Job ID = 6456438 SRX = SRX3404033 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:02:02 prefetch.2.10.7: 1) Downloading 'SRR6303510'... 2020-06-21T11:02:02 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:02:33 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:02:34 prefetch.2.10.7: 'SRR6303510' is valid 2020-06-21T11:02:34 prefetch.2.10.7: 1) 'SRR6303510' was downloaded successfully 2020-06-21T11:02:34 prefetch.2.10.7: 'SRR6303510' has 0 unresolved dependencies Read 4636303 spots for SRR6303510/SRR6303510.sra Written 4636303 spots for SRR6303510/SRR6303510.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: 00:02:07 4636303 reads; of these: 4636303 (100.00%) were unpaired; of these: 772786 (16.67%) aligned 0 times 1440363 (31.07%) aligned exactly 1 time 2423154 (52.26%) aligned >1 times 83.33% overall alignment rate Time searching: 00:02:07 Overall time: 00:02:07 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] 1918769 / 3863517 = 0.4966 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 20:06:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3404033/SRX3404033.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3404033/SRX3404033.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3404033/SRX3404033.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3404033/SRX3404033.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 20:06:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:06:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:06:21: 1000000 INFO @ Sun, 21 Jun 2020 20:06:27: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:06:27: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:06:27: #1 total tags in treatment: 1944748 INFO @ Sun, 21 Jun 2020 20:06:27: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:06:27: #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 20:06:27: #1 tags after filtering in treatment: 1944453 INFO @ Sun, 21 Jun 2020 20:06:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:06:27: #1 finished! INFO @ Sun, 21 Jun 2020 20:06:27: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:06:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:06:28: #2 number of paired peaks: 1789 INFO @ Sun, 21 Jun 2020 20:06:28: start model_add_line... INFO @ Sun, 21 Jun 2020 20:06:28: start X-correlation... INFO @ Sun, 21 Jun 2020 20:06:28: end of X-cor INFO @ Sun, 21 Jun 2020 20:06:28: #2 finished! INFO @ Sun, 21 Jun 2020 20:06:28: #2 predicted fragment length is 116 bps INFO @ Sun, 21 Jun 2020 20:06:28: #2 alternative fragment length(s) may be 116 bps INFO @ Sun, 21 Jun 2020 20:06:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3404033/SRX3404033.05_model.r INFO @ Sun, 21 Jun 2020 20:06:28: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:06:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:06:33: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:06:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3404033/SRX3404033.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:06:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3404033/SRX3404033.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:06:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3404033/SRX3404033.05_summits.bed INFO @ Sun, 21 Jun 2020 20:06:36: Done! pass1 - making usageList (356 chroms): 1 millis pass2 - checking and writing primary data (1475 records, 4 fields): 15 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 20:06:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3404033/SRX3404033.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3404033/SRX3404033.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3404033/SRX3404033.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3404033/SRX3404033.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 20:06:46: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:06:46: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:06:51: 1000000 INFO @ Sun, 21 Jun 2020 20:06:57: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:06:57: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:06:57: #1 total tags in treatment: 1944748 INFO @ Sun, 21 Jun 2020 20:06:57: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:06:57: #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 20:06:58: #1 tags after filtering in treatment: 1944453 INFO @ Sun, 21 Jun 2020 20:06:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:06:58: #1 finished! INFO @ Sun, 21 Jun 2020 20:06:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:06:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:06:58: #2 number of paired peaks: 1789 INFO @ Sun, 21 Jun 2020 20:06:58: start model_add_line... INFO @ Sun, 21 Jun 2020 20:06:58: start X-correlation... INFO @ Sun, 21 Jun 2020 20:06:58: end of X-cor INFO @ Sun, 21 Jun 2020 20:06:58: #2 finished! INFO @ Sun, 21 Jun 2020 20:06:58: #2 predicted fragment length is 116 bps INFO @ Sun, 21 Jun 2020 20:06:58: #2 alternative fragment length(s) may be 116 bps INFO @ Sun, 21 Jun 2020 20:06:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3404033/SRX3404033.10_model.r INFO @ Sun, 21 Jun 2020 20:06:58: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:06:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:07:04: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:07:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3404033/SRX3404033.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:07:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3404033/SRX3404033.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:07:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3404033/SRX3404033.10_summits.bed INFO @ Sun, 21 Jun 2020 20:07:06: Done! pass1 - making usageList (195 chroms): 3 millis pass2 - checking and writing primary data (649 records, 4 fields): 8 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 20:07:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3404033/SRX3404033.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3404033/SRX3404033.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3404033/SRX3404033.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3404033/SRX3404033.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 20:07:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:07:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:07:22: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:07:28: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:07:28: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:07:28: #1 total tags in treatment: 1944748 INFO @ Sun, 21 Jun 2020 20:07:28: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:07:28: #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 20:07:28: #1 tags after filtering in treatment: 1944453 INFO @ Sun, 21 Jun 2020 20:07:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:07:28: #1 finished! INFO @ Sun, 21 Jun 2020 20:07:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:07:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:07:28: #2 number of paired peaks: 1789 INFO @ Sun, 21 Jun 2020 20:07:28: start model_add_line... INFO @ Sun, 21 Jun 2020 20:07:28: start X-correlation... INFO @ Sun, 21 Jun 2020 20:07:28: end of X-cor INFO @ Sun, 21 Jun 2020 20:07:28: #2 finished! INFO @ Sun, 21 Jun 2020 20:07:28: #2 predicted fragment length is 116 bps INFO @ Sun, 21 Jun 2020 20:07:28: #2 alternative fragment length(s) may be 116 bps INFO @ Sun, 21 Jun 2020 20:07:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3404033/SRX3404033.20_model.r INFO @ Sun, 21 Jun 2020 20:07:29: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:07:29: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:07:34: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:07:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3404033/SRX3404033.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:07:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3404033/SRX3404033.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:07:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3404033/SRX3404033.20_summits.bed INFO @ Sun, 21 Jun 2020 20:07:37: Done! pass1 - making usageList (134 chroms): 1 millis pass2 - checking and writing primary data (282 records, 4 fields): 5 millis CompletedMACS2peakCalling