Job ID = 6452937 SRX = SRX050603 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:06:53 prefetch.2.10.7: 1) Downloading 'SRR139085'... 2020-06-21T08:06:53 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:08:14 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:08:15 prefetch.2.10.7: 'SRR139085' is valid 2020-06-21T08:08:15 prefetch.2.10.7: 1) 'SRR139085' was downloaded successfully Read 7259465 spots for SRR139085/SRR139085.sra Written 7259465 spots for SRR139085/SRR139085.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: 00:01:13 7259465 reads; of these: 7259465 (100.00%) were unpaired; of these: 229063 (3.16%) aligned 0 times 6041689 (83.22%) aligned exactly 1 time 988713 (13.62%) aligned >1 times 96.84% overall alignment rate Time searching: 00:01:13 Overall time: 00:01:13 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] 1034152 / 7030402 = 0.1471 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 17:11:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX050603/SRX050603.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX050603/SRX050603.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX050603/SRX050603.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX050603/SRX050603.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 17:11:43: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:11:43: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:11:49: 1000000 INFO @ Sun, 21 Jun 2020 17:11:54: 2000000 INFO @ Sun, 21 Jun 2020 17:12:00: 3000000 INFO @ Sun, 21 Jun 2020 17:12:06: 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 17:12:12: 5000000 INFO @ Sun, 21 Jun 2020 17:12:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX050603/SRX050603.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX050603/SRX050603.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX050603/SRX050603.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX050603/SRX050603.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 17:12:14: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:12:14: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:12:18: #1 tag size is determined as 30 bps INFO @ Sun, 21 Jun 2020 17:12:18: #1 tag size = 30 INFO @ Sun, 21 Jun 2020 17:12:18: #1 total tags in treatment: 5996250 INFO @ Sun, 21 Jun 2020 17:12:18: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:12:18: #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 17:12:18: #1 tags after filtering in treatment: 5996129 INFO @ Sun, 21 Jun 2020 17:12:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:12:18: #1 finished! INFO @ Sun, 21 Jun 2020 17:12:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:12:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:12:19: #2 number of paired peaks: 3276 INFO @ Sun, 21 Jun 2020 17:12:19: start model_add_line... INFO @ Sun, 21 Jun 2020 17:12:19: start X-correlation... INFO @ Sun, 21 Jun 2020 17:12:19: end of X-cor INFO @ Sun, 21 Jun 2020 17:12:19: #2 finished! INFO @ Sun, 21 Jun 2020 17:12:19: #2 predicted fragment length is 98 bps INFO @ Sun, 21 Jun 2020 17:12:19: #2 alternative fragment length(s) may be 98 bps INFO @ Sun, 21 Jun 2020 17:12:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX050603/SRX050603.05_model.r INFO @ Sun, 21 Jun 2020 17:12:19: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:12:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:12:20: 1000000 INFO @ Sun, 21 Jun 2020 17:12:26: 2000000 INFO @ Sun, 21 Jun 2020 17:12:32: 3000000 INFO @ Sun, 21 Jun 2020 17:12:33: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:12:38: 4000000 INFO @ Sun, 21 Jun 2020 17:12:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX050603/SRX050603.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:12:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX050603/SRX050603.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:12:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX050603/SRX050603.05_summits.bed INFO @ Sun, 21 Jun 2020 17:12:40: Done! pass1 - making usageList (122 chroms): 1 millis pass2 - checking and writing primary data (7704 records, 4 fields): 12 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 17:12:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX050603/SRX050603.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX050603/SRX050603.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX050603/SRX050603.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX050603/SRX050603.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 17:12:43: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:12:43: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:12:44: 5000000 INFO @ Sun, 21 Jun 2020 17:12:49: 1000000 INFO @ Sun, 21 Jun 2020 17:12:50: #1 tag size is determined as 30 bps INFO @ Sun, 21 Jun 2020 17:12:50: #1 tag size = 30 INFO @ Sun, 21 Jun 2020 17:12:50: #1 total tags in treatment: 5996250 INFO @ Sun, 21 Jun 2020 17:12:50: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:12:50: #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 17:12:51: #1 tags after filtering in treatment: 5996129 INFO @ Sun, 21 Jun 2020 17:12:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:12:51: #1 finished! INFO @ Sun, 21 Jun 2020 17:12:51: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:12:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:12:51: #2 number of paired peaks: 3276 INFO @ Sun, 21 Jun 2020 17:12:51: start model_add_line... INFO @ Sun, 21 Jun 2020 17:12:51: start X-correlation... INFO @ Sun, 21 Jun 2020 17:12:51: end of X-cor INFO @ Sun, 21 Jun 2020 17:12:51: #2 finished! INFO @ Sun, 21 Jun 2020 17:12:51: #2 predicted fragment length is 98 bps INFO @ Sun, 21 Jun 2020 17:12:51: #2 alternative fragment length(s) may be 98 bps INFO @ Sun, 21 Jun 2020 17:12:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX050603/SRX050603.10_model.r INFO @ Sun, 21 Jun 2020 17:12:51: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:12:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:12:55: 2000000 INFO @ Sun, 21 Jun 2020 17:13:01: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:13:06: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:13:07: 4000000 INFO @ Sun, 21 Jun 2020 17:13:13: 5000000 INFO @ Sun, 21 Jun 2020 17:13:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX050603/SRX050603.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:13:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX050603/SRX050603.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:13:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX050603/SRX050603.10_summits.bed INFO @ Sun, 21 Jun 2020 17:13:13: Done! pass1 - making usageList (76 chroms): 1 millis pass2 - checking and writing primary data (5087 records, 4 fields): 9 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:13:19: #1 tag size is determined as 30 bps INFO @ Sun, 21 Jun 2020 17:13:19: #1 tag size = 30 INFO @ Sun, 21 Jun 2020 17:13:19: #1 total tags in treatment: 5996250 INFO @ Sun, 21 Jun 2020 17:13:19: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:13:19: #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 17:13:19: #1 tags after filtering in treatment: 5996129 INFO @ Sun, 21 Jun 2020 17:13:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:13:19: #1 finished! INFO @ Sun, 21 Jun 2020 17:13:19: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:13:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:13:20: #2 number of paired peaks: 3276 INFO @ Sun, 21 Jun 2020 17:13:20: start model_add_line... INFO @ Sun, 21 Jun 2020 17:13:20: start X-correlation... INFO @ Sun, 21 Jun 2020 17:13:20: end of X-cor INFO @ Sun, 21 Jun 2020 17:13:20: #2 finished! INFO @ Sun, 21 Jun 2020 17:13:20: #2 predicted fragment length is 98 bps INFO @ Sun, 21 Jun 2020 17:13:20: #2 alternative fragment length(s) may be 98 bps INFO @ Sun, 21 Jun 2020 17:13:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX050603/SRX050603.20_model.r INFO @ Sun, 21 Jun 2020 17:13:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:13:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:13:34: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:13:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX050603/SRX050603.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:13:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX050603/SRX050603.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:13:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX050603/SRX050603.20_summits.bed INFO @ Sun, 21 Jun 2020 17:13:42: Done! pass1 - making usageList (54 chroms): 1 millis pass2 - checking and writing primary data (3189 records, 4 fields): 6 millis CompletedMACS2peakCalling