Job ID = 6457547 SRX = SRX4669036 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:33:25 prefetch.2.10.7: 1) Downloading 'SRR7817561'... 2020-06-21T11:33:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:34:14 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:34:15 prefetch.2.10.7: 'SRR7817561' is valid 2020-06-21T11:34:15 prefetch.2.10.7: 1) 'SRR7817561' was downloaded successfully 2020-06-21T11:34:15 prefetch.2.10.7: 'SRR7817561' has 0 unresolved dependencies Read 9894520 spots for SRR7817561/SRR7817561.sra Written 9894520 spots for SRR7817561/SRR7817561.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: 00:02:40 9894520 reads; of these: 9894520 (100.00%) were unpaired; of these: 440920 (4.46%) aligned 0 times 5741283 (58.02%) aligned exactly 1 time 3712317 (37.52%) aligned >1 times 95.54% overall alignment rate Time searching: 00:02:40 Overall time: 00:02:40 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] 1997355 / 9453600 = 0.2113 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 20:40:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4669036/SRX4669036.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4669036/SRX4669036.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4669036/SRX4669036.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4669036/SRX4669036.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 20:40:05: #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 20:40:21: 3000000 INFO @ Sun, 21 Jun 2020 20:40:26: 4000000 INFO @ Sun, 21 Jun 2020 20:40:32: 5000000 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/SRX4669036/SRX4669036.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4669036/SRX4669036.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4669036/SRX4669036.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4669036/SRX4669036.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 20:40:35: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:40:35: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:40:38: 6000000 INFO @ Sun, 21 Jun 2020 20:40:40: 1000000 INFO @ Sun, 21 Jun 2020 20:40:43: 7000000 INFO @ Sun, 21 Jun 2020 20:40:46: 2000000 INFO @ Sun, 21 Jun 2020 20:40:46: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:40:46: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:40:46: #1 total tags in treatment: 7456245 INFO @ Sun, 21 Jun 2020 20:40:46: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:40:46: #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 20:40:47: #1 tags after filtering in treatment: 7456200 INFO @ Sun, 21 Jun 2020 20:40:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:40:47: #1 finished! INFO @ Sun, 21 Jun 2020 20:40:47: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:40:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:40:48: #2 number of paired peaks: 2309 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 104 bps INFO @ Sun, 21 Jun 2020 20:40:48: #2 alternative fragment length(s) may be 4,104 bps INFO @ Sun, 21 Jun 2020 20:40:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4669036/SRX4669036.05_model.r INFO @ Sun, 21 Jun 2020 20:40:48: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:40:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:40:51: 3000000 INFO @ Sun, 21 Jun 2020 20:40:57: 4000000 INFO @ Sun, 21 Jun 2020 20:41:02: 5000000 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 20:41:04: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:41:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4669036/SRX4669036.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4669036/SRX4669036.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4669036/SRX4669036.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4669036/SRX4669036.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 20:41:05: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:41:05: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:41:08: 6000000 INFO @ Sun, 21 Jun 2020 20:41:11: 1000000 INFO @ Sun, 21 Jun 2020 20:41:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4669036/SRX4669036.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:41:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4669036/SRX4669036.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:41:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4669036/SRX4669036.05_summits.bed INFO @ Sun, 21 Jun 2020 20:41:12: Done! pass1 - making usageList (509 chroms): 1 millis pass2 - checking and writing primary data (5291 records, 4 fields): 33 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:41:14: 7000000 INFO @ Sun, 21 Jun 2020 20:41:17: 2000000 INFO @ Sun, 21 Jun 2020 20:41:17: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:41:17: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:41:17: #1 total tags in treatment: 7456245 INFO @ Sun, 21 Jun 2020 20:41:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:41:17: #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 20:41:18: #1 tags after filtering in treatment: 7456200 INFO @ Sun, 21 Jun 2020 20:41:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:41:18: #1 finished! INFO @ Sun, 21 Jun 2020 20:41:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:41:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:41:19: #2 number of paired peaks: 2309 INFO @ Sun, 21 Jun 2020 20:41:19: start model_add_line... INFO @ Sun, 21 Jun 2020 20:41:19: start X-correlation... INFO @ Sun, 21 Jun 2020 20:41:19: end of X-cor INFO @ Sun, 21 Jun 2020 20:41:19: #2 finished! INFO @ Sun, 21 Jun 2020 20:41:19: #2 predicted fragment length is 104 bps INFO @ Sun, 21 Jun 2020 20:41:19: #2 alternative fragment length(s) may be 4,104 bps INFO @ Sun, 21 Jun 2020 20:41:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4669036/SRX4669036.10_model.r INFO @ Sun, 21 Jun 2020 20:41:19: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:41:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:41:22: 3000000 INFO @ Sun, 21 Jun 2020 20:41:27: 4000000 INFO @ Sun, 21 Jun 2020 20:41:33: 5000000 INFO @ Sun, 21 Jun 2020 20:41:35: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:41:39: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:41:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4669036/SRX4669036.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:41:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4669036/SRX4669036.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:41:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4669036/SRX4669036.10_summits.bed INFO @ Sun, 21 Jun 2020 20:41:44: Done! pass1 - making usageList (309 chroms): 1 millis pass2 - checking and writing primary data (1825 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:41:44: 7000000 INFO @ Sun, 21 Jun 2020 20:41:47: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:41:47: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:41:47: #1 total tags in treatment: 7456245 INFO @ Sun, 21 Jun 2020 20:41:47: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:41:47: #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 20:41:48: #1 tags after filtering in treatment: 7456200 INFO @ Sun, 21 Jun 2020 20:41:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:41:48: #1 finished! INFO @ Sun, 21 Jun 2020 20:41:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:41:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:41:49: #2 number of paired peaks: 2309 INFO @ Sun, 21 Jun 2020 20:41:49: start model_add_line... INFO @ Sun, 21 Jun 2020 20:41:49: start X-correlation... INFO @ Sun, 21 Jun 2020 20:41:49: end of X-cor INFO @ Sun, 21 Jun 2020 20:41:49: #2 finished! INFO @ Sun, 21 Jun 2020 20:41:49: #2 predicted fragment length is 104 bps INFO @ Sun, 21 Jun 2020 20:41:49: #2 alternative fragment length(s) may be 4,104 bps INFO @ Sun, 21 Jun 2020 20:41:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4669036/SRX4669036.20_model.r INFO @ Sun, 21 Jun 2020 20:41:49: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:41:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:42:05: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:42:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4669036/SRX4669036.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:42:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4669036/SRX4669036.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:42:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4669036/SRX4669036.20_summits.bed INFO @ Sun, 21 Jun 2020 20:42:13: Done! pass1 - making usageList (185 chroms): 1 millis pass2 - checking and writing primary data (504 records, 4 fields): 12 millis CompletedMACS2peakCalling