Job ID = 6453735 SRX = SRX1433373 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:37:11 prefetch.2.10.7: 1) Downloading 'SRR2919838'... 2020-06-21T08:37:11 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:43:33 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:43:33 prefetch.2.10.7: 1) 'SRR2919838' was downloaded successfully Read 43421345 spots for SRR2919838/SRR2919838.sra Written 43421345 spots for SRR2919838/SRR2919838.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: 00:06:43 43421345 reads; of these: 43421345 (100.00%) were unpaired; of these: 32684925 (75.27%) aligned 0 times 8427869 (19.41%) aligned exactly 1 time 2308551 (5.32%) aligned >1 times 24.73% overall alignment rate Time searching: 00:06:43 Overall time: 00:06:43 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] 5271320 / 10736420 = 0.4910 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 17:54:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1433373/SRX1433373.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1433373/SRX1433373.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1433373/SRX1433373.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1433373/SRX1433373.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 17:54:59: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:54:59: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:55:05: 1000000 INFO @ Sun, 21 Jun 2020 17:55:10: 2000000 INFO @ Sun, 21 Jun 2020 17:55:16: 3000000 INFO @ Sun, 21 Jun 2020 17:55:21: 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 17:55:27: 5000000 INFO @ Sun, 21 Jun 2020 17:55:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1433373/SRX1433373.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1433373/SRX1433373.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1433373/SRX1433373.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1433373/SRX1433373.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 17:55:29: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:55:29: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:55:30: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:55:30: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:55:30: #1 total tags in treatment: 5465100 INFO @ Sun, 21 Jun 2020 17:55:30: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:55:30: #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 17:55:31: #1 tags after filtering in treatment: 5464959 INFO @ Sun, 21 Jun 2020 17:55:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:55:31: #1 finished! INFO @ Sun, 21 Jun 2020 17:55:31: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:55:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:55:31: #2 number of paired peaks: 1686 INFO @ Sun, 21 Jun 2020 17:55:31: start model_add_line... INFO @ Sun, 21 Jun 2020 17:55:31: start X-correlation... INFO @ Sun, 21 Jun 2020 17:55:31: end of X-cor INFO @ Sun, 21 Jun 2020 17:55:31: #2 finished! INFO @ Sun, 21 Jun 2020 17:55:31: #2 predicted fragment length is 166 bps INFO @ Sun, 21 Jun 2020 17:55:31: #2 alternative fragment length(s) may be 166 bps INFO @ Sun, 21 Jun 2020 17:55:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1433373/SRX1433373.05_model.r INFO @ Sun, 21 Jun 2020 17:55:31: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:55:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:55:35: 1000000 INFO @ Sun, 21 Jun 2020 17:55:41: 2000000 INFO @ Sun, 21 Jun 2020 17:55:45: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:55:47: 3000000 INFO @ Sun, 21 Jun 2020 17:55:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1433373/SRX1433373.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:55:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1433373/SRX1433373.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:55:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1433373/SRX1433373.05_summits.bed INFO @ Sun, 21 Jun 2020 17:55:51: Done! pass1 - making usageList (523 chroms): 1 millis pass2 - checking and writing primary data (2644 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:55:52: 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 17:55:58: 5000000 INFO @ Sun, 21 Jun 2020 17:55:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1433373/SRX1433373.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1433373/SRX1433373.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1433373/SRX1433373.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1433373/SRX1433373.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 17:55:59: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:55:59: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:56:01: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:56:01: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:56:01: #1 total tags in treatment: 5465100 INFO @ Sun, 21 Jun 2020 17:56:01: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:56:01: #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 17:56:02: #1 tags after filtering in treatment: 5464959 INFO @ Sun, 21 Jun 2020 17:56:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:56:02: #1 finished! INFO @ Sun, 21 Jun 2020 17:56:02: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:56:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:56:02: #2 number of paired peaks: 1686 INFO @ Sun, 21 Jun 2020 17:56:02: start model_add_line... INFO @ Sun, 21 Jun 2020 17:56:02: start X-correlation... INFO @ Sun, 21 Jun 2020 17:56:02: end of X-cor INFO @ Sun, 21 Jun 2020 17:56:02: #2 finished! INFO @ Sun, 21 Jun 2020 17:56:02: #2 predicted fragment length is 166 bps INFO @ Sun, 21 Jun 2020 17:56:02: #2 alternative fragment length(s) may be 166 bps INFO @ Sun, 21 Jun 2020 17:56:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1433373/SRX1433373.10_model.r INFO @ Sun, 21 Jun 2020 17:56:02: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:56:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:56:05: 1000000 INFO @ Sun, 21 Jun 2020 17:56:11: 2000000 INFO @ Sun, 21 Jun 2020 17:56:15: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:56:17: 3000000 INFO @ Sun, 21 Jun 2020 17:56:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1433373/SRX1433373.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:56:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1433373/SRX1433373.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:56:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1433373/SRX1433373.10_summits.bed INFO @ Sun, 21 Jun 2020 17:56:22: Done! pass1 - making usageList (326 chroms): 1 millis pass2 - checking and writing primary data (1089 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:56:23: 4000000 INFO @ Sun, 21 Jun 2020 17:56:29: 5000000 INFO @ Sun, 21 Jun 2020 17:56:31: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:56:31: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:56:31: #1 total tags in treatment: 5465100 INFO @ Sun, 21 Jun 2020 17:56:31: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:56:31: #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 17:56:32: #1 tags after filtering in treatment: 5464959 INFO @ Sun, 21 Jun 2020 17:56:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:56:32: #1 finished! INFO @ Sun, 21 Jun 2020 17:56:32: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:56:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:56:32: #2 number of paired peaks: 1686 INFO @ Sun, 21 Jun 2020 17:56:32: start model_add_line... INFO @ Sun, 21 Jun 2020 17:56:32: start X-correlation... INFO @ Sun, 21 Jun 2020 17:56:32: end of X-cor INFO @ Sun, 21 Jun 2020 17:56:32: #2 finished! INFO @ Sun, 21 Jun 2020 17:56:32: #2 predicted fragment length is 166 bps INFO @ Sun, 21 Jun 2020 17:56:32: #2 alternative fragment length(s) may be 166 bps INFO @ Sun, 21 Jun 2020 17:56:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1433373/SRX1433373.20_model.r INFO @ Sun, 21 Jun 2020 17:56:32: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:56:32: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:56:46: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:56:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1433373/SRX1433373.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:56:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1433373/SRX1433373.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:56:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1433373/SRX1433373.20_summits.bed INFO @ Sun, 21 Jun 2020 17:56:52: Done! pass1 - making usageList (114 chroms): 1 millis pass2 - checking and writing primary data (316 records, 4 fields): 5 millis CompletedMACS2peakCalling