Job ID = 6452793 SRX = SRX033316 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:10:04 prefetch.2.10.7: 1) Downloading 'SRR080710'... 2020-06-21T08:10:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:11:56 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:11:56 prefetch.2.10.7: 'SRR080710' is valid 2020-06-21T08:11:56 prefetch.2.10.7: 1) 'SRR080710' was downloaded successfully Read 12893541 spots for SRR080710/SRR080710.sra Written 12893541 spots for SRR080710/SRR080710.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: 00:02:09 12893541 reads; of these: 12893541 (100.00%) were unpaired; of these: 4167824 (32.32%) aligned 0 times 6395827 (49.60%) aligned exactly 1 time 2329890 (18.07%) aligned >1 times 67.68% overall alignment rate Time searching: 00:02:09 Overall time: 00:02:09 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] 2708853 / 8725717 = 0.3104 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 17:17:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX033316/SRX033316.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX033316/SRX033316.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX033316/SRX033316.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX033316/SRX033316.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 17:17:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:17:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:17:09: 1000000 INFO @ Sun, 21 Jun 2020 17:17:15: 2000000 INFO @ Sun, 21 Jun 2020 17:17:21: 3000000 INFO @ Sun, 21 Jun 2020 17:17:27: 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 17:17:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX033316/SRX033316.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX033316/SRX033316.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX033316/SRX033316.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX033316/SRX033316.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 17:17:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:17:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:17:33: 5000000 INFO @ Sun, 21 Jun 2020 17:17:39: 1000000 INFO @ Sun, 21 Jun 2020 17:17:40: 6000000 INFO @ Sun, 21 Jun 2020 17:17:40: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:17:40: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:17:40: #1 total tags in treatment: 6016864 INFO @ Sun, 21 Jun 2020 17:17:40: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:17:40: #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 17:17:40: #1 tags after filtering in treatment: 6016827 INFO @ Sun, 21 Jun 2020 17:17:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:17:40: #1 finished! INFO @ Sun, 21 Jun 2020 17:17:40: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:17:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:17:41: #2 number of paired peaks: 1246 INFO @ Sun, 21 Jun 2020 17:17:41: start model_add_line... INFO @ Sun, 21 Jun 2020 17:17:41: start X-correlation... INFO @ Sun, 21 Jun 2020 17:17:41: end of X-cor INFO @ Sun, 21 Jun 2020 17:17:41: #2 finished! INFO @ Sun, 21 Jun 2020 17:17:41: #2 predicted fragment length is 139 bps INFO @ Sun, 21 Jun 2020 17:17:41: #2 alternative fragment length(s) may be 126,139 bps INFO @ Sun, 21 Jun 2020 17:17:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX033316/SRX033316.05_model.r INFO @ Sun, 21 Jun 2020 17:17:41: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:17:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:17:44: 2000000 INFO @ Sun, 21 Jun 2020 17:17:49: 3000000 INFO @ Sun, 21 Jun 2020 17:17:54: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:17:54: 4000000 INFO @ Sun, 21 Jun 2020 17:17:59: 5000000 INFO @ Sun, 21 Jun 2020 17:18:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX033316/SRX033316.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:18:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX033316/SRX033316.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:18:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX033316/SRX033316.05_summits.bed INFO @ Sun, 21 Jun 2020 17:18:01: Done! pass1 - making usageList (412 chroms): 1 millis pass2 - checking and writing primary data (1515 records, 4 fields): 13 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 17:18:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX033316/SRX033316.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX033316/SRX033316.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX033316/SRX033316.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX033316/SRX033316.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 17:18:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:18:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:18:05: 6000000 INFO @ Sun, 21 Jun 2020 17:18:05: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:18:05: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:18:05: #1 total tags in treatment: 6016864 INFO @ Sun, 21 Jun 2020 17:18:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:18:05: #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 17:18:05: #1 tags after filtering in treatment: 6016827 INFO @ Sun, 21 Jun 2020 17:18:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:18:05: #1 finished! INFO @ Sun, 21 Jun 2020 17:18:05: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:18:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:18:06: #2 number of paired peaks: 1246 INFO @ Sun, 21 Jun 2020 17:18:06: start model_add_line... INFO @ Sun, 21 Jun 2020 17:18:06: start X-correlation... INFO @ Sun, 21 Jun 2020 17:18:06: end of X-cor INFO @ Sun, 21 Jun 2020 17:18:06: #2 finished! INFO @ Sun, 21 Jun 2020 17:18:06: #2 predicted fragment length is 139 bps INFO @ Sun, 21 Jun 2020 17:18:06: #2 alternative fragment length(s) may be 126,139 bps INFO @ Sun, 21 Jun 2020 17:18:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX033316/SRX033316.10_model.r INFO @ Sun, 21 Jun 2020 17:18:06: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:18:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:18:08: 1000000 INFO @ Sun, 21 Jun 2020 17:18:13: 2000000 INFO @ Sun, 21 Jun 2020 17:18:18: 3000000 INFO @ Sun, 21 Jun 2020 17:18:20: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:18:23: 4000000 INFO @ Sun, 21 Jun 2020 17:18:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX033316/SRX033316.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:18:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX033316/SRX033316.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:18:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX033316/SRX033316.10_summits.bed INFO @ Sun, 21 Jun 2020 17:18:27: Done! pass1 - making usageList (316 chroms): 1 millis BedGraph に変換しました。 BigWig に変換中... pass2 - checking and writing primary data (819 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:18:29: 5000000 INFO @ Sun, 21 Jun 2020 17:18:34: 6000000 INFO @ Sun, 21 Jun 2020 17:18:34: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:18:34: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:18:34: #1 total tags in treatment: 6016864 INFO @ Sun, 21 Jun 2020 17:18:34: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:18:34: #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 17:18:34: #1 tags after filtering in treatment: 6016827 INFO @ Sun, 21 Jun 2020 17:18:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:18:34: #1 finished! INFO @ Sun, 21 Jun 2020 17:18:34: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:18:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:18:35: #2 number of paired peaks: 1246 INFO @ Sun, 21 Jun 2020 17:18:35: start model_add_line... INFO @ Sun, 21 Jun 2020 17:18:35: start X-correlation... INFO @ Sun, 21 Jun 2020 17:18:35: end of X-cor INFO @ Sun, 21 Jun 2020 17:18:35: #2 finished! INFO @ Sun, 21 Jun 2020 17:18:35: #2 predicted fragment length is 139 bps INFO @ Sun, 21 Jun 2020 17:18:35: #2 alternative fragment length(s) may be 126,139 bps INFO @ Sun, 21 Jun 2020 17:18:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX033316/SRX033316.20_model.r INFO @ Sun, 21 Jun 2020 17:18:35: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:18:35: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:18:49: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:18:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX033316/SRX033316.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:18:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX033316/SRX033316.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:18:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX033316/SRX033316.20_summits.bed INFO @ Sun, 21 Jun 2020 17:18:56: Done! pass1 - making usageList (213 chroms): 1 millis pass2 - checking and writing primary data (395 records, 4 fields): 7 millis CompletedMACS2peakCalling