Job ID = 6457056 SRX = SRX4375823 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:34:40 prefetch.2.10.7: 1) Downloading 'SRR7506477'... 2020-06-21T11:34:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:36:08 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:36:08 prefetch.2.10.7: 'SRR7506477' is valid 2020-06-21T11:36:08 prefetch.2.10.7: 1) 'SRR7506477' was downloaded successfully Read 11346508 spots for SRR7506477/SRR7506477.sra Written 11346508 spots for SRR7506477/SRR7506477.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: 00:01:31 11346508 reads; of these: 11346508 (100.00%) were unpaired; of these: 7434472 (65.52%) aligned 0 times 3026333 (26.67%) aligned exactly 1 time 885703 (7.81%) aligned >1 times 34.48% overall alignment rate Time searching: 00:01:31 Overall time: 00:01:31 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] 1707050 / 3912036 = 0.4364 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 20:39:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4375823/SRX4375823.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4375823/SRX4375823.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4375823/SRX4375823.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4375823/SRX4375823.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 20:39:35: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:39:35: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:39:40: 1000000 INFO @ Sun, 21 Jun 2020 20:39:46: 2000000 INFO @ Sun, 21 Jun 2020 20:39:47: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:39:47: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:39:47: #1 total tags in treatment: 2204986 INFO @ Sun, 21 Jun 2020 20:39:47: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:39:47: #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 20:39:47: #1 tags after filtering in treatment: 2204563 INFO @ Sun, 21 Jun 2020 20:39:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:39:47: #1 finished! INFO @ Sun, 21 Jun 2020 20:39:47: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:39:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:39:48: #2 number of paired peaks: 5771 INFO @ Sun, 21 Jun 2020 20:39:48: start model_add_line... INFO @ Sun, 21 Jun 2020 20:39:48: start X-correlation... INFO @ Sun, 21 Jun 2020 20:39:48: end of X-cor INFO @ Sun, 21 Jun 2020 20:39:48: #2 finished! INFO @ Sun, 21 Jun 2020 20:39:48: #2 predicted fragment length is 228 bps INFO @ Sun, 21 Jun 2020 20:39:48: #2 alternative fragment length(s) may be 228 bps INFO @ Sun, 21 Jun 2020 20:39:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4375823/SRX4375823.05_model.r INFO @ Sun, 21 Jun 2020 20:39:48: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:39:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:39:55: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:39:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4375823/SRX4375823.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:39:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4375823/SRX4375823.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:39:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4375823/SRX4375823.05_summits.bed INFO @ Sun, 21 Jun 2020 20:39:58: Done! pass1 - making usageList (160 chroms): 2 millis pass2 - checking and writing primary data (5896 records, 4 fields): 12 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 20:40:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4375823/SRX4375823.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4375823/SRX4375823.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4375823/SRX4375823.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4375823/SRX4375823.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 20:40:05: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:40:05: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:40:10: 1000000 INFO @ Sun, 21 Jun 2020 20:40:16: 2000000 INFO @ Sun, 21 Jun 2020 20:40:17: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:40:17: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:40:17: #1 total tags in treatment: 2204986 INFO @ Sun, 21 Jun 2020 20:40:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:40:17: #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 20:40:17: #1 tags after filtering in treatment: 2204563 INFO @ Sun, 21 Jun 2020 20:40:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:40:17: #1 finished! INFO @ Sun, 21 Jun 2020 20:40:17: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:40:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:40:18: #2 number of paired peaks: 5771 INFO @ Sun, 21 Jun 2020 20:40:18: start model_add_line... INFO @ Sun, 21 Jun 2020 20:40:18: start X-correlation... INFO @ Sun, 21 Jun 2020 20:40:18: end of X-cor INFO @ Sun, 21 Jun 2020 20:40:18: #2 finished! INFO @ Sun, 21 Jun 2020 20:40:18: #2 predicted fragment length is 228 bps INFO @ Sun, 21 Jun 2020 20:40:18: #2 alternative fragment length(s) may be 228 bps INFO @ Sun, 21 Jun 2020 20:40:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4375823/SRX4375823.10_model.r INFO @ Sun, 21 Jun 2020 20:40:18: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:40:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:40:25: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:40:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4375823/SRX4375823.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:40:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4375823/SRX4375823.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:40:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4375823/SRX4375823.10_summits.bed INFO @ Sun, 21 Jun 2020 20:40:28: Done! pass1 - making usageList (95 chroms): 2 millis pass2 - checking and writing primary data (4577 records, 4 fields): 8 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 20:40:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4375823/SRX4375823.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4375823/SRX4375823.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4375823/SRX4375823.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4375823/SRX4375823.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 20:40:35: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:40:35: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:40:41: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:40:47: 2000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:40:48: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:40:48: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:40:48: #1 total tags in treatment: 2204986 INFO @ Sun, 21 Jun 2020 20:40:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:40:48: #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 20:40:48: #1 tags after filtering in treatment: 2204563 INFO @ Sun, 21 Jun 2020 20:40:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:40:48: #1 finished! INFO @ Sun, 21 Jun 2020 20:40:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:40:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:40:48: #2 number of paired peaks: 5771 INFO @ Sun, 21 Jun 2020 20:40:48: start model_add_line... INFO @ Sun, 21 Jun 2020 20:40:48: start X-correlation... INFO @ Sun, 21 Jun 2020 20:40:48: end of X-cor INFO @ Sun, 21 Jun 2020 20:40:48: #2 finished! INFO @ Sun, 21 Jun 2020 20:40:48: #2 predicted fragment length is 228 bps INFO @ Sun, 21 Jun 2020 20:40:48: #2 alternative fragment length(s) may be 228 bps INFO @ Sun, 21 Jun 2020 20:40:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4375823/SRX4375823.20_model.r INFO @ Sun, 21 Jun 2020 20:40:48: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:40:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:40:55: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:40:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4375823/SRX4375823.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:40:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4375823/SRX4375823.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:40:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4375823/SRX4375823.20_summits.bed INFO @ Sun, 21 Jun 2020 20:40:58: Done! pass1 - making usageList (62 chroms): 1 millis pass2 - checking and writing primary data (3234 records, 4 fields): 6 millis CompletedMACS2peakCalling