Job ID = 6459230 SRX = SRX645427 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:59:16 prefetch.2.10.7: 1) Downloading 'SRR1506118'... 2020-06-21T12:59:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:01:56 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:01:57 prefetch.2.10.7: 'SRR1506118' is valid 2020-06-21T13:01:57 prefetch.2.10.7: 1) 'SRR1506118' was downloaded successfully Read 14181487 spots for SRR1506118/SRR1506118.sra Written 14181487 spots for SRR1506118/SRR1506118.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: 00:02:48 14181487 reads; of these: 14181487 (100.00%) were unpaired; of these: 3805658 (26.84%) aligned 0 times 9205650 (64.91%) aligned exactly 1 time 1170179 (8.25%) aligned >1 times 73.16% overall alignment rate Time searching: 00:02:48 Overall time: 00:02:48 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] 3678266 / 10375829 = 0.3545 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 22:08:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX645427/SRX645427.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX645427/SRX645427.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX645427/SRX645427.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX645427/SRX645427.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 22:08:19: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:08:19: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:08:25: 1000000 INFO @ Sun, 21 Jun 2020 22:08:32: 2000000 INFO @ Sun, 21 Jun 2020 22:08:39: 3000000 INFO @ Sun, 21 Jun 2020 22:08:45: 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 22:08:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX645427/SRX645427.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX645427/SRX645427.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX645427/SRX645427.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX645427/SRX645427.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 22:08:49: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:08:49: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:08:52: 5000000 INFO @ Sun, 21 Jun 2020 22:08:55: 1000000 INFO @ Sun, 21 Jun 2020 22:08:59: 6000000 INFO @ Sun, 21 Jun 2020 22:09:02: 2000000 INFO @ Sun, 21 Jun 2020 22:09:04: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:09:04: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:09:04: #1 total tags in treatment: 6697563 INFO @ Sun, 21 Jun 2020 22:09:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:09:04: #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 22:09:05: #1 tags after filtering in treatment: 6697487 INFO @ Sun, 21 Jun 2020 22:09:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:09:05: #1 finished! INFO @ Sun, 21 Jun 2020 22:09:05: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:09:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:09:05: #2 number of paired peaks: 1896 INFO @ Sun, 21 Jun 2020 22:09:05: start model_add_line... INFO @ Sun, 21 Jun 2020 22:09:05: start X-correlation... INFO @ Sun, 21 Jun 2020 22:09:05: end of X-cor INFO @ Sun, 21 Jun 2020 22:09:05: #2 finished! INFO @ Sun, 21 Jun 2020 22:09:05: #2 predicted fragment length is 173 bps INFO @ Sun, 21 Jun 2020 22:09:05: #2 alternative fragment length(s) may be 173 bps INFO @ Sun, 21 Jun 2020 22:09:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX645427/SRX645427.05_model.r INFO @ Sun, 21 Jun 2020 22:09:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:09:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:09:08: 3000000 INFO @ Sun, 21 Jun 2020 22:09:14: 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 22:09:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX645427/SRX645427.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX645427/SRX645427.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX645427/SRX645427.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX645427/SRX645427.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 22:09:19: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:09:19: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:09:19: 5000000 INFO @ Sun, 21 Jun 2020 22:09:21: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:09:25: 1000000 INFO @ Sun, 21 Jun 2020 22:09:26: 6000000 INFO @ Sun, 21 Jun 2020 22:09:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX645427/SRX645427.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:09:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX645427/SRX645427.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:09:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX645427/SRX645427.05_summits.bed INFO @ Sun, 21 Jun 2020 22:09:29: Done! pass1 - making usageList (385 chroms): 2 millis pass2 - checking and writing primary data (6815 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:09:30: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:09:30: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:09:30: #1 total tags in treatment: 6697563 INFO @ Sun, 21 Jun 2020 22:09:30: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:09:30: #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 22:09:31: #1 tags after filtering in treatment: 6697487 INFO @ Sun, 21 Jun 2020 22:09:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:09:31: #1 finished! INFO @ Sun, 21 Jun 2020 22:09:31: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:09:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:09:31: #2 number of paired peaks: 1896 INFO @ Sun, 21 Jun 2020 22:09:31: start model_add_line... INFO @ Sun, 21 Jun 2020 22:09:31: start X-correlation... INFO @ Sun, 21 Jun 2020 22:09:31: end of X-cor INFO @ Sun, 21 Jun 2020 22:09:31: #2 finished! INFO @ Sun, 21 Jun 2020 22:09:31: #2 predicted fragment length is 173 bps INFO @ Sun, 21 Jun 2020 22:09:31: #2 alternative fragment length(s) may be 173 bps INFO @ Sun, 21 Jun 2020 22:09:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX645427/SRX645427.10_model.r INFO @ Sun, 21 Jun 2020 22:09:31: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:09:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:09:32: 2000000 INFO @ Sun, 21 Jun 2020 22:09:38: 3000000 INFO @ Sun, 21 Jun 2020 22:09:44: 4000000 INFO @ Sun, 21 Jun 2020 22:09:46: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:09:50: 5000000 INFO @ Sun, 21 Jun 2020 22:09:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX645427/SRX645427.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:09:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX645427/SRX645427.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:09:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX645427/SRX645427.10_summits.bed INFO @ Sun, 21 Jun 2020 22:09:54: Done! pass1 - making usageList (209 chroms): 1 millis pass2 - checking and writing primary data (3593 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:09:56: 6000000 INFO @ Sun, 21 Jun 2020 22:10:00: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:10:00: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:10:00: #1 total tags in treatment: 6697563 INFO @ Sun, 21 Jun 2020 22:10:00: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:10:00: #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 22:10:00: #1 tags after filtering in treatment: 6697487 INFO @ Sun, 21 Jun 2020 22:10:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:10:00: #1 finished! INFO @ Sun, 21 Jun 2020 22:10:00: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:10:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:10:01: #2 number of paired peaks: 1896 INFO @ Sun, 21 Jun 2020 22:10:01: start model_add_line... INFO @ Sun, 21 Jun 2020 22:10:01: start X-correlation... INFO @ Sun, 21 Jun 2020 22:10:01: end of X-cor INFO @ Sun, 21 Jun 2020 22:10:01: #2 finished! INFO @ Sun, 21 Jun 2020 22:10:01: #2 predicted fragment length is 173 bps INFO @ Sun, 21 Jun 2020 22:10:01: #2 alternative fragment length(s) may be 173 bps INFO @ Sun, 21 Jun 2020 22:10:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX645427/SRX645427.20_model.r INFO @ Sun, 21 Jun 2020 22:10:01: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:10:01: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:10:17: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:10:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX645427/SRX645427.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:10:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX645427/SRX645427.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:10:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX645427/SRX645427.20_summits.bed INFO @ Sun, 21 Jun 2020 22:10:25: Done! pass1 - making usageList (92 chroms): 1 millis pass2 - checking and writing primary data (1707 records, 4 fields): 5 millis CompletedMACS2peakCalling