Job ID = 6454221 SRX = SRX191914 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 'SRR580344'... 2020-06-21T08:56:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:00:43 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:00:43 prefetch.2.10.7: 1) 'SRR580344' was downloaded successfully Read 19432784 spots for SRR580344/SRR580344.sra Written 19432784 spots for SRR580344/SRR580344.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: 00:03:30 19432784 reads; of these: 19432784 (100.00%) were unpaired; of these: 2268453 (11.67%) aligned 0 times 14513139 (74.68%) aligned exactly 1 time 2651192 (13.64%) aligned >1 times 88.33% overall alignment rate Time searching: 00:03:30 Overall time: 00:03:30 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_sort_core] merging from 8 files... [bam_rmdupse_core] 12541775 / 17164331 = 0.7307 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 18:09:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX191914/SRX191914.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX191914/SRX191914.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX191914/SRX191914.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX191914/SRX191914.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 18:09:05: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:09:05: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:09:11: 1000000 INFO @ Sun, 21 Jun 2020 18:09:16: 2000000 INFO @ Sun, 21 Jun 2020 18:09:22: 3000000 INFO @ Sun, 21 Jun 2020 18:09:28: 4000000 INFO @ Sun, 21 Jun 2020 18:09:31: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:09:31: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:09:31: #1 total tags in treatment: 4622556 INFO @ Sun, 21 Jun 2020 18:09:31: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:09:31: #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 18:09:31: #1 tags after filtering in treatment: 4622384 INFO @ Sun, 21 Jun 2020 18:09:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:09:31: #1 finished! INFO @ Sun, 21 Jun 2020 18:09:31: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:09:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:09:32: #2 number of paired peaks: 2372 INFO @ Sun, 21 Jun 2020 18:09:32: start model_add_line... INFO @ Sun, 21 Jun 2020 18:09:32: start X-correlation... INFO @ Sun, 21 Jun 2020 18:09:32: end of X-cor INFO @ Sun, 21 Jun 2020 18:09:32: #2 finished! INFO @ Sun, 21 Jun 2020 18:09:32: #2 predicted fragment length is 126 bps INFO @ Sun, 21 Jun 2020 18:09:32: #2 alternative fragment length(s) may be 126 bps INFO @ Sun, 21 Jun 2020 18:09:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX191914/SRX191914.05_model.r INFO @ Sun, 21 Jun 2020 18:09:32: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:09:32: #3 Pre-compute pvalue-qvalue table... 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 18:09:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX191914/SRX191914.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX191914/SRX191914.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX191914/SRX191914.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX191914/SRX191914.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 18:09:35: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:09:35: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:09:41: 1000000 INFO @ Sun, 21 Jun 2020 18:09:45: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:09:46: 2000000 INFO @ Sun, 21 Jun 2020 18:09:52: 3000000 INFO @ Sun, 21 Jun 2020 18:09:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX191914/SRX191914.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:09:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX191914/SRX191914.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:09:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX191914/SRX191914.05_summits.bed INFO @ Sun, 21 Jun 2020 18:09:52: Done! pass1 - making usageList (407 chroms): 2 millis pass2 - checking and writing primary data (4890 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:09:58: 4000000 INFO @ Sun, 21 Jun 2020 18:10:01: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:10:01: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:10:01: #1 total tags in treatment: 4622556 INFO @ Sun, 21 Jun 2020 18:10:01: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:10:01: #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 18:10:02: #1 tags after filtering in treatment: 4622384 INFO @ Sun, 21 Jun 2020 18:10:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:10:02: #1 finished! INFO @ Sun, 21 Jun 2020 18:10:02: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:10:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:10:02: #2 number of paired peaks: 2372 INFO @ Sun, 21 Jun 2020 18:10:02: start model_add_line... INFO @ Sun, 21 Jun 2020 18:10:02: start X-correlation... INFO @ Sun, 21 Jun 2020 18:10:02: end of X-cor INFO @ Sun, 21 Jun 2020 18:10:02: #2 finished! INFO @ Sun, 21 Jun 2020 18:10:02: #2 predicted fragment length is 126 bps INFO @ Sun, 21 Jun 2020 18:10:02: #2 alternative fragment length(s) may be 126 bps INFO @ Sun, 21 Jun 2020 18:10:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX191914/SRX191914.10_model.r INFO @ Sun, 21 Jun 2020 18:10:02: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:10:02: #3 Pre-compute pvalue-qvalue table... 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 18:10:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX191914/SRX191914.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX191914/SRX191914.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX191914/SRX191914.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX191914/SRX191914.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 18:10:05: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:10:05: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:10:11: 1000000 INFO @ Sun, 21 Jun 2020 18:10:16: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:10:16: 2000000 INFO @ Sun, 21 Jun 2020 18:10:22: 3000000 INFO @ Sun, 21 Jun 2020 18:10:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX191914/SRX191914.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:10:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX191914/SRX191914.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:10:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX191914/SRX191914.10_summits.bed INFO @ Sun, 21 Jun 2020 18:10:22: Done! pass1 - making usageList (296 chroms): 2 millis pass2 - checking and writing primary data (3028 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:10:28: 4000000 INFO @ Sun, 21 Jun 2020 18:10:31: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:10:31: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:10:31: #1 total tags in treatment: 4622556 INFO @ Sun, 21 Jun 2020 18:10:31: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:10:31: #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 18:10:32: #1 tags after filtering in treatment: 4622384 INFO @ Sun, 21 Jun 2020 18:10:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:10:32: #1 finished! INFO @ Sun, 21 Jun 2020 18:10:32: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:10:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:10:32: #2 number of paired peaks: 2372 INFO @ Sun, 21 Jun 2020 18:10:32: start model_add_line... INFO @ Sun, 21 Jun 2020 18:10:32: start X-correlation... INFO @ Sun, 21 Jun 2020 18:10:32: end of X-cor INFO @ Sun, 21 Jun 2020 18:10:32: #2 finished! INFO @ Sun, 21 Jun 2020 18:10:32: #2 predicted fragment length is 126 bps INFO @ Sun, 21 Jun 2020 18:10:32: #2 alternative fragment length(s) may be 126 bps INFO @ Sun, 21 Jun 2020 18:10:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX191914/SRX191914.20_model.r INFO @ Sun, 21 Jun 2020 18:10:32: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:10:32: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:10:45: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:10:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX191914/SRX191914.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:10:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX191914/SRX191914.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:10:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX191914/SRX191914.20_summits.bed INFO @ Sun, 21 Jun 2020 18:10:51: Done! pass1 - making usageList (204 chroms): 2 millis pass2 - checking and writing primary data (1897 records, 4 fields): 9 millis CompletedMACS2peakCalling