Job ID = 6456941 SRX = SRX4158168 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:19:57 prefetch.2.10.7: 1) Downloading 'SRR7253448'... 2020-06-21T11:19:57 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:20:37 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:20:37 prefetch.2.10.7: 'SRR7253448' is valid 2020-06-21T11:20:37 prefetch.2.10.7: 1) 'SRR7253448' was downloaded successfully Read 3408371 spots for SRR7253448/SRR7253448.sra Written 3408371 spots for SRR7253448/SRR7253448.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: 00:00:50 3408371 reads; of these: 3408371 (100.00%) were unpaired; of these: 80109 (2.35%) aligned 0 times 3014145 (88.43%) aligned exactly 1 time 314117 (9.22%) aligned >1 times 97.65% overall alignment rate Time searching: 00:00:50 Overall time: 00:00:50 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_rmdupse_core] 126316 / 3328262 = 0.0380 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 20:23:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4158168/SRX4158168.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4158168/SRX4158168.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4158168/SRX4158168.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4158168/SRX4158168.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 20:23:09: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:23:09: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:23:14: 1000000 INFO @ Sun, 21 Jun 2020 20:23:20: 2000000 INFO @ Sun, 21 Jun 2020 20:23:27: 3000000 INFO @ Sun, 21 Jun 2020 20:23:28: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 20:23:28: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 20:23:28: #1 total tags in treatment: 3201946 INFO @ Sun, 21 Jun 2020 20:23:28: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:23:28: #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 20:23:28: #1 tags after filtering in treatment: 3201397 INFO @ Sun, 21 Jun 2020 20:23:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:23:28: #1 finished! INFO @ Sun, 21 Jun 2020 20:23:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:23:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:23:29: #2 number of paired peaks: 7535 INFO @ Sun, 21 Jun 2020 20:23:29: start model_add_line... INFO @ Sun, 21 Jun 2020 20:23:29: start X-correlation... INFO @ Sun, 21 Jun 2020 20:23:29: end of X-cor INFO @ Sun, 21 Jun 2020 20:23:29: #2 finished! INFO @ Sun, 21 Jun 2020 20:23:29: #2 predicted fragment length is 147 bps INFO @ Sun, 21 Jun 2020 20:23:29: #2 alternative fragment length(s) may be 4,147 bps INFO @ Sun, 21 Jun 2020 20:23:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4158168/SRX4158168.05_model.r INFO @ Sun, 21 Jun 2020 20:23:29: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:23:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:23:36: #3 Call peaks for each chromosome... 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 20:23:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4158168/SRX4158168.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4158168/SRX4158168.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4158168/SRX4158168.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4158168/SRX4158168.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 20:23:39: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:23:39: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:23:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4158168/SRX4158168.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:23:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4158168/SRX4158168.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:23:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4158168/SRX4158168.05_summits.bed INFO @ Sun, 21 Jun 2020 20:23:41: Done! pass1 - making usageList (67 chroms): 1 millis pass2 - checking and writing primary data (2775 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:23:44: 1000000 INFO @ Sun, 21 Jun 2020 20:23:50: 2000000 INFO @ Sun, 21 Jun 2020 20:23:56: 3000000 INFO @ Sun, 21 Jun 2020 20:23:58: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 20:23:58: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 20:23:58: #1 total tags in treatment: 3201946 INFO @ Sun, 21 Jun 2020 20:23:58: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:23:58: #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 20:23:58: #1 tags after filtering in treatment: 3201397 INFO @ Sun, 21 Jun 2020 20:23:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:23:58: #1 finished! INFO @ Sun, 21 Jun 2020 20:23:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:23:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:23:58: #2 number of paired peaks: 7535 INFO @ Sun, 21 Jun 2020 20:23:58: start model_add_line... INFO @ Sun, 21 Jun 2020 20:23:59: start X-correlation... INFO @ Sun, 21 Jun 2020 20:23:59: end of X-cor INFO @ Sun, 21 Jun 2020 20:23:59: #2 finished! INFO @ Sun, 21 Jun 2020 20:23:59: #2 predicted fragment length is 147 bps INFO @ Sun, 21 Jun 2020 20:23:59: #2 alternative fragment length(s) may be 4,147 bps INFO @ Sun, 21 Jun 2020 20:23:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4158168/SRX4158168.10_model.r INFO @ Sun, 21 Jun 2020 20:23:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:23:59: #3 Pre-compute pvalue-qvalue table... 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 20:24:07: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:24:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4158168/SRX4158168.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4158168/SRX4158168.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4158168/SRX4158168.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4158168/SRX4158168.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 20:24:09: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:24:09: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:24:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4158168/SRX4158168.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:24:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4158168/SRX4158168.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:24:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4158168/SRX4158168.10_summits.bed INFO @ Sun, 21 Jun 2020 20:24:11: Done! pass1 - making usageList (43 chroms): 0 millis pass2 - checking and writing primary data (484 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:24:14: 1000000 INFO @ Sun, 21 Jun 2020 20:24:20: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:24:26: 3000000 INFO @ Sun, 21 Jun 2020 20:24:27: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 20:24:27: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 20:24:27: #1 total tags in treatment: 3201946 INFO @ Sun, 21 Jun 2020 20:24:27: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:24:27: #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 20:24:28: #1 tags after filtering in treatment: 3201397 INFO @ Sun, 21 Jun 2020 20:24:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:24:28: #1 finished! INFO @ Sun, 21 Jun 2020 20:24:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:24:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:24:28: #2 number of paired peaks: 7535 INFO @ Sun, 21 Jun 2020 20:24:28: start model_add_line... INFO @ Sun, 21 Jun 2020 20:24:28: start X-correlation... INFO @ Sun, 21 Jun 2020 20:24:28: end of X-cor INFO @ Sun, 21 Jun 2020 20:24:28: #2 finished! INFO @ Sun, 21 Jun 2020 20:24:28: #2 predicted fragment length is 147 bps INFO @ Sun, 21 Jun 2020 20:24:28: #2 alternative fragment length(s) may be 4,147 bps INFO @ Sun, 21 Jun 2020 20:24:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4158168/SRX4158168.20_model.r INFO @ Sun, 21 Jun 2020 20:24:28: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:24:28: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:24:36: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:24:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4158168/SRX4158168.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:24:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4158168/SRX4158168.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:24:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4158168/SRX4158168.20_summits.bed INFO @ Sun, 21 Jun 2020 20:24:40: Done! pass1 - making usageList (28 chroms): 1 millis pass2 - checking and writing primary data (79 records, 4 fields): 2 millis CompletedMACS2peakCalling