Job ID = 6452603 SRX = SRX017854 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:31:42 prefetch.2.10.7: 1) Downloading 'SRR038289'... 2020-06-21T07:31:42 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:33:02 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:33:02 prefetch.2.10.7: 'SRR038289' is valid 2020-06-21T07:33:02 prefetch.2.10.7: 1) 'SRR038289' was downloaded successfully Read 7432600 spots for SRR038289/SRR038289.sra Written 7432600 spots for SRR038289/SRR038289.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: 00:00:40 7432600 reads; of these: 7432600 (100.00%) were unpaired; of these: 5805263 (78.11%) aligned 0 times 1152609 (15.51%) aligned exactly 1 time 474728 (6.39%) aligned >1 times 21.89% overall alignment rate Time searching: 00:00:40 Overall time: 00:00:40 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] 95358 / 1627337 = 0.0586 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 16:34:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX017854/SRX017854.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX017854/SRX017854.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX017854/SRX017854.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX017854/SRX017854.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 16:34:53: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:34:53: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:34:57: 1000000 INFO @ Sun, 21 Jun 2020 16:35:00: #1 tag size is determined as 25 bps INFO @ Sun, 21 Jun 2020 16:35:00: #1 tag size = 25 INFO @ Sun, 21 Jun 2020 16:35:00: #1 total tags in treatment: 1531979 INFO @ Sun, 21 Jun 2020 16:35:00: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:35:00: #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 16:35:00: #1 tags after filtering in treatment: 1531915 INFO @ Sun, 21 Jun 2020 16:35:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:35:00: #1 finished! INFO @ Sun, 21 Jun 2020 16:35:00: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:35:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:35:00: #2 number of paired peaks: 1698 INFO @ Sun, 21 Jun 2020 16:35:00: start model_add_line... INFO @ Sun, 21 Jun 2020 16:35:00: start X-correlation... INFO @ Sun, 21 Jun 2020 16:35:00: end of X-cor INFO @ Sun, 21 Jun 2020 16:35:00: #2 finished! INFO @ Sun, 21 Jun 2020 16:35:00: #2 predicted fragment length is 100 bps INFO @ Sun, 21 Jun 2020 16:35:00: #2 alternative fragment length(s) may be 100 bps INFO @ Sun, 21 Jun 2020 16:35:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX017854/SRX017854.05_model.r INFO @ Sun, 21 Jun 2020 16:35:00: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:35:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:35:04: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:35:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX017854/SRX017854.05_peaks.xls INFO @ Sun, 21 Jun 2020 16:35:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX017854/SRX017854.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:35:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX017854/SRX017854.05_summits.bed INFO @ Sun, 21 Jun 2020 16:35:06: Done! pass1 - making usageList (333 chroms): 2 millis pass2 - checking and writing primary data (1011 records, 4 fields): 11 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 16:35:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX017854/SRX017854.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX017854/SRX017854.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX017854/SRX017854.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX017854/SRX017854.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 16:35:23: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:35:23: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:35:27: 1000000 INFO @ Sun, 21 Jun 2020 16:35:31: #1 tag size is determined as 25 bps INFO @ Sun, 21 Jun 2020 16:35:31: #1 tag size = 25 INFO @ Sun, 21 Jun 2020 16:35:31: #1 total tags in treatment: 1531979 INFO @ Sun, 21 Jun 2020 16:35:31: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:35:31: #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 16:35:31: #1 tags after filtering in treatment: 1531915 INFO @ Sun, 21 Jun 2020 16:35:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:35:31: #1 finished! INFO @ Sun, 21 Jun 2020 16:35:31: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:35:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:35:31: #2 number of paired peaks: 1698 INFO @ Sun, 21 Jun 2020 16:35:31: start model_add_line... INFO @ Sun, 21 Jun 2020 16:35:31: start X-correlation... INFO @ Sun, 21 Jun 2020 16:35:31: end of X-cor INFO @ Sun, 21 Jun 2020 16:35:31: #2 finished! INFO @ Sun, 21 Jun 2020 16:35:31: #2 predicted fragment length is 100 bps INFO @ Sun, 21 Jun 2020 16:35:31: #2 alternative fragment length(s) may be 100 bps INFO @ Sun, 21 Jun 2020 16:35:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX017854/SRX017854.10_model.r INFO @ Sun, 21 Jun 2020 16:35:31: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:35:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:35:35: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:35:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX017854/SRX017854.10_peaks.xls INFO @ Sun, 21 Jun 2020 16:35:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX017854/SRX017854.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:35:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX017854/SRX017854.10_summits.bed INFO @ Sun, 21 Jun 2020 16:35:37: Done! pass1 - making usageList (120 chroms): 1 millis pass2 - checking and writing primary data (253 records, 4 fields): 5 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 16:35:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX017854/SRX017854.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX017854/SRX017854.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX017854/SRX017854.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX017854/SRX017854.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 16:35:53: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:35:53: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 16:35:58: 1000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 16:36:01: #1 tag size is determined as 25 bps INFO @ Sun, 21 Jun 2020 16:36:01: #1 tag size = 25 INFO @ Sun, 21 Jun 2020 16:36:01: #1 total tags in treatment: 1531979 INFO @ Sun, 21 Jun 2020 16:36:01: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:36:01: #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 16:36:01: #1 tags after filtering in treatment: 1531915 INFO @ Sun, 21 Jun 2020 16:36:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:36:01: #1 finished! INFO @ Sun, 21 Jun 2020 16:36:01: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:36:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:36:01: #2 number of paired peaks: 1698 INFO @ Sun, 21 Jun 2020 16:36:01: start model_add_line... INFO @ Sun, 21 Jun 2020 16:36:01: start X-correlation... INFO @ Sun, 21 Jun 2020 16:36:01: end of X-cor INFO @ Sun, 21 Jun 2020 16:36:01: #2 finished! INFO @ Sun, 21 Jun 2020 16:36:01: #2 predicted fragment length is 100 bps INFO @ Sun, 21 Jun 2020 16:36:01: #2 alternative fragment length(s) may be 100 bps INFO @ Sun, 21 Jun 2020 16:36:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX017854/SRX017854.20_model.r INFO @ Sun, 21 Jun 2020 16:36:01: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:36:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:36:05: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:36:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX017854/SRX017854.20_peaks.xls INFO @ Sun, 21 Jun 2020 16:36:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX017854/SRX017854.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:36:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX017854/SRX017854.20_summits.bed INFO @ Sun, 21 Jun 2020 16:36:07: Done! pass1 - making usageList (75 chroms): 1 millis pass2 - checking and writing primary data (106 records, 4 fields): 3 millis CompletedMACS2peakCalling