Job ID = 6453895 SRX = SRX1561064 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:56:49 prefetch.2.10.7: 1) Downloading 'SRR3145066'... 2020-06-21T08:56:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:57:21 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:57:21 prefetch.2.10.7: 'SRR3145066' is valid 2020-06-21T08:57:21 prefetch.2.10.7: 1) 'SRR3145066' was downloaded successfully Read 4556468 spots for SRR3145066/SRR3145066.sra Written 4556468 spots for SRR3145066/SRR3145066.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: 00:00:30 4556468 reads; of these: 4556468 (100.00%) were unpaired; of these: 3344707 (73.41%) aligned 0 times 1087041 (23.86%) aligned exactly 1 time 124720 (2.74%) aligned >1 times 26.59% overall alignment rate Time searching: 00:00:30 Overall time: 00:00:30 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] 355837 / 1211761 = 0.2937 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 17:58:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1561064/SRX1561064.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1561064/SRX1561064.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1561064/SRX1561064.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1561064/SRX1561064.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 17:58:56: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:58:56: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:59:01: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:59:01: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:59:01: #1 total tags in treatment: 855924 INFO @ Sun, 21 Jun 2020 17:59:01: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:59:01: #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 17:59:01: #1 tags after filtering in treatment: 855216 INFO @ Sun, 21 Jun 2020 17:59:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:59:01: #1 finished! INFO @ Sun, 21 Jun 2020 17:59:01: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:59:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:59:01: #2 number of paired peaks: 4436 INFO @ Sun, 21 Jun 2020 17:59:01: start model_add_line... INFO @ Sun, 21 Jun 2020 17:59:01: start X-correlation... INFO @ Sun, 21 Jun 2020 17:59:01: end of X-cor INFO @ Sun, 21 Jun 2020 17:59:01: #2 finished! INFO @ Sun, 21 Jun 2020 17:59:01: #2 predicted fragment length is 175 bps INFO @ Sun, 21 Jun 2020 17:59:01: #2 alternative fragment length(s) may be 175 bps INFO @ Sun, 21 Jun 2020 17:59:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1561064/SRX1561064.05_model.r INFO @ Sun, 21 Jun 2020 17:59:01: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:59:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:59:04: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:59:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1561064/SRX1561064.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:59:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1561064/SRX1561064.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:59:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1561064/SRX1561064.05_summits.bed INFO @ Sun, 21 Jun 2020 17:59:05: Done! pass1 - making usageList (52 chroms): 1 millis pass2 - checking and writing primary data (2447 records, 4 fields): 7 millis CompletedMACS2peakCalling 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 17:59:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1561064/SRX1561064.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1561064/SRX1561064.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1561064/SRX1561064.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1561064/SRX1561064.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 17:59:26: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:59:26: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:59:31: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:59:31: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:59:31: #1 total tags in treatment: 855924 INFO @ Sun, 21 Jun 2020 17:59:31: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:59:31: #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 17:59:31: #1 tags after filtering in treatment: 855216 INFO @ Sun, 21 Jun 2020 17:59:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:59:31: #1 finished! INFO @ Sun, 21 Jun 2020 17:59:31: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:59:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:59:31: #2 number of paired peaks: 4436 INFO @ Sun, 21 Jun 2020 17:59:31: start model_add_line... INFO @ Sun, 21 Jun 2020 17:59:31: start X-correlation... INFO @ Sun, 21 Jun 2020 17:59:31: end of X-cor INFO @ Sun, 21 Jun 2020 17:59:31: #2 finished! INFO @ Sun, 21 Jun 2020 17:59:31: #2 predicted fragment length is 175 bps INFO @ Sun, 21 Jun 2020 17:59:31: #2 alternative fragment length(s) may be 175 bps INFO @ Sun, 21 Jun 2020 17:59:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1561064/SRX1561064.10_model.r INFO @ Sun, 21 Jun 2020 17:59:31: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:59:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:59:34: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:59:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1561064/SRX1561064.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:59:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1561064/SRX1561064.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:59:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1561064/SRX1561064.10_summits.bed INFO @ Sun, 21 Jun 2020 17:59:35: Done! pass1 - making usageList (39 chroms): 1 millis pass2 - checking and writing primary data (1269 records, 4 fields): 4 millis CompletedMACS2peakCalling 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 17:59:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1561064/SRX1561064.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1561064/SRX1561064.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1561064/SRX1561064.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1561064/SRX1561064.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 17:59:56: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:59:56: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:00:01: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:00:01: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:00:01: #1 total tags in treatment: 855924 INFO @ Sun, 21 Jun 2020 18:00:01: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:00:01: #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 18:00:01: #1 tags after filtering in treatment: 855216 INFO @ Sun, 21 Jun 2020 18:00:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:00:01: #1 finished! INFO @ Sun, 21 Jun 2020 18:00:01: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:00:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:00:01: #2 number of paired peaks: 4436 INFO @ Sun, 21 Jun 2020 18:00:01: start model_add_line... INFO @ Sun, 21 Jun 2020 18:00:01: start X-correlation... INFO @ Sun, 21 Jun 2020 18:00:01: end of X-cor INFO @ Sun, 21 Jun 2020 18:00:01: #2 finished! INFO @ Sun, 21 Jun 2020 18:00:01: #2 predicted fragment length is 175 bps INFO @ Sun, 21 Jun 2020 18:00:01: #2 alternative fragment length(s) may be 175 bps INFO @ Sun, 21 Jun 2020 18:00:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1561064/SRX1561064.20_model.r INFO @ Sun, 21 Jun 2020 18:00:01: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:00:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:00:04: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:00:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1561064/SRX1561064.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:00:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1561064/SRX1561064.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:00:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1561064/SRX1561064.20_summits.bed INFO @ Sun, 21 Jun 2020 18:00:05: Done! pass1 - making usageList (31 chroms): 1 millis pass2 - checking and writing primary data (499 records, 4 fields): 3 millis CompletedMACS2peakCalling