Job ID = 6453021 SRX = SRX099639 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:47:30 prefetch.2.10.7: 1) Downloading 'SRR350629'... 2020-06-21T07:47:30 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:49:34 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:49:35 prefetch.2.10.7: 'SRR350629' is valid 2020-06-21T07:49:35 prefetch.2.10.7: 1) 'SRR350629' was downloaded successfully Read 11208065 spots for SRR350629/SRR350629.sra Written 11208065 spots for SRR350629/SRR350629.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: 00:00:01 Multiseed full-index search: 00:03:03 11208065 reads; of these: 11208065 (100.00%) were unpaired; of these: 1621545 (14.47%) aligned 0 times 1871144 (16.69%) aligned exactly 1 time 7715376 (68.84%) aligned >1 times 85.53% overall alignment rate Time searching: 00:03:04 Overall time: 00:03:04 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] 9055390 / 9586520 = 0.9446 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 16:55:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX099639/SRX099639.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX099639/SRX099639.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX099639/SRX099639.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX099639/SRX099639.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 16:55:07: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:55:07: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:55:10: #1 tag size is determined as 55 bps INFO @ Sun, 21 Jun 2020 16:55:10: #1 tag size = 55 INFO @ Sun, 21 Jun 2020 16:55:10: #1 total tags in treatment: 531130 INFO @ Sun, 21 Jun 2020 16:55:10: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:55:10: #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 16:55:11: #1 tags after filtering in treatment: 530615 INFO @ Sun, 21 Jun 2020 16:55:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:55:11: #1 finished! INFO @ Sun, 21 Jun 2020 16:55:11: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:55:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:55:11: #2 number of paired peaks: 1960 INFO @ Sun, 21 Jun 2020 16:55:11: start model_add_line... INFO @ Sun, 21 Jun 2020 16:55:11: start X-correlation... INFO @ Sun, 21 Jun 2020 16:55:11: end of X-cor INFO @ Sun, 21 Jun 2020 16:55:11: #2 finished! INFO @ Sun, 21 Jun 2020 16:55:11: #2 predicted fragment length is 152 bps INFO @ Sun, 21 Jun 2020 16:55:11: #2 alternative fragment length(s) may be 152 bps INFO @ Sun, 21 Jun 2020 16:55:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX099639/SRX099639.05_model.r INFO @ Sun, 21 Jun 2020 16:55:11: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:55:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:55:13: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:55:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX099639/SRX099639.05_peaks.xls INFO @ Sun, 21 Jun 2020 16:55:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX099639/SRX099639.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:55:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX099639/SRX099639.05_summits.bed INFO @ Sun, 21 Jun 2020 16:55:14: Done! pass1 - making usageList (181 chroms): 1 millis pass2 - checking and writing primary data (2958 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 16:55:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX099639/SRX099639.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX099639/SRX099639.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX099639/SRX099639.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX099639/SRX099639.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 16:55:37: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:55:37: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:55:41: #1 tag size is determined as 55 bps INFO @ Sun, 21 Jun 2020 16:55:41: #1 tag size = 55 INFO @ Sun, 21 Jun 2020 16:55:41: #1 total tags in treatment: 531130 INFO @ Sun, 21 Jun 2020 16:55:41: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:55:41: #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 16:55:41: #1 tags after filtering in treatment: 530615 INFO @ Sun, 21 Jun 2020 16:55:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:55:41: #1 finished! INFO @ Sun, 21 Jun 2020 16:55:41: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:55:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:55:41: #2 number of paired peaks: 1960 INFO @ Sun, 21 Jun 2020 16:55:41: start model_add_line... INFO @ Sun, 21 Jun 2020 16:55:41: start X-correlation... INFO @ Sun, 21 Jun 2020 16:55:41: end of X-cor INFO @ Sun, 21 Jun 2020 16:55:41: #2 finished! INFO @ Sun, 21 Jun 2020 16:55:41: #2 predicted fragment length is 152 bps INFO @ Sun, 21 Jun 2020 16:55:41: #2 alternative fragment length(s) may be 152 bps INFO @ Sun, 21 Jun 2020 16:55:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX099639/SRX099639.10_model.r INFO @ Sun, 21 Jun 2020 16:55:41: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:55:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:55:43: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:55:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX099639/SRX099639.10_peaks.xls INFO @ Sun, 21 Jun 2020 16:55:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX099639/SRX099639.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:55:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX099639/SRX099639.10_summits.bed INFO @ Sun, 21 Jun 2020 16:55:44: Done! pass1 - making usageList (134 chroms): 1 millis pass2 - checking and writing primary data (2256 records, 4 fields): 6 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 16:56:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX099639/SRX099639.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX099639/SRX099639.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX099639/SRX099639.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX099639/SRX099639.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 16:56:07: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:56:07: #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 16:56:11: #1 tag size is determined as 55 bps INFO @ Sun, 21 Jun 2020 16:56:11: #1 tag size = 55 INFO @ Sun, 21 Jun 2020 16:56:11: #1 total tags in treatment: 531130 INFO @ Sun, 21 Jun 2020 16:56:11: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:56:11: #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 16:56:11: #1 tags after filtering in treatment: 530615 INFO @ Sun, 21 Jun 2020 16:56:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:56:11: #1 finished! INFO @ Sun, 21 Jun 2020 16:56:11: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:56:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:56:11: #2 number of paired peaks: 1960 INFO @ Sun, 21 Jun 2020 16:56:11: start model_add_line... INFO @ Sun, 21 Jun 2020 16:56:11: start X-correlation... INFO @ Sun, 21 Jun 2020 16:56:11: end of X-cor INFO @ Sun, 21 Jun 2020 16:56:11: #2 finished! INFO @ Sun, 21 Jun 2020 16:56:11: #2 predicted fragment length is 152 bps INFO @ Sun, 21 Jun 2020 16:56:11: #2 alternative fragment length(s) may be 152 bps INFO @ Sun, 21 Jun 2020 16:56:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX099639/SRX099639.20_model.r INFO @ Sun, 21 Jun 2020 16:56:11: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:56:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:56:13: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:56:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX099639/SRX099639.20_peaks.xls INFO @ Sun, 21 Jun 2020 16:56:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX099639/SRX099639.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:56:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX099639/SRX099639.20_summits.bed INFO @ Sun, 21 Jun 2020 16:56:14: Done! pass1 - making usageList (109 chroms): 1 millis pass2 - checking and writing primary data (1725 records, 4 fields): 5 millis CompletedMACS2peakCalling