Job ID = 6454831 SRX = SRX2592427 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:40:25 prefetch.2.10.7: 1) Downloading 'SRR5289704'... 2020-06-21T09:40:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:41:56 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:41:57 prefetch.2.10.7: 'SRR5289704' is valid 2020-06-21T09:41:57 prefetch.2.10.7: 1) 'SRR5289704' was downloaded successfully Read 8417050 spots for SRR5289704/SRR5289704.sra Written 8417050 spots for SRR5289704/SRR5289704.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 8417050 reads; of these: 8417050 (100.00%) were unpaired; of these: 683269 (8.12%) aligned 0 times 6260698 (74.38%) aligned exactly 1 time 1473083 (17.50%) aligned >1 times 91.88% 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] 2082925 / 7733781 = 0.2693 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 18:47:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592427/SRX2592427.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592427/SRX2592427.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592427/SRX2592427.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592427/SRX2592427.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 18:47:39: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:47:39: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:47:45: 1000000 INFO @ Sun, 21 Jun 2020 18:47:50: 2000000 INFO @ Sun, 21 Jun 2020 18:47:56: 3000000 INFO @ Sun, 21 Jun 2020 18:48:02: 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 18:48:08: 5000000 INFO @ Sun, 21 Jun 2020 18:48:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592427/SRX2592427.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592427/SRX2592427.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592427/SRX2592427.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592427/SRX2592427.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 18:48:09: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:48:09: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:48:12: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:48:12: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:48:12: #1 total tags in treatment: 5650856 INFO @ Sun, 21 Jun 2020 18:48:12: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:48:12: #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 18:48:12: #1 tags after filtering in treatment: 5650632 INFO @ Sun, 21 Jun 2020 18:48:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:48:12: #1 finished! INFO @ Sun, 21 Jun 2020 18:48:12: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:48:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:48:13: #2 number of paired peaks: 228 WARNING @ Sun, 21 Jun 2020 18:48:13: Fewer paired peaks (228) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 228 pairs to build model! INFO @ Sun, 21 Jun 2020 18:48:13: start model_add_line... INFO @ Sun, 21 Jun 2020 18:48:13: start X-correlation... INFO @ Sun, 21 Jun 2020 18:48:13: end of X-cor INFO @ Sun, 21 Jun 2020 18:48:13: #2 finished! INFO @ Sun, 21 Jun 2020 18:48:13: #2 predicted fragment length is 103 bps INFO @ Sun, 21 Jun 2020 18:48:13: #2 alternative fragment length(s) may be 103 bps INFO @ Sun, 21 Jun 2020 18:48:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592427/SRX2592427.05_model.r INFO @ Sun, 21 Jun 2020 18:48:13: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:48:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:48:15: 1000000 INFO @ Sun, 21 Jun 2020 18:48:21: 2000000 INFO @ Sun, 21 Jun 2020 18:48:26: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:48:27: 3000000 INFO @ Sun, 21 Jun 2020 18:48:32: 4000000 INFO @ Sun, 21 Jun 2020 18:48:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592427/SRX2592427.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:48:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592427/SRX2592427.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:48:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592427/SRX2592427.05_summits.bed INFO @ Sun, 21 Jun 2020 18:48:34: Done! pass1 - making usageList (289 chroms): 3 millis pass2 - checking and writing primary data (14046 records, 4 fields): 23 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 18:48:39: 5000000 INFO @ Sun, 21 Jun 2020 18:48:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592427/SRX2592427.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592427/SRX2592427.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592427/SRX2592427.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592427/SRX2592427.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 18:48:39: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:48:39: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:48:43: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:48:43: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:48:43: #1 total tags in treatment: 5650856 INFO @ Sun, 21 Jun 2020 18:48:43: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:48:43: #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 18:48:43: #1 tags after filtering in treatment: 5650632 INFO @ Sun, 21 Jun 2020 18:48:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:48:43: #1 finished! INFO @ Sun, 21 Jun 2020 18:48:43: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:48:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:48:44: #2 number of paired peaks: 228 WARNING @ Sun, 21 Jun 2020 18:48:44: Fewer paired peaks (228) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 228 pairs to build model! INFO @ Sun, 21 Jun 2020 18:48:44: start model_add_line... INFO @ Sun, 21 Jun 2020 18:48:44: start X-correlation... INFO @ Sun, 21 Jun 2020 18:48:44: end of X-cor INFO @ Sun, 21 Jun 2020 18:48:44: #2 finished! INFO @ Sun, 21 Jun 2020 18:48:44: #2 predicted fragment length is 103 bps INFO @ Sun, 21 Jun 2020 18:48:44: #2 alternative fragment length(s) may be 103 bps INFO @ Sun, 21 Jun 2020 18:48:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592427/SRX2592427.10_model.r INFO @ Sun, 21 Jun 2020 18:48:44: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:48:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:48:45: 1000000 INFO @ Sun, 21 Jun 2020 18:48:51: 2000000 INFO @ Sun, 21 Jun 2020 18:48:57: 3000000 INFO @ Sun, 21 Jun 2020 18:48:58: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:49:03: 4000000 INFO @ Sun, 21 Jun 2020 18:49:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592427/SRX2592427.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:49:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592427/SRX2592427.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:49:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592427/SRX2592427.10_summits.bed INFO @ Sun, 21 Jun 2020 18:49:06: Done! pass1 - making usageList (199 chroms): 2 millis pass2 - checking and writing primary data (10459 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:49:09: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:49:12: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:49:12: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:49:12: #1 total tags in treatment: 5650856 INFO @ Sun, 21 Jun 2020 18:49:12: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:49:12: #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 18:49:13: #1 tags after filtering in treatment: 5650632 INFO @ Sun, 21 Jun 2020 18:49:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:49:13: #1 finished! INFO @ Sun, 21 Jun 2020 18:49:13: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:49:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:49:14: #2 number of paired peaks: 228 WARNING @ Sun, 21 Jun 2020 18:49:14: Fewer paired peaks (228) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 228 pairs to build model! INFO @ Sun, 21 Jun 2020 18:49:14: start model_add_line... INFO @ Sun, 21 Jun 2020 18:49:14: start X-correlation... INFO @ Sun, 21 Jun 2020 18:49:14: end of X-cor INFO @ Sun, 21 Jun 2020 18:49:14: #2 finished! INFO @ Sun, 21 Jun 2020 18:49:14: #2 predicted fragment length is 103 bps INFO @ Sun, 21 Jun 2020 18:49:14: #2 alternative fragment length(s) may be 103 bps INFO @ Sun, 21 Jun 2020 18:49:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592427/SRX2592427.20_model.r INFO @ Sun, 21 Jun 2020 18:49:14: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:49:14: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:49:28: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:49:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592427/SRX2592427.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:49:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592427/SRX2592427.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:49:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592427/SRX2592427.20_summits.bed INFO @ Sun, 21 Jun 2020 18:49:35: Done! pass1 - making usageList (122 chroms): 2 millis pass2 - checking and writing primary data (6597 records, 4 fields): 12 millis CompletedMACS2peakCalling