Job ID = 6456419 SRX = SRX3404015 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:00:16 prefetch.2.10.7: 1) Downloading 'SRR6303492'... 2020-06-21T11:00:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:03:43 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:03:44 prefetch.2.10.7: 'SRR6303492' is valid 2020-06-21T11:03:44 prefetch.2.10.7: 1) 'SRR6303492' was downloaded successfully 2020-06-21T11:03:44 prefetch.2.10.7: 'SRR6303492' has 0 unresolved dependencies Read 25924790 spots for SRR6303492/SRR6303492.sra Written 25924790 spots for SRR6303492/SRR6303492.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: 00:05:52 25924790 reads; of these: 25924790 (100.00%) were unpaired; of these: 6325474 (24.40%) aligned 0 times 14607804 (56.35%) aligned exactly 1 time 4991512 (19.25%) aligned >1 times 75.60% overall alignment rate Time searching: 00:05:52 Overall time: 00:05:52 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] 4866949 / 19599316 = 0.2483 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 20:15:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3404015/SRX3404015.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3404015/SRX3404015.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3404015/SRX3404015.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3404015/SRX3404015.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 20:15:18: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:15:18: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:15:23: 1000000 INFO @ Sun, 21 Jun 2020 20:15:28: 2000000 INFO @ Sun, 21 Jun 2020 20:15:32: 3000000 INFO @ Sun, 21 Jun 2020 20:15:37: 4000000 INFO @ Sun, 21 Jun 2020 20:15:41: 5000000 INFO @ Sun, 21 Jun 2020 20:15:46: 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 20:15:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3404015/SRX3404015.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3404015/SRX3404015.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3404015/SRX3404015.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3404015/SRX3404015.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 20:15:48: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:15:48: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:15:50: 7000000 INFO @ Sun, 21 Jun 2020 20:15:53: 1000000 INFO @ Sun, 21 Jun 2020 20:15:55: 8000000 INFO @ Sun, 21 Jun 2020 20:15:58: 2000000 INFO @ Sun, 21 Jun 2020 20:16:00: 9000000 INFO @ Sun, 21 Jun 2020 20:16:02: 3000000 INFO @ Sun, 21 Jun 2020 20:16:05: 10000000 INFO @ Sun, 21 Jun 2020 20:16:07: 4000000 INFO @ Sun, 21 Jun 2020 20:16:09: 11000000 INFO @ Sun, 21 Jun 2020 20:16:12: 5000000 INFO @ Sun, 21 Jun 2020 20:16:14: 12000000 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 20:16:16: 6000000 INFO @ Sun, 21 Jun 2020 20:16:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3404015/SRX3404015.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3404015/SRX3404015.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3404015/SRX3404015.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3404015/SRX3404015.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 20:16:18: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:16:18: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:16:19: 13000000 INFO @ Sun, 21 Jun 2020 20:16:21: 7000000 INFO @ Sun, 21 Jun 2020 20:16:24: 1000000 INFO @ Sun, 21 Jun 2020 20:16:24: 14000000 INFO @ Sun, 21 Jun 2020 20:16:26: 8000000 INFO @ Sun, 21 Jun 2020 20:16:28: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:16:28: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:16:28: #1 total tags in treatment: 14732367 INFO @ Sun, 21 Jun 2020 20:16:28: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:16:28: #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 20:16:29: #1 tags after filtering in treatment: 14732285 INFO @ Sun, 21 Jun 2020 20:16:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:16:29: #1 finished! INFO @ Sun, 21 Jun 2020 20:16:29: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:16:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:16:29: 2000000 INFO @ Sun, 21 Jun 2020 20:16:30: #2 number of paired peaks: 1833 INFO @ Sun, 21 Jun 2020 20:16:30: start model_add_line... INFO @ Sun, 21 Jun 2020 20:16:30: start X-correlation... INFO @ Sun, 21 Jun 2020 20:16:30: end of X-cor INFO @ Sun, 21 Jun 2020 20:16:30: #2 finished! INFO @ Sun, 21 Jun 2020 20:16:30: #2 predicted fragment length is 155 bps INFO @ Sun, 21 Jun 2020 20:16:30: #2 alternative fragment length(s) may be 155 bps INFO @ Sun, 21 Jun 2020 20:16:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3404015/SRX3404015.05_model.r INFO @ Sun, 21 Jun 2020 20:16:30: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:16:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:16:31: 9000000 INFO @ Sun, 21 Jun 2020 20:16:35: 3000000 INFO @ Sun, 21 Jun 2020 20:16:35: 10000000 INFO @ Sun, 21 Jun 2020 20:16:40: 4000000 INFO @ Sun, 21 Jun 2020 20:16:40: 11000000 INFO @ Sun, 21 Jun 2020 20:16:45: 12000000 INFO @ Sun, 21 Jun 2020 20:16:46: 5000000 INFO @ Sun, 21 Jun 2020 20:16:50: 13000000 INFO @ Sun, 21 Jun 2020 20:16:51: 6000000 INFO @ Sun, 21 Jun 2020 20:16:55: 14000000 INFO @ Sun, 21 Jun 2020 20:16:57: 7000000 INFO @ Sun, 21 Jun 2020 20:16:59: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:16:59: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:16:59: #1 total tags in treatment: 14732367 INFO @ Sun, 21 Jun 2020 20:16:59: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:16:59: #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 20:17:00: #1 tags after filtering in treatment: 14732285 INFO @ Sun, 21 Jun 2020 20:17:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:17:00: #1 finished! INFO @ Sun, 21 Jun 2020 20:17:00: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:17:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:17:01: #2 number of paired peaks: 1833 INFO @ Sun, 21 Jun 2020 20:17:01: start model_add_line... INFO @ Sun, 21 Jun 2020 20:17:01: start X-correlation... INFO @ Sun, 21 Jun 2020 20:17:01: end of X-cor INFO @ Sun, 21 Jun 2020 20:17:01: #2 finished! INFO @ Sun, 21 Jun 2020 20:17:01: #2 predicted fragment length is 155 bps INFO @ Sun, 21 Jun 2020 20:17:01: #2 alternative fragment length(s) may be 155 bps INFO @ Sun, 21 Jun 2020 20:17:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3404015/SRX3404015.10_model.r INFO @ Sun, 21 Jun 2020 20:17:01: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:17:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:17:02: 8000000 INFO @ Sun, 21 Jun 2020 20:17:05: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:17:07: 9000000 INFO @ Sun, 21 Jun 2020 20:17:12: 10000000 INFO @ Sun, 21 Jun 2020 20:17:18: 11000000 INFO @ Sun, 21 Jun 2020 20:17:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3404015/SRX3404015.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:17:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3404015/SRX3404015.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:17:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3404015/SRX3404015.05_summits.bed INFO @ Sun, 21 Jun 2020 20:17:22: Done! pass1 - making usageList (495 chroms): 2 millis pass2 - checking and writing primary data (5596 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:17:23: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:17:29: 13000000 INFO @ Sun, 21 Jun 2020 20:17:34: 14000000 INFO @ Sun, 21 Jun 2020 20:17:35: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:17:38: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:17:38: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:17:38: #1 total tags in treatment: 14732367 INFO @ Sun, 21 Jun 2020 20:17:38: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:17:38: #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 20:17:39: #1 tags after filtering in treatment: 14732285 INFO @ Sun, 21 Jun 2020 20:17:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:17:39: #1 finished! INFO @ Sun, 21 Jun 2020 20:17:39: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:17:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:17:40: #2 number of paired peaks: 1833 INFO @ Sun, 21 Jun 2020 20:17:40: start model_add_line... INFO @ Sun, 21 Jun 2020 20:17:40: start X-correlation... INFO @ Sun, 21 Jun 2020 20:17:40: end of X-cor INFO @ Sun, 21 Jun 2020 20:17:40: #2 finished! INFO @ Sun, 21 Jun 2020 20:17:40: #2 predicted fragment length is 155 bps INFO @ Sun, 21 Jun 2020 20:17:40: #2 alternative fragment length(s) may be 155 bps INFO @ Sun, 21 Jun 2020 20:17:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3404015/SRX3404015.20_model.r INFO @ Sun, 21 Jun 2020 20:17:40: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:17:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:17:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3404015/SRX3404015.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:17:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3404015/SRX3404015.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:17:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3404015/SRX3404015.10_summits.bed INFO @ Sun, 21 Jun 2020 20:17:52: Done! pass1 - making usageList (341 chroms): 2 millis pass2 - checking and writing primary data (4116 records, 4 fields): 16 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:18:12: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:18:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3404015/SRX3404015.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:18:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3404015/SRX3404015.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:18:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3404015/SRX3404015.20_summits.bed INFO @ Sun, 21 Jun 2020 20:18:29: Done! pass1 - making usageList (225 chroms): 1 millis pass2 - checking and writing primary data (3068 records, 4 fields): 12 millis CompletedMACS2peakCalling