Job ID = 6454884 SRX = SRX2592472 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:51:40 prefetch.2.10.7: 1) Downloading 'SRR5289749'... 2020-06-21T09:51:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:54:46 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:54:47 prefetch.2.10.7: 'SRR5289749' is valid 2020-06-21T09:54:47 prefetch.2.10.7: 1) 'SRR5289749' was downloaded successfully Read 13485141 spots for SRR5289749/SRR5289749.sra Written 13485141 spots for SRR5289749/SRR5289749.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: 00:02:54 13485141 reads; of these: 13485141 (100.00%) were unpaired; of these: 2080373 (15.43%) aligned 0 times 9443630 (70.03%) aligned exactly 1 time 1961138 (14.54%) aligned >1 times 84.57% overall alignment rate Time searching: 00:02:54 Overall time: 00:02:54 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] 4028586 / 11404768 = 0.3532 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 19:02:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592472/SRX2592472.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592472/SRX2592472.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592472/SRX2592472.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592472/SRX2592472.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 19:02:20: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:02:20: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:02:25: 1000000 INFO @ Sun, 21 Jun 2020 19:02:31: 2000000 INFO @ Sun, 21 Jun 2020 19:02:36: 3000000 INFO @ Sun, 21 Jun 2020 19:02:42: 4000000 INFO @ Sun, 21 Jun 2020 19:02:47: 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 19:02:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592472/SRX2592472.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592472/SRX2592472.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592472/SRX2592472.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592472/SRX2592472.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 19:02:50: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:02:50: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:02:54: 6000000 INFO @ Sun, 21 Jun 2020 19:02:56: 1000000 INFO @ Sun, 21 Jun 2020 19:02:59: 7000000 INFO @ Sun, 21 Jun 2020 19:03:02: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:03:02: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:03:02: #1 total tags in treatment: 7376182 INFO @ Sun, 21 Jun 2020 19:03:02: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:03:02: #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 19:03:02: 2000000 INFO @ Sun, 21 Jun 2020 19:03:02: #1 tags after filtering in treatment: 7375953 INFO @ Sun, 21 Jun 2020 19:03:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:03:02: #1 finished! INFO @ Sun, 21 Jun 2020 19:03:02: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:03:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:03:03: #2 number of paired peaks: 8591 INFO @ Sun, 21 Jun 2020 19:03:03: start model_add_line... INFO @ Sun, 21 Jun 2020 19:03:04: start X-correlation... INFO @ Sun, 21 Jun 2020 19:03:04: end of X-cor INFO @ Sun, 21 Jun 2020 19:03:04: #2 finished! INFO @ Sun, 21 Jun 2020 19:03:04: #2 predicted fragment length is 199 bps INFO @ Sun, 21 Jun 2020 19:03:04: #2 alternative fragment length(s) may be 199 bps INFO @ Sun, 21 Jun 2020 19:03:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592472/SRX2592472.05_model.r INFO @ Sun, 21 Jun 2020 19:03:04: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:03:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:03:08: 3000000 INFO @ Sun, 21 Jun 2020 19:03:14: 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 19:03:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592472/SRX2592472.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592472/SRX2592472.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592472/SRX2592472.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592472/SRX2592472.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 19:03:20: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:03:20: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:03:20: 5000000 INFO @ Sun, 21 Jun 2020 19:03:27: 1000000 INFO @ Sun, 21 Jun 2020 19:03:27: 6000000 INFO @ Sun, 21 Jun 2020 19:03:31: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:03:33: 2000000 INFO @ Sun, 21 Jun 2020 19:03:34: 7000000 INFO @ Sun, 21 Jun 2020 19:03:37: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:03:37: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:03:37: #1 total tags in treatment: 7376182 INFO @ Sun, 21 Jun 2020 19:03:37: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:03:37: #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 19:03:37: #1 tags after filtering in treatment: 7375953 INFO @ Sun, 21 Jun 2020 19:03:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:03:37: #1 finished! INFO @ Sun, 21 Jun 2020 19:03:37: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:03:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:03:39: #2 number of paired peaks: 8591 INFO @ Sun, 21 Jun 2020 19:03:39: start model_add_line... INFO @ Sun, 21 Jun 2020 19:03:39: start X-correlation... INFO @ Sun, 21 Jun 2020 19:03:39: end of X-cor INFO @ Sun, 21 Jun 2020 19:03:39: #2 finished! INFO @ Sun, 21 Jun 2020 19:03:39: #2 predicted fragment length is 199 bps INFO @ Sun, 21 Jun 2020 19:03:39: #2 alternative fragment length(s) may be 199 bps INFO @ Sun, 21 Jun 2020 19:03:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592472/SRX2592472.10_model.r INFO @ Sun, 21 Jun 2020 19:03:39: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:03:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:03:40: 3000000 INFO @ Sun, 21 Jun 2020 19:03:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592472/SRX2592472.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:03:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592472/SRX2592472.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:03:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592472/SRX2592472.05_summits.bed INFO @ Sun, 21 Jun 2020 19:03:40: Done! pass1 - making usageList (151 chroms): 3 millis pass2 - checking and writing primary data (8449 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:03:46: 4000000 INFO @ Sun, 21 Jun 2020 19:03:52: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:03:59: 6000000 INFO @ Sun, 21 Jun 2020 19:04:05: 7000000 INFO @ Sun, 21 Jun 2020 19:04:07: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:04:08: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:04:08: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:04:08: #1 total tags in treatment: 7376182 INFO @ Sun, 21 Jun 2020 19:04:08: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:04:08: #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 19:04:08: #1 tags after filtering in treatment: 7375953 INFO @ Sun, 21 Jun 2020 19:04:08: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:04:08: #1 finished! INFO @ Sun, 21 Jun 2020 19:04:08: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:04:08: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:04:09: #2 number of paired peaks: 8591 INFO @ Sun, 21 Jun 2020 19:04:09: start model_add_line... INFO @ Sun, 21 Jun 2020 19:04:09: start X-correlation... INFO @ Sun, 21 Jun 2020 19:04:09: end of X-cor INFO @ Sun, 21 Jun 2020 19:04:09: #2 finished! INFO @ Sun, 21 Jun 2020 19:04:09: #2 predicted fragment length is 199 bps INFO @ Sun, 21 Jun 2020 19:04:09: #2 alternative fragment length(s) may be 199 bps INFO @ Sun, 21 Jun 2020 19:04:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592472/SRX2592472.20_model.r INFO @ Sun, 21 Jun 2020 19:04:09: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:04:09: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:04:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592472/SRX2592472.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:04:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592472/SRX2592472.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:04:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592472/SRX2592472.10_summits.bed INFO @ Sun, 21 Jun 2020 19:04:15: Done! pass1 - making usageList (125 chroms): 2 millis pass2 - checking and writing primary data (6822 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:04:37: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:04:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592472/SRX2592472.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:04:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592472/SRX2592472.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:04:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592472/SRX2592472.20_summits.bed INFO @ Sun, 21 Jun 2020 19:04:46: Done! pass1 - making usageList (96 chroms): 1 millis pass2 - checking and writing primary data (5205 records, 4 fields): 13 millis CompletedMACS2peakCalling