Job ID = 6458587 SRX = SRX5343123 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:33:07 prefetch.2.10.7: 1) Downloading 'SRR8540823'... 2020-06-21T12:33:07 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:34:05 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:34:05 prefetch.2.10.7: 'SRR8540823' is valid 2020-06-21T12:34:05 prefetch.2.10.7: 1) 'SRR8540823' was downloaded successfully 2020-06-21T12:34:05 prefetch.2.10.7: 'SRR8540823' has 0 unresolved dependencies Read 5871137 spots for SRR8540823/SRR8540823.sra Written 5871137 spots for SRR8540823/SRR8540823.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: 00:01:19 5871137 reads; of these: 5871137 (100.00%) were unpaired; of these: 2042066 (34.78%) aligned 0 times 3372837 (57.45%) aligned exactly 1 time 456234 (7.77%) aligned >1 times 65.22% overall alignment rate Time searching: 00:01:19 Overall time: 00:01:19 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] 2064386 / 3829071 = 0.5391 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 21:37:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343123/SRX5343123.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343123/SRX5343123.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343123/SRX5343123.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343123/SRX5343123.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 21:37:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:37:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:37:15: 1000000 INFO @ Sun, 21 Jun 2020 21:37:19: #1 tag size is determined as 65 bps INFO @ Sun, 21 Jun 2020 21:37:19: #1 tag size = 65 INFO @ Sun, 21 Jun 2020 21:37:19: #1 total tags in treatment: 1764685 INFO @ Sun, 21 Jun 2020 21:37:19: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:37:19: #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 21:37:19: #1 tags after filtering in treatment: 1764439 INFO @ Sun, 21 Jun 2020 21:37:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:37:19: #1 finished! INFO @ Sun, 21 Jun 2020 21:37:19: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:37:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:37:20: #2 number of paired peaks: 8350 INFO @ Sun, 21 Jun 2020 21:37:20: start model_add_line... INFO @ Sun, 21 Jun 2020 21:37:20: start X-correlation... INFO @ Sun, 21 Jun 2020 21:37:20: end of X-cor INFO @ Sun, 21 Jun 2020 21:37:20: #2 finished! INFO @ Sun, 21 Jun 2020 21:37:20: #2 predicted fragment length is 175 bps INFO @ Sun, 21 Jun 2020 21:37:20: #2 alternative fragment length(s) may be 175 bps INFO @ Sun, 21 Jun 2020 21:37:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343123/SRX5343123.05_model.r INFO @ Sun, 21 Jun 2020 21:37:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:37:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:37:24: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:37:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343123/SRX5343123.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:37:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343123/SRX5343123.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:37:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343123/SRX5343123.05_summits.bed INFO @ Sun, 21 Jun 2020 21:37:27: Done! pass1 - making usageList (124 chroms): 1 millis pass2 - checking and writing primary data (5774 records, 4 fields): 10 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 21:37:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343123/SRX5343123.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343123/SRX5343123.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343123/SRX5343123.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343123/SRX5343123.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 21:37:39: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:37:39: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:37:45: 1000000 INFO @ Sun, 21 Jun 2020 21:37:50: #1 tag size is determined as 65 bps INFO @ Sun, 21 Jun 2020 21:37:50: #1 tag size = 65 INFO @ Sun, 21 Jun 2020 21:37:50: #1 total tags in treatment: 1764685 INFO @ Sun, 21 Jun 2020 21:37:50: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:37:50: #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 21:37:50: #1 tags after filtering in treatment: 1764439 INFO @ Sun, 21 Jun 2020 21:37:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:37:50: #1 finished! INFO @ Sun, 21 Jun 2020 21:37:50: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:37:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:37:51: #2 number of paired peaks: 8350 INFO @ Sun, 21 Jun 2020 21:37:51: start model_add_line... INFO @ Sun, 21 Jun 2020 21:37:51: start X-correlation... INFO @ Sun, 21 Jun 2020 21:37:51: end of X-cor INFO @ Sun, 21 Jun 2020 21:37:51: #2 finished! INFO @ Sun, 21 Jun 2020 21:37:51: #2 predicted fragment length is 175 bps INFO @ Sun, 21 Jun 2020 21:37:51: #2 alternative fragment length(s) may be 175 bps INFO @ Sun, 21 Jun 2020 21:37:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343123/SRX5343123.10_model.r INFO @ Sun, 21 Jun 2020 21:37:51: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:37:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:37:56: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:37:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343123/SRX5343123.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:37:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343123/SRX5343123.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:37:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343123/SRX5343123.10_summits.bed INFO @ Sun, 21 Jun 2020 21:37:58: Done! pass1 - making usageList (108 chroms): 2 millis pass2 - checking and writing primary data (4046 records, 4 fields): 7 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 21:38:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343123/SRX5343123.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343123/SRX5343123.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343123/SRX5343123.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343123/SRX5343123.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 21:38:09: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:38:09: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:38:14: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:38:18: #1 tag size is determined as 65 bps INFO @ Sun, 21 Jun 2020 21:38:18: #1 tag size = 65 INFO @ Sun, 21 Jun 2020 21:38:18: #1 total tags in treatment: 1764685 INFO @ Sun, 21 Jun 2020 21:38:18: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:38:18: #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 21:38:19: #1 tags after filtering in treatment: 1764439 INFO @ Sun, 21 Jun 2020 21:38:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:38:19: #1 finished! INFO @ Sun, 21 Jun 2020 21:38:19: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:38:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:38:19: #2 number of paired peaks: 8350 INFO @ Sun, 21 Jun 2020 21:38:19: start model_add_line... INFO @ Sun, 21 Jun 2020 21:38:19: start X-correlation... INFO @ Sun, 21 Jun 2020 21:38:19: end of X-cor INFO @ Sun, 21 Jun 2020 21:38:19: #2 finished! INFO @ Sun, 21 Jun 2020 21:38:19: #2 predicted fragment length is 175 bps INFO @ Sun, 21 Jun 2020 21:38:19: #2 alternative fragment length(s) may be 175 bps INFO @ Sun, 21 Jun 2020 21:38:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343123/SRX5343123.20_model.r INFO @ Sun, 21 Jun 2020 21:38:19: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:38:19: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:38:23: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:38:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343123/SRX5343123.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:38:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343123/SRX5343123.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:38:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343123/SRX5343123.20_summits.bed INFO @ Sun, 21 Jun 2020 21:38:25: Done! pass1 - making usageList (81 chroms): 1 millis pass2 - checking and writing primary data (1507 records, 4 fields): 5 millis CompletedMACS2peakCalling