed INFO @ Sat, 27 Jun 2020 00:08:44: Done! INFO @ Sat, 27 Jun 2020 00:08:44: 12000000 pass1 - making usageList (212 chroms): 2 millis pass2 - checking and writing primary data (8047 records, 4 fields): 37 millis CompletedMACS2peakCalling INFO @ Sat, 27 Jun 2020 00:08:51: 13000000 INFO @ Sat, 27 Jun 2020 00:08:54: #1 tag size is determined as 50 bps INFO @ Sat, 27 Jun 2020 00:08:54: #1 tag size = 50 INFO @ Sat, 27 Jun 2020 00:08:54: #1 total tags in treatment: 13393029 INFO @ Sat, 27 Jun 2020 00:08:54: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:08:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:08:54: #1 tags after filtering in treatment: 13392941 INFO @ Sat, 27 Jun 2020 00:08:54: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:08:54: #1 finished! INFO @ Sat, 27 Jun 2020 00:08:54: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:08:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:08:55: #2 number of paired peaks: 1807 INFO @ Sat, 27 Jun 2020 00:08:55: start model_add_line... INFO @ Sat, 27 Jun 2020 00:08:56: start X-correlation... INFO @ Sat, 27 Jun 2020 00:08:56: end of X-cor INFO @ Sat, 27 Jun 2020 00:08:56: #2 finished! INFO @ Sat, 27 Jun 2020 00:08:56: #2 predicted fragment length is 169 bps INFO @ Sat, 27 Jun 2020 00:08:56: #2 alternative fragment length(s) may be 4,169,178,181 bps INFO @ Sat, 27 Jun 2020 00:08:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX467113/SRX467113.20_model.r INFO @ Sat, 27 Jun 2020 00:08:56: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:08:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:09:16: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:09:30: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:09:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX467113/SRX467113.10_peaks.xls INFO @ Sat, 27 Jun 2020 00:09:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX467113/SRX467113.10_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:09:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX467113/SRX467113.10_summits.bed INFO @ Sat, 27 Jun 2020 00:09:35: Done! pass1 - making usageList (173 chroms): 2 millis pass2 - checking and writing primary data (4754 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sat, 27 Jun 2020 00:09:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX467113/SRX467113.20_peaks.xls INFO @ Sat, 27 Jun 2020 00:09:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX467113/SRX467113.20_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:09:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX467113/SRX467113.20_summits.bed INFO @ Sat, 27 Jun 2020 00:09:48: Done! pass1 - making usageList (123 chroms): 1 millis pass2 - checking and writing primary data (1701 records, 4 fields): 8 millis CompletedMACS2peakCalling