Job ID = 6453899 SRX = SRX1561067 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:54:19 prefetch.2.10.7: 1) Downloading 'SRR3145070'... 2020-06-21T08:54:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:56:08 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:56:09 prefetch.2.10.7: 'SRR3145070' is valid 2020-06-21T08:56:09 prefetch.2.10.7: 1) 'SRR3145070' was downloaded successfully Read 9795504 spots for SRR3145070/SRR3145070.sra Written 9795504 spots for SRR3145070/SRR3145070.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: 00:01:49 9795504 reads; of these: 9795504 (100.00%) were unpaired; of these: 3099039 (31.64%) aligned 0 times 5908180 (60.32%) aligned exactly 1 time 788285 (8.05%) aligned >1 times 68.36% overall alignment rate Time searching: 00:01:49 Overall time: 00:01:49 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] 988331 / 6696465 = 0.1476 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 18:00:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1561067/SRX1561067.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1561067/SRX1561067.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1561067/SRX1561067.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1561067/SRX1561067.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 18:00:34: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:00:34: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:00:40: 1000000 INFO @ Sun, 21 Jun 2020 18:00:46: 2000000 INFO @ Sun, 21 Jun 2020 18:00:51: 3000000 INFO @ Sun, 21 Jun 2020 18:00:57: 4000000 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 18:01:03: 5000000 INFO @ Sun, 21 Jun 2020 18:01:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1561067/SRX1561067.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1561067/SRX1561067.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1561067/SRX1561067.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1561067/SRX1561067.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 18:01:04: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:01:04: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:01:07: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:01:07: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:01:07: #1 total tags in treatment: 5708134 INFO @ Sun, 21 Jun 2020 18:01:07: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:01:07: #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 18:01:07: #1 tags after filtering in treatment: 5708059 INFO @ Sun, 21 Jun 2020 18:01:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:01:07: #1 finished! INFO @ Sun, 21 Jun 2020 18:01:07: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:01:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:01:08: #2 number of paired peaks: 4750 INFO @ Sun, 21 Jun 2020 18:01:08: start model_add_line... INFO @ Sun, 21 Jun 2020 18:01:08: start X-correlation... INFO @ Sun, 21 Jun 2020 18:01:08: end of X-cor INFO @ Sun, 21 Jun 2020 18:01:08: #2 finished! INFO @ Sun, 21 Jun 2020 18:01:08: #2 predicted fragment length is 128 bps INFO @ Sun, 21 Jun 2020 18:01:08: #2 alternative fragment length(s) may be 128 bps INFO @ Sun, 21 Jun 2020 18:01:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1561067/SRX1561067.05_model.r INFO @ Sun, 21 Jun 2020 18:01:08: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:01:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:01:10: 1000000 INFO @ Sun, 21 Jun 2020 18:01:16: 2000000 INFO @ Sun, 21 Jun 2020 18:01:21: 3000000 INFO @ Sun, 21 Jun 2020 18:01:22: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:01:27: 4000000 INFO @ Sun, 21 Jun 2020 18:01:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1561067/SRX1561067.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:01:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1561067/SRX1561067.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:01:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1561067/SRX1561067.05_summits.bed INFO @ Sun, 21 Jun 2020 18:01:29: Done! pass1 - making usageList (321 chroms): 2 millis pass2 - checking and writing primary data (9965 records, 4 fields): 18 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 18:01:33: 5000000 INFO @ Sun, 21 Jun 2020 18:01:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1561067/SRX1561067.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1561067/SRX1561067.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1561067/SRX1561067.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1561067/SRX1561067.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 18:01:34: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:01:34: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:01:37: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:01:37: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:01:37: #1 total tags in treatment: 5708134 INFO @ Sun, 21 Jun 2020 18:01:37: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:01:37: #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 18:01:38: #1 tags after filtering in treatment: 5708059 INFO @ Sun, 21 Jun 2020 18:01:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:01:38: #1 finished! INFO @ Sun, 21 Jun 2020 18:01:38: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:01:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:01:38: #2 number of paired peaks: 4750 INFO @ Sun, 21 Jun 2020 18:01:38: start model_add_line... INFO @ Sun, 21 Jun 2020 18:01:39: start X-correlation... INFO @ Sun, 21 Jun 2020 18:01:39: end of X-cor INFO @ Sun, 21 Jun 2020 18:01:39: #2 finished! INFO @ Sun, 21 Jun 2020 18:01:39: #2 predicted fragment length is 128 bps INFO @ Sun, 21 Jun 2020 18:01:39: #2 alternative fragment length(s) may be 128 bps INFO @ Sun, 21 Jun 2020 18:01:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1561067/SRX1561067.10_model.r INFO @ Sun, 21 Jun 2020 18:01:39: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:01:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:01:41: 1000000 INFO @ Sun, 21 Jun 2020 18:01:49: 2000000 INFO @ Sun, 21 Jun 2020 18:01:52: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:01:55: 3000000 INFO @ Sun, 21 Jun 2020 18:01:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1561067/SRX1561067.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:01:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1561067/SRX1561067.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:01:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1561067/SRX1561067.10_summits.bed INFO @ Sun, 21 Jun 2020 18:01:59: Done! pass1 - making usageList (153 chroms): 1 millis pass2 - checking and writing primary data (6614 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:02:02: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:02:09: 5000000 INFO @ Sun, 21 Jun 2020 18:02:14: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:02:14: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:02:14: #1 total tags in treatment: 5708134 INFO @ Sun, 21 Jun 2020 18:02:14: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:02:14: #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 18:02:14: #1 tags after filtering in treatment: 5708059 INFO @ Sun, 21 Jun 2020 18:02:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:02:14: #1 finished! INFO @ Sun, 21 Jun 2020 18:02:14: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:02:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:02:15: #2 number of paired peaks: 4750 INFO @ Sun, 21 Jun 2020 18:02:15: start model_add_line... INFO @ Sun, 21 Jun 2020 18:02:15: start X-correlation... INFO @ Sun, 21 Jun 2020 18:02:15: end of X-cor INFO @ Sun, 21 Jun 2020 18:02:15: #2 finished! INFO @ Sun, 21 Jun 2020 18:02:15: #2 predicted fragment length is 128 bps INFO @ Sun, 21 Jun 2020 18:02:15: #2 alternative fragment length(s) may be 128 bps INFO @ Sun, 21 Jun 2020 18:02:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1561067/SRX1561067.20_model.r INFO @ Sun, 21 Jun 2020 18:02:15: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:02:15: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:02:28: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:02:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1561067/SRX1561067.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:02:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1561067/SRX1561067.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:02:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1561067/SRX1561067.20_summits.bed INFO @ Sun, 21 Jun 2020 18:02:35: Done! pass1 - making usageList (89 chroms): 1 millis pass2 - checking and writing primary data (3711 records, 4 fields): 7 millis CompletedMACS2peakCalling